Self-Study Report Department of Biochemistry and Biophysics External Academic Program Review, April 2021

Home , Fred Hutchinson, Gene Reynolds, Gordon Hammes, John Mason Ward, LA Knight, Marlan Scully

This document was prepared in 2021 Academic Program Review (APR) Ad hoc. committee

Betty Cotton Justine deGruyter Timothy Devarenne Ping He Kaitlyn McGaff Jean-Philippe Pellois Michael Polymenis Josh Wand 2

TABLE OF CONTENTS List of Figures 6 List of Tables 8 Charge to the Peer Review Team 10 Itinerary for Virtual Visit for the External Review Team 11 Executive Summary 18 Introduction to the Department 20 Departmental history 20 Mission, strategic plan and goals 21 Administrative Structure 21 Leadership 22 Faculty departmental committees 24 Permanent committees 24 Standing committees 24 Ad hoc. committees 24 Administrative support staff 25 Undergraduate office staff 25 Graduate office staff 25 Web presence 25 Facilities management staff 25 Stockroom staff 26 COALS administrative staff 26 Business Office 26 Information Technology 27 Academic Advising 27 Research Staff 27 Departmental Resources 28 Facilities 28 Main BCBP Building 28 NMR Annex 28 Borlaug Center 29 Interdisciplinary Life Sciences Building (ILSB) 29 Research Infrastructure 29 Center for Phage Technology 29 Center for Structural Biology 30 Common use equipment system (CUE) 30

Biomolecular NMR laboratory 31 Protein Chemistry Lab (PCL) 31 Integrated metabolomics analysis core (IMAC) 31 Response to previous APR critiques 31 Analysis 32 Academic Programs 33 Graduate Programs 33 PhD in Biochemistry 33 Program Curricula 35 Rotations and Laboratory Selection 36 Courses 37 Teaching Assistantship and Relationship to the Undergraduate Programs 37 Research Proposal and Preliminary Examination 37 Annual Committee Meetings and Thesis Committee 39 Seminar Series 39 Dissertation and Thesis Defense 40 Graduate Training Programs 40 Number of Degrees Awarded Per Year 40 Average Time to Degree 41 Academic Enhancements and High-Impact Opportunities for Students 41 Town Halls 42 Assessment of Student Learning Outcomes 42 Admissions and Admissions Criteria 43 Response to previous APR critiques 44 Analysis 47 Interdisciplinary Program (IDP) in Genetics 48 Undergraduate Programs 49 Academic Programs and Curricula 49 Accreditations 49 Program curricula in Biochemistry 50 Program curricula in Genetics 50 Courses/Degree Plans 51 BS in Biochemistry 51 BS in Genetics 52 Admission Criteria 53 Number of Degrees Awarded per year 54

Average Time to Degree 55 Academic Enhancements 55 Assessment of Student Learning Outcomes 56 Assessment of Biochemistry Program 56 Assessment of Genetics Program 58 Response to previous APR critiques 58 Analysis of Biochemistry Program 58 Analysis of Genetics Program 59 Faculty Profile 60 Tenured and tenure-track Ad loc. faculty 60 Demographics of Ad loc. faculty 61 Faculty diversity 61 Faculty qualifications 62 Participation in interdepartmental and interdisciplinary programs 63 Joint faculty 63 Non-tenure track Research Faculty 64 Academic Professional Track Faculty 64 Fields of study of research-active faculty 64 Interactions among research-active faculty 65 Research productivity of the Ad loc. faculty 66 Publications 66 Funding 68 Teaching Productivity of Ad loc. and non-tenure track faculty 70 Student:Faculty ratio 70 Teaching load 71 Service productivity 72 Awards 73 Response to previous APR critiques 73 Analysis 74 Comparison to peer institutions by Academic Analytics 75 Student Profiles 76 Graduate Students 76 Student Profile (Current) 76 Student Profile (20-Year Trends) 77 Class size 77 GRE and GPR/A scores 78

Race and ethnicity 78 Federal designation and gender distributions 80 Geographic diversity of domestic students 80 Attrition 80 Analysis 81 PhD completion rates 81 Student productivity 82 Distribution of graduate students within the department and in research laboratories 83 Undergraduate Students 84 Enrollment 84 Student Diversity/Demographics 86 Retention Rates 87 Number of Degrees Awarded per Year 87 Graduation Rates 87 Average Time to Degree (most recent 5 years) 88 Analysis 88 Conclusions and Action Plan 89 Appendices 92

List of Figures

FIGURE 1. Organizational chart of the Departmental administration.

FIGURE 2. Organizational chart of the College-administered Business, IT, and Advising Offices.

FIGURE 3. Typical schedule of Advisory Committee meetings.

FIGURE 4. Number of PhD degrees awarded by year for the past 30 years.

FIGURE 5. Average year-to-degree for students who entered the program between 2000 and 2013.

FIGURE 6. Number of applicants to the PhD program since 2010.

FIGURE 7. Distribution of year-to-degree (YTD) and year-to-preliminary-exam (YTPE) for BCBP PhD students who graduated during the 2000-2015 period.

FIGURE 8. Implemented changes to improve advising and decrease the time to degree.

FIGURE 9. PhD candidates currently in the program distributed as a function of the academic year they entered the program.

FIGURE 10. Number of BICH and GENE transfer students admitted for AY 2015-2019.

FIGURE 11. Performance of TAMU BICH students on ASBMB Degree Certification Exam.

FIGURE 12. Age and rank distribution of Ad loc. faculty over the review period.

FIGURE 13. Network of co-authorships among research-active faculty since 2015.

FIGURE 14. Publications of Ad loc. faculty over the review period.

FIGURE 15. Cumulative literature impact of Ad loc. and Joint faculty.

FIGURE 16. Funding of Ad loc. faculty over the review period.

FIGURE 17. Student:Faculty ratio over the review period.

FIGURE 18. Radar chart of BCBP performance among peer biochemistry departments identified by Academic Analytics.

FIGURE 19. Distribution of gender for students currently enrolled in the program by matriculation year.

FIGURE 20. Box and whisker plot for the graduate GPA of students currently in the program and enrolled since 2015.

FIGURE 21. Class size by matriculation year.

FIGURE 22. GRE verbal (V) and GPR of PhD cohorts.

FIGURE 23. Ethnicity distribution of students entering the BCBP graduate program.

FIGURE 24. Distribution of matriculating cohorts by gender and federal designation.

FIGURE 25. Geographic diversity of admitted domestic students.

FIGURE 26. Attrition and PhD completion rates in real numbers and percent attrition and PhD completion.

FIGURE 27. Percent graduation rates by gender and percent graduate rates by federal designation.

FIGURE 29. Student publications.

FIGURE 30. Proportion of graduate students within research personnel.

FIGURE 31. Freshman BICH and GENE Enrollment for AY 2015-2019.

FIGURE 32. Total BICH and GENE Undergraduate Enrollment for AY 2015-2019.

FIGURE 33. Non-Major vs. Total Department Undergraduates Taught for AY 2015-2019.

FIGURE 34. Percent of Freshman BICH and GENE students retained in the department after the first year.

FIGURE 35. BICH and GENE graduation rates in comparison to other science majors for AY 2015-2019.

List of Tables

TABLE 1. Semester demand on Teaching Assistantships since 2018.

TABLE 2. Preliminary examination proposal components.

TABLE 3. Thesis working committee composition and structure.

TABLE 4. Biochemistry BS Curriculum.

TABLE 5. Genetics BS Curriculum.

TABLE 6. Number of BICH and GENE degrees awarded for AY 2015-2019.

TABLE 7. Graduation statistics for BICH and GENE majors for AY 2015-2109.

TABLE 8. Ad loc. faculty.

TABLE 9. Joint faculty.

TABLE 10. Non-tenure track research faculty.

TABLE 11. Academic Professional Track Faculty.

TABLE 12. Research areas of the Department.

TABLE 13. Publication output of Ad loc. faculty.

TABLE 14. External Grand Research Expenditures from Ad loc. faculty.

TABLE 15. Sources of research funding (n = Ad. loc faculty) for the 2015-2020 period.

TABLE 16. Lecture/Lab sections taught for AY2020-21.

TABLE 17. Current departmental committee membership.

TABLE 18. BCBP Ad loc. faculty intramural awards since 2015.

TABLE 19. BCBP Ad loc. faculty extramural awards since 2015.

TABLE 20. Number of large collaborative proposals to NIH at peer departments.

TABLE 21. Total department attrition rates for students matriculating between 2000–2020.

TABLE 22. Demographics of BICH and GENE Majors for AY 2016–2019.

Texas A&M University

Academic Program Review (APR)

Charge to the Peer Review Team

The Academic Program Review (APR) process at Texas A&M University provides the occasion for academic units to plan strategically, assess the quality and efficiency of their programs, and determine the best courses of action for ongoing improvement. APR is at the heart of our institutional commitment to excellence, and we sincerely thank you for assisting us. This letter provides you with the charge to the committee and a brief overview of the department.

Peer Review Team Charge Please examine the department and its programs and make recommendations that will help in planning improvements. Your resources are a self-study report prepared by the department, copies of materials from the program’s last review, information you gain through personal interactions while visiting Texas A&M University, copies of strategic plans and goal-setting documents at the department, college, and/or university level, and any additional information requested by you or by the department. Within the broad charge of recommending ways the department can continue to improve are some specific questions that we would like you to address:

● Based on the data / information provided in the self-study report or gathered by the review team, what are the department’s overall strengths and weaknesses?

● How well do the department’s strategic goals align with those of its college and with those of Texas A&M University?

● How would you compare this department with its peers? Specifically, is the curriculum directly related and appropriate to the mission and goals of this institution?

● What improvement (including student learning and faculty development) has the department made since the previous program review?

● With only current resources or a modest infusion of new ones, what specific recommendations could improve the department’s performance, marginally or significantly?

We look forward to meeting with you during your time on campus. If you have any questions or require additional information prior to your visit, Ms. Bettyann Zio, APR Program Coordinator, at [email protected].

Thank you.

Itinerary for Virtual Visit by the External Review Team for the 2021 Academic Program Review (APR) Department of Biochemistry and Biophysics College of Agriculture and Life Sciences Texas A&M University April 18-21, 2021

External Review Team

Members Institution Email Address Mobile Number University of California, Susan Marqusee, Chair [email protected] (510) 666-3383 Berkeley University of Texas, Daniel Leahy [email protected] (512) 471-2575 Austin Brian Fox University of Wisconsin- [email protected] (608) 262-9708 Madison The Ohio State University Michael Ibba [email protected] (614) 688-3908

BCBP Self-Study Committee

Members Office Location Email Address Telephone Number Josh Wand, Chair 103E BICH [email protected] (979) 845-2772 Jean-Philippe Pellois 436A BICH [email protected] (979) 450-4817 Tim Devarenne N218A BICH [email protected] (979) 862-6509 Michael Polymenis 333A BICH [email protected] (979) 458-3259 Ping He 129 BORL [email protected] (979) 458-1368 Justine deGruyter 103C BICH [email protected] (979) 458-0631 Kaitlyn McGaff 104 BICH [email protected] (979) 458-1136 Betty Cotton 103D BICH [email protected] (979) 458-0630

* Emergency contacts: Josh Wand (215) 756-1018-cell (979) 845-2544-office; Betty Cotton (979) 218-9575-cell, (979) 458-0630

Monday, April 19, 2021

All Times listed in Central Time Participants 8:00 a.m. – 9:00 a.m. Entry Meeting: External Review Team and Provost’s Administrative Team Join Zoom Meeting Patrick Louchouarn, Interim Vice Provost – Faculty Affairs and https://tamu.zoom.us/j/9416850 Interdisciplinary Initiatives 7538?pwd=U0xHczBLeGp3eG George Cunningham, Senior Associate Dean, Graduate and Professional 1LL0NjaSs1UGx3dz09 Studies Valerie Balester, Assistant Provost, Academic Success Center Meeting ID: 941 6850 7538 Passcode: 439838 9:15 a.m. – 10:00 a.m.

Join Zoom Meeting https://tamu.zoom.us/j/9460154 Meet with Department Head of Biochemistry and Biophysics 7753?pwd=aEg5RzBpOWNoVl Josh Wand, Professor and Head JEbXBtdVBWRlNtUT09

Meeting ID: 946 0154 7753 Passcode: 495469 10:15 a.m. – 11:00 a.m.

Join Zoom Meeting Meet with College of Agriculture and Life Science’s Administration https://tamu.zoom.us/j/9258639 Patrick Stover, Vice Chancellor and Dean for Agriculture and Life Sciences 4236?pwd=bWR1Y2VOVUdZ and Director, Texas A&M AgriLife Research (potentially serving on Jury TFFkRW95VHpSZVdZQT09 Duty) Clare Gill, Executive Associate Dean and Associate Dean for Research Meeting ID: 925 8639 4236 Passcode: 776726 11:15 a.m. – 12:00 p.m. Meet with Self-Study Committee Josh Wand, Professor and Head Join Zoom Meeting Jean-Philippe Pellois, Professor and Associate Head https://tamu.zoom.us/j/9397315 Tim Devarenne, Associate Professor and Associate Head 5791?pwd=ZTF5SzR3Ymp3L0 Michael Polymenis, Professor d4SWc4OHM3aHgwZz09 Ping He, Professor (will join late after teaching) Justine deGruyer, Administrative Postdoctoral Associate Meeting ID: 939 7315 5791 Kaitlyn McGaff, Program Assistant Passcode: 563995 Betty Cotton, Administrator I 12:00 p.m. – 1:00 p.m. Lunch 1:00 p.m. – 1:45 p.m. Meet with Graduate Program Leadership Team

Jean-Philippe Pellois, Chair of the Graduate Program Join Zoom Meeting Tatyana Igumenova, Graduate Admissions Chair (will leave early to teach) https://tamu.zoom.us/j/9899550 Lanying Zeng, Chair of the Advisory Committee 5197?pwd=S09WVzdlbFJqWW Justine deGruyter, Recruitment and Outreach, Chair d2ZHZ4dHRGZlZMdz09 Cecilia Tommos, Member of Advisory Committee

Megan Teel, Academic Advisor, III Meeting ID: 989 9550 5197

Passcode: 749210 2:00 p.m. – 2:45 p.m. Meet with Assistant and Associate Professors Dmitry Kurouski, Assistant Professor Join Zoom Meeting Jae-Hyun Cho, Assistant Professor https://tamu.zoom.us/j/9134914337 Mary Bryk, 25% Associate Professor and 75% Associate Dean for Academic 3?pwd=SlM5Y2E4MUhvZ3dGMmoxU Affairs G1tTDR1Zz09 Timothy Devarenne, Associate Professor and Associate Head Margy Glasner, Associate Professor Meeting ID: 913 4914 3373 Vishal Gohil, Associate Professor Passcode: 806209 Jennifer Herman, Associate Professor Hays Rye, Associate Professor Paul Straight, Associate Professor Sing-hoi Sze, 40% BCBP Associate Professor, 60% Computer Science Lanying Zeng, Associate Professor Junjie Zhang, Associate Professor 3:00 p.m. – 3:45 p.m. Meet with Professors Jorge Cruz-Reyes, Professor Join Zoom Meeting Suma Datta, 100% Assistant Provost, Honors Program and Professor https://tamu.zoom.us/j/9905904519 Ping He, Presidential Impact Fellow, Professor 6?pwd=c2JGcmVudXloWDlHa0dwUG Pingwei Li, Professor I2U1IzQT09 Tom Meek, Professor John Mullet, Perry L. Adkisson Chair in Agricultural Biology and Professor Meeting ID: 990 5904 5196 Vlad Panin, Professor Passcode: 598328 Bill Park, Professor Michael Polymenis, Professor Jim Sacchettini, Professor and Wolfe Welch Chair Libo Shan, Christine Richardson Professor in Agriculture, Professor (potentially serving on Jury Duty) Dorothy Shippen, University Distinguished Professor and Regents Professor David Threadgill, University Distinguished Professor, Tom and Jean McMullin Chair, 49% BCBP Professor and 51% Molecular and Cellular Medicine Cecilia Tommos, Professor Ry Young, Sadie Hatfield Professor in Agriculture, University Distinguished Professor and Regents Professor Xiuren Zhang, Chancellor EDGES Fellow, University Faculty Fellow 3:45 p.m. – 4:30 p.m.

Join Zoom Meeting https://tamu.zoom.us/j/9304786770 Meet with Graduate Students 6?pwd=L0JMNDBWcVEvVU5lQlpNUn To be named. JmOTNNZz09

Meeting ID: 930 4786 7706 Passcode: 698027 4:30 – 5:15 p.m. Meet with Academic Professional Track Faculty Nicola Ayres, Senior Lecturer (might be late) Join Zoom Meeting Chave Carr, Senior Lecturer https://tamu.zoom.us/j/9994261862 Megan Reynolds, Senior Lecturer 5?pwd=d1laZVA3VUxhV2NBM3hDNz Shelley Pozzi, Senior Lecturer BTclpRUT09 Bryant Miles, Senior Lecturer Meeting ID: 999 4261 8625 Jane Pishko, Lecturer Passcode: 435276 Stephanie Perez, Lecturer

Tuesday, April 20, 2021

8:00 a.m. – 8:45 a.m. Meet with Joint Faculty Jeff Kapler, Chair, Department of Molecular & Cellular Medicine, Professor, Molecular & Cellular Medicine, Biochemistry & Biophysics Join Zoom Meeting Wenshe Liu, Gradipore Chair, Chemistry Biochemistry & Biophysics, https://tamu.zoom.us/j/97379918 Molecular and Cellular Medicine, Director, Texas A&M Drug Discovery 105?pwd=WEtKSzhWQklpa0dt Laboratory dWdzUmhWRmdZdz09 Frank Raushel, Distinguished Professor of Chemistry and Powell Professor of Science Meeting ID: 973 7991 8105 Steve Safe, University Distinguished Professor, Syd Kyle Chair, Veterinary Passcode: 266425 Medicine, Professor Veterinary Physiology & Pharmacology, Biochemistry & Biophysics, Molecular & Cellular Medicine Vytas Bankaitis, University Distinguished Professor, E.L. Wehner-Welch Foundation Chair, Chemistry Professor, Molecular and Cellular Medicine, Biochemistry and Biophysics, Chemistry 9:00 a.m. – 9:45 a.m. Meet with Undergraduate Committee Tim Devarenne, Chair, Professor and Associate Head Join Zoom Meeting Pingwei Li, Professor https://tamu.zoom.us/j/95955496224 Margy Glasner, Associate Professor ?pwd=bzlXUzdpVkQyd1RLUGhiajdEZn Gary Kunkel, Sr. Associate Professor F0Zz09 David Threadgill, Professor Vlad Panin, Professor Meeting ID: 959 5549 6224 Paul Straight, Associate Professor Passcode: 849790 Bryant Miles, Senior Lecturer Khara Spears, Academic Advisor, II Megan Teel, Academic Advisor, III Kaitlyn McGaff, Program Assistant 10:00 a.m. – 10:45 a.m.

Join Zoom Meeting https://tamu.zoom.us/j/91740104170 Meet with Undergraduate Students ?pwd=dmNBTzhuQVlqVmtsYVR1bmFv To be named. QUpJUT09

Meeting ID: 917 4010 4170 Passcode: 755361 11:00 a.m. – 11:45 a.m. Meet with Department Heads in Agriculture and Life Sciences Mark Waller, Acting Head of Agricultural Economics Join Zoom Meeting Matt Baker, Head Agricultural Leadership, Education & Communications https://tamu.zoom.us/j/95458196101 Cliff Lamb, Head of Animal Science and Interim Head of Rangeland, Wildlife ?pwd=MCtJQXdaazdENjJRaHdpTXJaV2 & Fisheries Management p1QT09 John Tracy, Interim Head of Biological Agricultural Engineering Kirk Winemiller, Interim Head of Ecology and Conservation Biology Meeting ID: 954 5819 6101 Phillip Kaufman, Head of Entomology Passcode: 978137 Bhimu Patil, Interim Head of Food Science and Technology Patricia Klein, Interim Head of Horticultural Sciences Leland (Sandy) Pierson, Head of Plant Pathology and Microbiology David Baltensperger, Head of Soil and Crop Sciences 12:00 p.m. – 1:00 p.m. Lunch 1:00 p.m. – 5:00 p.m. External Review Team meeting and work on draft report

Join Zoom Meeting https://tamu.zoom.us/j/92512713823 ?pwd=Yk1SMHpzQThZV0FwUlE5NlFjN 3l2dz09

Meeting ID: 925 1271 3823 Passcode: 884629

Wednesday, April 21, 2021

8:00 a.m. – 8:45 a.m. Exit Meeting with Provost’s Administrative Team and College Dean

Join Zoom Meeting Mark Weichold, Interim Provost and Executive Vice President https://tamu.zoom.us/j/94897182791?p Patrick Louchouarn, Interim Vice Provost – Faculty Affairs and wd=bDNBYzFXOWR4dW5hVE9qcUZ Interdisciplinary Initiatives ZeXhMdz09 Karen Butler-Purry, Asst. Provost for Graduate & Professional Studies Valerie Balester, Assistant Provost, Academic Success Center Meeting ID: 948 9718 2791 Patrick Stover, Vice Chancellor and Dean for Agriculture and Life Passcode: 478676 Sciences and Director, Texas A&M AgriLife Research Clare Gill, Executive Associate Dean and Associate Dean for Research 9:00 a.m. – 9:45 a.m. Reviewers debrief Graduate Program Leadership and Head Josh Wand, Professor and Head Join Zoom Meeting Jean-Philippe Pellois, Chair of the Graduate Program https://tamu.zoom.us/j/96256295358?pw Tatyana Igumenova, Graduate Admissions Chair d=U1NDeHlFOVNvZFN2UkFIMS8wVy9hQT0 Lanying Zeng, Chair of the Advisory Committee (will leave early to teach) 9 Justine deGruyter, Recruitment and Outreach, Chair Cecilia Tommos, Member of Advisory Committee Meeting ID: 962 5629 5358 Megan Teel, Academic Advisor, III Passcode: 564294 10:00 a.m. – 10:45 a.m. Reviewers debrief faculty, staff, and student on final report Join Zoom Meeting https://tamu.zoom.us/j/91512912958?pw Everyone welcomed and encouraged to attend. d=Q1d4K1d6d2dHNnQ1d2RlU3ZjZ25Mdz09

Meeting ID: 915 1291 2958 Passcode: 817815 11:00 a.m. – 11:45 a.m.

Join Zoom Meeting https://tamu.zoom.us/j/93587915365?pw Reviewers make final changes to report as necessary and submit d=ZHFjMXZKWjNoRHB6dUd2Zk9DbzNWZz

Meeting ID: 935 8791 5365 Passcode: 164329

Executive Summary This report describes the Department of Biochemistry and Biophysics at Texas A&M as of January 2021. As the PhD is a research degree and because the Department's undergraduate majors require independent research, this self-study covers the research environment and productivity of the Department.1

New leadership of the Department and its Undergraduate and Graduate programs have recently been installed. The Department and its programs are in a state of transition. Issues raised by the previous APR review have motivated some of the changes being made, but most seek to resolve new realities and developments. This instance of review is primarily motivated by a requirement for the periodic evaluation of our graduate program. Over the past decade or so, but particularly over the most recent few years, structural and programmatic weaknesses in many aspects of the graduate program have been revealed. In response, the graduate program structure and its staff have been completely revamped to correct a disturbing trend towards higher attrition, longer time to degree for those who survive, and increasing disaffection for the graduate program by the faculty and students alike. In addition, the program is being enriched in content and the mechanisms of delivery. Importantly, more extensive faculty involvement in advising and clearer and more uniform expectations for both research mentors and trainees are being installed. A significant concern stated in the previous review was the need to improve the quality of matriculating graduate students by increasing the program's attractiveness by improving the admission, recruitment, and outreach activities of the Department. We will describe below the tremendous strides, led by Dr. Justine deGruyter and Dr. Jean-Philippe Pellois, taken towards the modernization of the graduate program and its effectiveness.

The cornerstone of any graduate program is the faculty. The Department's faculty is large and varied, with over thirty Ad loc. research-active, tenure-track faculty, seven non-tenured academic professional teaching faculty, two research-track faculty, and nine adjunct/joint faculty. All contribute to the teaching mandate of the Department, most at both the undergraduate and graduate levels. The faculty spans an unusually broad range of topics in biochemistry, biophysics, and molecular genetics and has impressive representation across the major subdisciplines. The Department is unusually strong in plant biochemistry and genetics. There are, however, notable deficiencies in emerging areas such as cryoelectron microscopy, computational biology, integrated biochemistry including metabolism, protein chemistry including design, epigenetics, and so on. How representation in these fields will be distributed across the University is unknown, but it is clear that this Department ought to take a lead role in many of them. The current faculty's age distribution implies a need for rolling faculty hires over the next decade, which positions us to keep pace with the disciplines through careful recruitment of junior faculty.

The Graduate Program is nominally titled "Biochemistry," though the Department covers topics in biophysics, medicinal chemistry, and allied fields as noted above. The graduate student population is drifting downwards and now number roughly 90. A plurality of matriculants come from Texas. We are taking steps to broaden our national appeal while also raising the bar for admission. We have begun to "break" the historical tendency to have teaching assistant requirements override the rigor of admissions to the program.

1 Though it is directed by a BCBP faculty member and is provided administrative space and support by the Department, the Interdisciplinary program in Genetics operates independently of the Associate Head for the BCBP Graduate Program and is therefore only described here in passing.

Graduate programs and research in Biochemistry are infrastructure intensive. Access to expensive instrumentation and modern space is often the difference between leading-edge efforts and ones that stumble. This Department often finds itself on a knife-edge in that respect. As noted in the last review, COALS and the University seemed not to appreciate the instability introduced into the research effort by inadequate support for expensive instrumentation. The NMR resource was raised as a particularly acute example. Since the prior review, there has been an institution-wide investment in "heavy instrumentation" and, in some cases, with on-going support. We will describe a truly impressive investment by the University in cryoelectron microscopy. A manageable mechanism to pay down t he debt accumulated by the NMR users over the prior decade has been provided by the Vice Chancellor. On the other hand, the Department's perhaps privileged position with respect to indirect cost return has been eliminated, and a significant reduction in the Department's base budget was instituted this past fiscal year. When combined with the costs associated with an unanticipated directive to repatriate three faculty from the Borlaug Center into the Department's main building, our ability to support research and graduate education in the near future vigorously is clouded. Indeed, it is vital that the Department look forward to providing faculty representation in exciting emerging fields of Biochemistry, Biophysics, and Molecular Genetics.

The physical plant available to the Department is quite heterogeneous in quality. The main building (BCBP) supports the majority of teaching and research space of the Ad loc. faculty. Roughly 10% and 15% of the Ad loc. faculty are in the relatively new Interdisciplinary Life Sciences Building (ILSB) and the NMR annex (NMR) of BCBP, respectively. Three faculty are being evicted from a rather derelict space in the Borlaug Center, which is to be renovated and repurposed. These faculty will be relocated to BCBP. BCBP generates the most concern. A 1980s vintage building, BCBP is simply worn out and needs a serious "facelift" and installation of modern infrastructure for both teaching and research. There are no plans for a replacement building. The rolling renovation of space to accommodate new faculty, even at the least extensive and least expensive level, represents a high cost, potentially on the order of $10–15M. This is a major challenge facing the Department.

Biochemistry and Genetics undergraduate majors currently number over 500, and the Department teaches over 6,000 "seats" of biochemistry and genetics each year. Growth in major and non-major course enrollments since the last review is an astounding 40%. This represents a heavy teaching load on both research-active and lecturer faculty, often to the detriment of the former. In addition, these majors are research-demanding. Thus, the students' quality and the quality of the undergraduate research experience that we can offer them have a large impact on the style and quality of the Department's research enterprise. Dr. Timothy Devarenne has recently assumed the role of Associate Head for Undergraduate Programs. He has led a modernization of the Genetics major and is now positioning the Department to do the same for the Biochemistry major. Lurking on the horizon is the desire to establish a new major to recognize the breadth of the educational mandate of the Department, i.e., in molecular biophysics.

The Department's goal is to be recognized as a consensus "top ten" biochemistry and biophysics department of prominent public universities. Over the past decade, the Department's external recognition has diminished. There are many contributing factors, all of which are correctable with modest investments by the institution and realignment of priorities, resources, and tactics by the Department and its faculty. In the pages below, we

will highlight our perceived strengths and weaknesses of the Department and its programs. Various plans and strategies for correcting current deficiencies, enhancing strengths, and creating new capabilities will be outlined in the concluding section. Introduction to the Department

Departmental history The Department of Biochemistry and Nutrition was established in 1947, with the first students awarded PhD degrees in June 1950. In 1966, the Department's name was changed to the Department of Biochemistry and Biophysics (BCBP). Its mission expanded to include the undergraduate curriculum in biochemistry. The Department's faculty increased dramatically, and the first BS in Biochemistry was awarded in May 1969.

Following a departmental review in 1979, Dr. Gene Sander was hired as Head of the Department in 1980. Dr. Sander recruited seven faculty during the period from 1980-1987 and incorporated molecular biology and plant biochemistry into the Department. Three of these hires (Drs. Mullet, Park, and Young) remain as faculty of the Department. Dr. Sander also initiated planning and obtained approval for the new Biochemistry and Biophysics Building on West Campus, completed in 1989. Dr. Sander was promoted to Vice-Chancellor and Director of the Institute for Bioscience and Technology shortly before he left to become Dean of the College of Agriculture at the University of Arizona.

As the Department developed over the next several years, affiliated faculty, whose primary academic appointment resided in other departments and colleges, were included as joint members to strengthen overall departmental activities. Dr. Jim Wild served as Interim Head from 1987-89, and Dr. Martyn Gunn served as Interim Head between 1989-90. In 1991, the Institute of Biosciences and Technology (IBT) was built in Houston to provide a vehicle to connect Texas A&M University with the Texas Medical Center. This added several tenure- track faculty members affiliated with the Department under the leadership of Dr. Robert Wells, as Head of the Department. Dr. Wells left in 1992 to pursue his duties as Director of the IBT in Houston. Dr. Martyn Gunn returned as Interim Head again from 1992-94, and Jim Wild served as Head from 1994 until 2000. During this period, the Department was provided an endowed position, the Wolfe-Welch Chair in Science, which was used to recruit Dr. Jim Sacchettini to the Department in 1996. Dr. John Mullet was awarded the Perry Adkisson Chair in Agricultural Biology the same year.

With the creation of The Texas A&M University System Health Science Center, the IBT in Houston became an independent unit within the HSC. The tenure and promotion activities associated with the tenure-track faculty members located at the IBT were no longer the Department's responsibility. One of the IBT faculty (Dr. Magnus Höök) is currently affiliated with the Department as a joint member.

Dr. Greg Reinhart became Head of the Department in 2000. The Department expanded its research expertise in structural biology and molecular biology, especially in plant and microbial systems. Dr. Reinhart led the effort to create an annex to the BCBP building that expanded the laboratory space of the Department and, importantly, provided spacious open laboratory space suitable for heavy instrumentation such as NMR spectrometers and cryoelectron microscopes. He was involved in planning the Interdisciplinary Life Sciences Building where 5 faculty of the Department now reside. Dr. Reinhart stepped down as Department Head in 2018 and retired in 2020. Dr. Dorothy Shippen served as Interim Head from 2018–19 until Dr. Josh Wand was hired as Head of the Department in late 2019.

The current faculty consists of 30 Ad loc. tenured or tenure-track faculty, 9 joint faculty, 7 academic professional-track faculty, and 2 research-track faculty. The 10 tenured joint faculty are administratively affiliated with 5 departments at TAMU-College Station (Chemistry, Computer Science, Molecular and Cellular Medicine, Nutrition and Food Science, and Veterinary Physiology and Pharmacology) and the Institute for Bioscience and Technology (IBT) in Houston. Among the 30 Ad loc. faculty, Dr. Sing-Hoi Sze has his formal appointment split between the Department of Computer Science (60%) and BCBP (40%), Dr. David Threadgill (The Tom and Jean McMullin Chair of Genetics) between Molecular and Cellular Medicine (51%) and BCBP (49%), and Dr. Mary Bryk between College administration (75%) and BCBP (25%). Except for Drs. Threadgill (housed in Molecular and Cellular Medicine) and Sze (housed in Computer Science), all other Ad loc. appointments are housed in four buildings: The Biochemistry and Biophysics (BCBP) Building; The NMR Building (opened in 2008); The Interdisciplinary Life Sciences Building (ILSB, opened in 2009), and the Borlaug Building. Three faculty members—Drs. Libo Shan (The Christine Richardson Professor in Agriculture), Ping He, and Xiuren Zhang—currently reside in the Borlaug Building. As will be described in more detail below, the closure of the Institute of Plant Genomics and Biotechnology and the capture of the Borlaug Building by AgriLife has required that all three of these faculty be repatriated to the main BCBP building. Mission, strategic plan and goals BCBP strives to be an intellectually robust and inclusive community of scholars with a common interest in integrating chemistry, biology, mathematics, and physics to understand the molecular basis of life. The historical strength of the Department in plant biochemistry and genetics; structural biology and molecular biophysics; drug discovery; enzymology; computation in various forms; metabolism from microbes to plant to humans; cell biochemistry and imaging, agricultural biotechnology, molecular genetics, and other allied areas of our core fields has resulted in research efforts that span a remarkable range of biochemistry and biophysics. Teaching and research are intimately intertwined, coupling modern didactic instruction, and extensive research experience for undergraduate students. The Department makes great efforts to introduce students to the wonders of biochemistry, biophysics, and molecular genetics and lay the foundation for a successful career in research or the allied professions. The Department's goal is to be recognized as a consensus ‘top ten’ biochemistry and biophysics department associated with prominent public universities. Over the past decade the Department’s external recognition has arguably diminished. There are many contributing factors, all of which are correctable with modest investments by the institution and realignment of priorities, resources and tactics by the Department and its faculty. Primary issues or weaknesses include a failing infrastructure, a struggling graduate program, an aging faculty with poor demographics and limited departmental resources to finance faculty recruitment, especially in instrument-intensive areas central to biochemistry and biophysics. Administrative Structure BCBP and the College of Agriculture and Life Sciences (COALS) have undergone significant organizational changes over the last three years. In 2019, Dr. Josh Wand was named Department Head. He was hired from the University of Pennsylvania, where he served as Benjamin Rush Professor of Biochemistry and Biophysics for 22 years. Dr. Wand initiated several large-scale reorganizations of the administrative structure and focus of that structure, many of which will be described in more detail below.

The same year, Dr. Patrick Stover was hired from Cornell University to become Vice-

Chancellor and Dean of COALS. Vice-Chancellor Stover has instituted many significant changes in the organization of both COALS and AgriLife that impact the Department significantly. In response to financial challenges brought about by the global pandemic, the Dean directed a significant reorganization of the administrative structure throughout the College and Texas A&M AgriLife Research. Staff who were laid off at the Department level were encouraged to reapply for similar positions created in the College. Departmental staff in the Business, IT, and Advising Offices now fall under the new structure. As a result, some professional staff administered directly by the Department are now centrally administered by the College. Some of that staff are not housed in BCBP (IT support, Academic Advising), while others (Business Office) are. Overall, 20 staff members are housed in BCBP, and they are distributed in the following administrative groups:

GROUP MEMBERS Leadership Dr. Josh Wand (Head) Drs. Tim Devarenne (Assoc. Head), Jean-Philippe Pellois (Assoc. Head) Faculty Committees Various Administrative Support Betty Cotton Tillie Rausch, Daisy Wilbert, Rene Patton Undergraduate Office Kaitlyn McGaff Graduate Office Dr. Justine deGruyter, Nowlan Savage Facilities Terry Lovingshimer, Austin Johnson, Raul Rodriguez Stockroom Divina Page, Sherry Barnett, Bruce Washington Business Staff* Sarah McLaughlin Jenny Ponzio, Sherry Coronado, Shelly Pasket, Kristin Vierus *these employees are housed in departmental space, but supervised by the Director of Business Services with “dotted line” reporting to the Department Head.

The administrative structure of BCBP is summarized in Figure 1.

FIGURE 1. Organizational chart of the Departmental administration. Leadership The Department Head (DH), Dr. Josh Wand, has a 40% administrative and 60% research appointment. It is also noted that Dr. Wand volunteers to teach 1/3 of the undergraduate major course BICH440 with Dr. Pellois. The DH provides leadership and facilitates

administrative support toward the achievement of the Department’s mission. Specifically, the DH: ● provides intellectual and philosophical leadership to synergize faculty, staff, and students in academic and research pursuits in the broad fields of biochemistry and biophysics; ● oversees the management of the Biochemistry and Genetics undergraduate programs and the Biochemistry graduate program; ● oversees and appoints departmental committees; ● manages the Department's human, physical, and fiscal resources, including coordination of major facility renovations; ● fosters a culture of inclusive excellence in support of a diverse faculty, staff, and student body; ● represents the Department in the COALS and Texas A&M AgriLife Research administrative structure, including Department advocacy in programmatic goals and strategies, including the Precision Nutrition initiative; ● represents the Department in dealings with state and federal agencies, private organizations, partners and collaborators, and key industry groups; and ● provides leadership for continued acquisition of internal and external resources to enhance departmental programs.

The Associate Department Head for Graduate Programs (ADHGP), Dr. Jean-Philippe Pellois, has a 15% administrative, 60% research, and 25% teaching appointment. The ADHGP: ● Oversees the administration of the Biochemistry graduate program, including the coordination of administrative and advising staff as appropriate; ● Actively pursues improvements in the graduate curriculum, including the development of a Biophysics graduate degree; ● Assists the DH in the development of teaching assignments and long-range planning of faculty teaching; ● Coordinates with the DH and ADHUP on the teaching assistant program, including teaching assistant assignments, the definition of duties, and oversight; ● Represents the interests of the Graduate Program at the Departmental, College, and University level, as appropriate; and ● Represents the Department on behalf of the Head at formal functions, meetings, and other administrative activities, as required.

The Associate Department Head for Undergraduate Programs (ADHUP), Dr. Tim Devarenne, has a 15% administrative, 60% research, and 25% teaching appointment. The ADHUP: ● Oversees the administration of the Biochemistry and Genetics undergraduate programs, including the coordination of administrative staff as appropriate; ● Actively pursues improvements in the undergraduate curriculum, including the development of a Biophysics undergraduate degree; ● Assists the DH in the development of teaching assignments and long-range planning of faculty teaching; ● Coordinates with the DH and Associate Head for Graduate Programs on the teaching assistant program, including teaching assistant assignments, the definition of duties, and oversight; ● Represents the interests of the Undergraduate Program at the Departmental, College, and University level, as appropriate; and

● Represents the Department on behalf of the Head at formal functions, meetings, and other administrative activities, as required.

Faculty departmental committees The Department has three Permanent Committees, with detailed rules governing their structure, as defined in the Departmental by-laws (see Appendix A). These committees are the Executive (EXCOM), Promotion and Tenure (PATC), and the Post-Tenure Review Committee (PTRC). At least some of their members are elected by the faculty. Changing the organization of the permanent committees requires an amendment in the by-laws. All other committees are put together by the Department Head as necessary, on a standing or Ad hoc. basis. As part of their service duties (see Appendix B), faculty participate in various committees. The committees of the faculty are listed below. The current members of each committee are described later, in Table 17, when the faculty's service productivity will be outlined. Permanent committees ● Executive Committee (EXCOM) ● Promotion and Tenure (PATC) ● Post Tenure Review (PTRC)

Standing committees Standing committees are appointed to manage the ongoing affairs of the Department. The current standing committees are listed below.

● Awards Committee ● Climate Committee ● Development ● Facilities-CUE ● Graduate Admissions (GRAC) ● Graduate Advising ● Graduate Outreach & Recruitment ● Executive Committee of the Graduate Program ● NMR Users Committee ● Seminar/Virtual Seminar ● Undergraduate Program Committee (UPC) ● Website

Ad hoc. committees Ad hoc. committees are appointed to manage temporary projects in the Department. The current Ad hoc. committees are listed below.

● APR self-study ● Covid-Safety Committee ● Departmental Study Section ● Facilities Renovation Committee

● Faculty Search Committee ● Junior Faculty Mentoring ● Non-Thesis Masters Committee

Administrative support staff The administrative support staff is led by Ms. Betty Cotton, who assists the DH and manages three Administrative Associates: Tillie Rausch, Daisy Wilbert, and Rene Patton. Ms. Cotton works directly with the DH to coordinate all Departmental administrative duties, including timely submission of required reports, scheduling, and document management. Each Administrative Associate is assigned to several faculty members to assist with teaching, research, and service duties. Undergraduate office staff The Associate Head of Undergraduate Programs (Dr. Tim Devarenne) leads the Undergraduate Programs’ Office. Dr. Devarenne is supported by Ms. Kaitlyn McGaff, Program Assistant. Together, they participate in weekly meetings with the COALS Advising Center Team 5 to coordinate the programs' academic advising and administrative support. In addition to general program administration, Ms. McGaff oversees undergraduate teaching evaluations, textbook adoptions, scholarship distributions, and other tasks as needed. Graduate office staff The Associate Head of the Graduate Program (Dr. Jean-Philippe Pellois) leads the Graduate Program Office. Dr. Pellois is supported by an Administrative Postdoctoral Associate, Dr. Justine deGruyter, and a Program Assistant, Mr. Nowlan Savage. Dr. deGruyter helps manage the Graduate Program and is responsible for program evaluations, teaching assistant assignments, course evaluations, course assignments and scheduling, and the graduate program's general administration. Dr. deGruyter also serves as the Chair of the Outreach and Recruitment Committee and as an ex officio member of the Advisory Committee and the Admissions Committee. Mr. Savage assists with general program administration and plays a crucial role in website administration. Web presence The Graduate Office also helps maintain the department web presence, including a complete overhaul of the Departmental website in Summer 2020 and facilitation of all social media accounts. Facilities management staff Mr. Terry Lovingshimer is charged with maintaining the main BCBP and associated NMR annex, including research laboratories and equipment. His team comprises Mrs. Austin Johnson, Facilities Coordinator II, and Raul Rodriguez, Laboratory Mechanic II. The Facilities Management Team oversees building maintenance and repairs in BICH and the NMR Facility; coordinates with SSC on complex repairs; maintains common-use equipment; coordinates laboratory and office rearrangements and/or evacuation; implements preventative maintenance systems and schedules; maintains equipment inventory. Mr. Lovingshimer’s talented team has proven to be a critical asset and often performs in-house maintenance or repairs, thereby saving the department on the order of millions of dollars. Mr. Lovingshimer is currently overseeing the building remodel initiated in

Fall 2020 with an anticipated completion of 2022. The remodel is delineated in Appendix C.

Stockroom staff Ms. Divina Page manages the BCBP Stockroom. Ms. Sherry Barnett and Mr. Bruce Washington support her. The Stockroom has been significantly reorganized over the past two years to position it to be a profit-center for the Department. The Stockroom maintains a large in-house inventory of scientific and office equipment while also coordinating specialty purchases from external vendors. COALS administrative staff As mentioned above, due to the College-wide restructuring that took place, additional Staff associated with BCBP operations are now centrally administered by the College. Some of that Staff (in the Business Office) are housed in the main BCBP building, but others (IT, Academic Advising) are not. The COALS administered staff groups are shown in Figure 2.

FIGURE 2. Organizational chart of the College-administered Business, IT, and Advising Offices.

Business Office The Business operation of the Department was centralized in 2020 under Mr. Robert Pottberg, COALS Director of Business Services. Around this time, the long-time business administrator of the Department (Ms. Melissa Kay) left to join the Department of Chemistry and Ms. Sarah McLaughlin (formerly College of Veterinary Medicine) took up the position as

Senior Business Administrator. Ms. McLaughlin reports to BCBP’s Department Head but remains under the formal supervision of Mr. Pottberg. The Business Office staff remains physically located in BCBP and is comprised of: ● Ms. Jenny Ponzio, maintains all account reconciliations and provides accounting reports for all grants. She also manages accounts payable and receivable and processes graduate student tuition/fees payments. ● Ms. Sherry Coronado, serves as the primary Human Resources and payroll representative for research staff, faculty, and students, including recruitment, reclassification, equities, and salary actions. She works alongside Sponsored Research Services (Mr. Dylan Gregg) to track cost-sharing requirements and investigate grant charges, including payroll and other posts. Ms. Coronado assists with graduate student tuition/fees and solves problems with student accounts, grant charges, and re-budgeting. She is the designated Absence Partner for the Department. Finally, Ms. Coronado also manages faculty budgets—including creating, re-budgeting, cost-sharing of funding—and oversees time and effort reporting for all PIs. ● Ms. Shelly Pasket, responsible for all purchasing over $10,000, approves all laboratory requisitions that route through AggieBuy, monitoring receiving and invoicing for AggieBuy purchases. She also prepares travel expense reports for all Department representatives. ● Ms. Kristin Vierus, assists Ms. Coronado with payroll and international documents. She is also responsible for formalizing the creation and posting of new positions, recruitment, hiring and termination, biweekly payroll, personal reimbursements, payroll corrections, and graduate student hiring. Ms. Vierus manages H1-B and J-1 document processing for international faculty and staff. Finally, she is responsible for the reconciliation and processing of purchases made with payment cards. Information Technology In 2019, administration of the local BCBP Information Technology (IT) team (3 employees) was transferred to the AgriLife IT Department. In 2020, IT was centralized across the College. The original BCBP IT staff has largely turned over with only one member remaining. BCBP IT is now handled by so-called Area 2 Support Staff, alongside the Departments of Horticulture Sciences, Plant Pathology and Microbiology, and Rangeland, Wildlife, and Fisheries Management. Mr. Alan Kurk and Mr. Tim Ramsey oversee AgriLife IT, while Mr. Aaron Rodriguez is the Area 2 Manager. Area 2 Staff remain in the main BCBP building. AgriLife IT supports faculty, student, and staff personal computers; accounting computers; classroom computers; and numerous servers associated with individual faculty research programs. In addition to AgriLife IT support, the University provides network infrastructure, email systems, and access to restricted resources, including online journals and learning management systems. The University also manages most classroom audio/visual resources. Academic Advising Undergraduate and graduate academic advising was also centralized at the College level. BCBP is assigned to AGLS Advising Center 5, along with the Departments of Entomology, Food Science and Technology, and Nutrition. Research Staff Finally, although not involved in administration, there are currently 92 non-faculty research staff members (research scientists, postdoctoral research associates, research assistants,

technicians, programmers, etc.) associated with various BCBP laboratories. Departmental Resources Facilities Faculty with primary appointments in the Department are located in four buildings: the main BCBP building and its annex, the Borlaug Center and the Interdisciplinary Life Sciences Building (ILSB). ILSB is located on the main campus while the others are located a brisk 10- minute walk away on the west campus. Main BCBP Building The Department of Biochemistry and Biophysics is physically located primarily in the BCBP Building, first occupied in 1989. The Department is assigned approximately 85,000 ft2 of usable space, with the remainder of the building (approximately 10,000 ft2, mostly on the first floor) occupied by general university functions, primarily the two large lecture halls, which are used quite heavily for undergraduate teaching, the Atrium foyer area and the Ag Cafe. Of the 85,000 ft2, approximately 57,000 ft2 is currently assigned to 15 of the 30 Ad loc. faculty as primary research laboratories, offices, equipment corridors, cold-freezer rooms, and specialized rooms for equipment, autoclaves, dishwashing, tissue culture, plant growth chambers, and biological isolation.

Most of the faculty research space is divided into modules of ~900 ft2 containing laboratories, equipment rooms, and offices. There are 48 of these modules on the third and fourth floors. Approximately half of the second floor is occupied by teaching laboratories (8 modules) and an open student lounge area. Still, there are also 14 more research modules plus some other research space not arranged in modules.

There are two major lecture halls on the first floor, a smaller classroom, and the West Campus Bioinformatics Classroom, with ~23 workstations for personal computing. The first floor also houses Departmental Administration offices and the Stockroom.

The average space allocation to a research-active faculty member is two modules, with the range between 1 and 4 modules, depending on the laboratory groups' funding and staffing levels. Of the remaining 20,000 ft2, approximately 10,000 ft2 is dedicated to teaching labs, lecture halls, and conference rooms. Departmental administration, accounting, academic counseling, and a stockroom occupy roughly 10,000 ft2. The map of each floor of the BCBP building is in Appendix D. NMR Annex Five faculty members (Drs. Igumenova, Cho, Devarenne, Wand, and Tommos) are housed in the NMR wing of the main BCBP building. The NMR wing houses the Biomolecular NMR laboratory. The five NMR spectrometers are overseen and funded by this user group as a “club” and are not operated as a classic core resource. It is self-supporting and receives no funding from the University or AgriLife. The map of each floor of the NMR building is in Appendix E. In 2020, the Department took steps to initiate a major investment in cryoelectron microscopy. With the strong participation of Chancellor Sharp, Vice-Chancellor Stover and then Provost Fierke, a Titan Krios G4 cryoEM instrument was purchased. Space was identified in the NMR laboratory as the most suitable for housing this instrument. The instrument has been delivered and is awaiting necessary renovations that will be completed in late 2021.

Borlaug Center Three faculty members (Drs. He, Shan and X. Zhang) are currently housed in the Borlaug Center which is a few minutes walk from BCBP. Drs. He, Shan, and Zhang were members of the Institute for Plant Genomics and Biotechnology (IPGB). The IPGB was dissolved in the Summer of 2020. Following a significant renovation in mid-2021, they will relocate to the BCBP building. Interdisciplinary Life Sciences Building (ILSB) The Interdisciplinary Life Sciences Building, opened in 2009, includes 220,000 gross sq ft for research laboratories, teaching, and related activities. The building houses around 30 flexible laboratory modules used by faculty from different departments, including BCBP, Chemistry, Biology, and Psychology. Five BCBP faculty members with primary appointments (Drs. Sacchettini, Li, Gohil, J. Zhang and Meek) reside in the ILSB and occupy 29,000 sf of laboratory and office space. The ILSB also houses several core facilities. The ILSB is located on the main campus across the railroad tracks from the other BCBP facilities on West Campus. The ILSB has a couple of dedicated visitor parking spaces for members of the Biochemistry Department. The completion of an underpass in 2013 makes walking to and from the ILSB much more convenient. Research Infrastructure The University supports a number of research resources that are particularly pertinent to the training and research environment of BCBP. Formal “centers” are generally recognized by the Board of Regents and provided, at least initially, with significant support by the office of the Vice President for Research. Two such centers are directed by Ad loc. BCBP faculty. Center for Phage Technology In 2009, the University held a campus-wide “white paper” competition, in which teams of faculty proposed new interdisciplinary research programs. After being chosen from over 120 submissions, the Center for Phage Technology (CPT) was officially created by the Texas A&M Board of Regents in May 2010, with University Distinguished Professor Ry Young as its Director. As the first state-funded phage research institute in the United States, the CPT's mission is to establish Texas A&M as the world’s premier center for bacteriophage research and its translational applications to practical problems in human, animal, and crop disease, as well as in industrial applications. In 2016, the CPT was a lead organization in the first modern application of phage therapy in the West to treat a desperately ill patient in California successfully (“the Tom Patterson Case”); this event is widely viewed as a watershed in modern antibacterial therapeutics. Interdepartmental recruiting involving four departments resulted in the hiring of four faculty Dr. Jason Gill (2013) in Animal Science and three in Biochemistry and Biophysics: Dr. Jennifer Herman (2011), Dr. Lanying Zeng (2012) and Dr. Junjie Zhang (2014). All have been promoted and tenured. The CPT operations budget supports various research and training activities involved in helping faculty develop grant proposals and carry out phage-related research, as well as developing a cadre of young phage biologists through the BICH464 Phage Genomics course. To date, many grants and contracts have been won based on CPT activities and sponsorship, including not only the core faculty of the CPT but also scientists from civil and chemical engineering. In addition, the existence of the CPT as a research focus has proven to be attractive to several doctoral program applicants from across the country.

Center for Structural Biology The Center for Structural Biology (CSB) is headed by Dr. Jim Sacchettini. The CSB provides x-ray crystallography equipment and expertise to the Texas A&M community. The Center is involved in a number of projects using structural biology to answer questions about different diseases that affect human health. Additional instrumentation and experienced support staff in high-throughput inhibitor screening, medicinal chemistry, and pharmacology are also part of the CSB. Current areas of interest include infectious disease, cancer, and metabolic diseases.

CSB has a 1,600 square feet area where two X-ray diffraction stations equipped with two R axis IV++ and one Bruker CCD detectors are located. Three walk-in crystallization rooms are located close to the diffractometer for protein crystal production and storage. An additional 1,500 square feet robotics facility includes a TTP Labtech Mosquito Liquid Handling System, Phoenix Liquid Handling System and TECAN Universal Plate Piercer.

The CSB medicinal chemistry facilities include a Shimadzu analytical LCMS system, a Thar SFC-MS system and two Mass Spectrometry Systems, a Genevac Evaporator System, a Bruker Microtof-Q spectrometer with Agilent HPLC, and a Bruker FTICR 9.4 GHz mass spectrometer, several Teledyne ISCO Silica flash columns, a 500mHz Varian NMR with auto sampler.

The CSB high throughput screening lab has three Cy-Bio automated liquid-handling robotic systems, two of them are in Biological Safety Cabinets: The CyBio Vario system handles high throughput plate assays. A CyBio 8plus1 integrated robotic system does hit picking, samples serial dilution, plates piercing, sealing and plate reading. 8plus1 has been connected to four CyBio stackers which can hold more than 100 plates and over 30,000 compounds at one time. The HTS lab also has several plate readers including Labtech CLARIOstar BMG plate reader for assay readouts and two Eppendorf epMotion 5075 LH automated pipetting systems which also can do the cherry picking. We also have a third Cy- Bio integrated robot with an InCell 2000 high throughput microscope.

The CSB pharmacology facility includes shared necropsy, procedure, and surgical suites as well as two animal housing rooms comprising OptiRat and OptiMice high density cage systems. Veterinary care and basic animal husbandry are continually provided (24-7, 365) via an agreement between CMP, the attending veterinarian, and Dr. Sacchettini’s preclinical trial staff. Specialty shared equipment includes Abaxis VetScan hematological analysis system, ECGenie electrocardiogram system, euthanasia stations, and anesthesia stations located in common equipment/procedure areas. Additional animal facility space is available at Laboratory Animal Care Building (LARR) on TAMU West. Common use equipment system (CUE) Before the Department moved into the Biochemistry and Biophysics Building during July/August 1989, 10% of the building cost ($2M) was set aside and designated for the purchase of movable equipment for teaching. A large portion of this equipment was used for teaching in the undergraduate laboratories. The remainder was dedicated to the graduate teaching function and is distributed throughout the building for common use. As the warranty periods for the new equipment expired, the CUE system was established to manage common use equipment for research groups in the Biochemistry Building. When the NMR building was added, the CUE system was extended to cover its occupants. CUE is overseen by the Common Use Equipment Tsar In Place (CUETIP), usually the sole member of the Facilities Committee. The following faculty members have served as 31

CUETIP: Drs. Ry Young (CUETIP the first), Gary Kunkel (CUETIP II), Ed Harris (CUETIP III), Donald Pettigrew (CUETIP IV), Gary Kunkel (CUETIP V) and currently Tom Meek and Bill Park (CUETIPs VI). CUE is maintained by a combination of service contracts and local maintenance coordinated by Mr. Terry Lovingshimer, the BCBP building proctor. CUE's philosophy is that everyone has equal access to CUE and pays an equal share of the maintenance cost. There is no opt-out of CUE for anyone whose laboratory is located in the BCBP and NMR Annex. The cost of equipment maintenance is apportioned based on the number of users in a research laboratory. A census of users is taken at the start of the fall semester and that census is used for the entire fiscal year. Faculty, postdoctoral associates, research staff, and graduate students count towards a head count that is used to determine a prorated share of the costs. There is some accommodation for equipment used disproportionately by a subset of faculty. Current CUE and its location are listed in Appendix F. Biomolecular NMR laboratory The Department has arguably the most comprehensive solution NMR resources of the southwestern United States. Bruker Avance III HD 800, 600 and 500 MHz and Bruker NEO 800 MHz and 600 MHz spectrometers form the NMR resource of the Biomolecular NMR Resource of the Department. All spectrometers comprise four independent channels for 1H, 13C, 15N and 2H and triple resonance probes. Both 800 MHz spectrometers and the Avance 600 and 500 MHz spectrometers are equipped with He-cooled with cryogenically cooled probes. The NEO 600 MHz instrument triple resonance probe is also 19F capable and is nitrogen cooled. Standard conventional room temperature triple resonance probes are also available for each spectrometer. The Wand group is the inventor of the current implementation of high-pressure NMR, which is used throughout the world. Accordingly, the laboratory is equipped with state-of-the-art high pressure NMR apparatus. The research laboratories of primary departmental faculty users (Drs. Wand, Tommos, Igumenova, Cho) are located in the NMR wing across the hall from the NMR instrument arena. Protein Chemistry Lab (PCL) The future of the PCL is in doubt. Historically, the PCL has provided state-of-the-art instrumentation, systems, software, technical expertise and training as a means to support cutting-edge research in various techniques in protein chemistry and proteomics. The emphasis has been in mass spectrometry. For some time, the PCL has been a University- recognized “core” facility. However, realignment by the office of the Vice President for Research has resulted in the PCL losing this designation and financial support. AgriLife declined to provide support as an AgriLife “core” and the responsibility of the PCL has fallen entirely to the Department. A reorganization is being attempted with the goal of providing a financial and demand justification for consideration of PCL as an AgriLife core resource. It is unclear whether this will be successful. Integrated metabolomics analysis core (IMAC) Established in 2016 with the TAMU Research Development Fund, the IMAC is a University “core” and is the result of a strategic investment in Metabolomics. The IMAC operates as a fee-for-service core facility. The IMAC is located in the main BCBP building. The Department provides administrative and business support but no financial underwriting. Response to previous APR critiques The IMAC and PCL are excellent examples of the University-wide effort to support research instrumentation infrastructure. Funded, in part, by capture of indirect cost, the Research Development Fund (RDF) provides competitive mechanisms for groups of researchers to

32 request support for purchase of expensive instrumentation. The RDF supported the purchase of an array of mass spectrometry instruments, much of which resides in the IMAC and PCL. In response to the previous review, the University and College provided $1.5M that was used towards replenishment of the CUE instruments, mostly involving the purchase of centrifuges. Analysis The dissolution of the IPGB and the necessary repatriation of three faculty to the main BCBP building presents a serious logistical, financial, and scientific challenge. The nature of the plant biochemistry research carried out by Drs. Shan, He and Zhang will require carefully controlled plant growth facilities local to their laboratories. This will require the installation of expensive growth chambers within the BCBP building. Even a modest “lowest level” renovation is priced at $150 sq ft. Purchase and installation of the required growth chambers will approach $2M. Thus, the overall cost to move these faculty into minimal quality space with the necessary infrastructure will approach $3.5M. This is well beyond the resources of the Department. It should be pointed out that these three faculty – Drs. Shan, He and X. Zhang – are truly mid-career superstars and need to be protected from destabilizing effects of this transition.

In the longer term it is clear that the ever-increasing array of expensive and complicated instrumentation (e.g., cryoEM, NMR spectrometers, calorimeters) and infrastructure (e.g., plant growth chambers) will outstrip the Department’s ability to support them. The University model for “core” support is outmoded and generally leads to a “death spiral” when applied to biochemical instrumentation. The “club” model used for the NMR resource is more cost effective but puts considerable strain on the users. This is a common issue and is not peculiar to Texas A&M. Regardless, accommodation in the financial model of the Department must be found to ensure the viability of leading-edge research utilizing expensive but critical instrumentation and infrastructure. 33

Academic Programs

Graduate Programs The Department of Biochemistry and Biophysics (BCBP) administers a PhD in Biochemistry. BCBP does not offer a standalone M.S. program, but thesis and non-thesis MS degrees are awarded to qualified students who opt to leave the PhD program. Degree programs in Biophysics (BS, PhD) are in development, with a projected launch of Fall 2023. PhD in Biochemistry The BCBP graduate program seeks to foster an inquisitive and diverse community of scholars with a common interest in the chemical and physicochemical processes that occur within living systems. Upon completing the program, students are equipped to solve scientific challenges by applying empirical and theoretical methods. The State of Texas specifies many of the items described below (Texas Administrative Code Rule §5.52).

Over the past year the BCBP graduate program has been completely overhauled. Almost every aspect of the program structure has been revisited and modified to some degree. Poor time-to-degree, attrition, graduate student recruitment and other critical criteria motivated a drastic intervention. The program is largely styled on that implemented by Dr. Wand at the University of Pennsylvania during his tenure as Chair of the Graduate Group of Biochemistry and Molecular Biophysics. Concomitant with the program implementation was a general refreshment of the graduate program office through the establishment of a postdoctoral-level coordinator ultimately filled by Dr. Justine deGruyter. Dr. deGruyter in conjunction with Dr. Wand and Dr. Pellois, recently appointed as Associate Head for the Graduate Program, have installed the new structure over the past year and a half. Dr. deGruyter is to be applauded for her imagination and dedication to this task.

The general theme of the new program structure is to enhance efficiency and predictability, which are identified as two issues that often lead to confusion and stress in graduate students. Specific steps taken include: introduction of a well-defined timeline to examination of candidacy for the PhD degree; removal of the inherent conflict-of-interest of the advising mentor in administrative guidance of dissertation research; introduction of a candidacy proposal writing course; creation of a pre-candidacy advisory committee of faculty that meets individually with students three times a year; continuing rationalization of course structures and topical content; among many other tactics and strategies.

The BCBP Graduate Office is led by the Associate Head of the Graduate Program and comprises three committees: Advisory, Admissions, and Outreach and Recruitment. The Associate Head of the Graduate Program (AHGP) and the Graduate Program Coordinator (GPC) serve as the primary program administrators. The Graduate Program Handbook has been rewritten to incorporate the vast number of changes and introduce the new philosophy. It is maintained by the GPC and defines the programmatic components of the doctoral degree (Appendix G). A current Handbook is issued to students on matriculation and reviewed in detail during Graduate Student Orientation. The Handbook's web version is updated immediately upon issuance of new department or university protocols, rules, and/or regulations.

The Advisory Committee guides pre-candidacy students in laboratory rotation, elective coursework, Journal Club, and thesis committee selection. This committee is a new committee and fulfills an important need for pre-candidacy students. The committee helps orient students to the program and assists in developing a tailored curriculum that

buttresses strengths and targets deficiencies. The Advisory Committee meets individually with students six times throughout the first two years of study (Figure 3). We note that our timeline is somewhat incongruent with the regulations of OGAPS/GPS, where an advisory committee and degree plan is to be established before the student passes the preliminary examination. This is more a logistical issue than a philosophical one. One approach is to have the standing BCBP Advisory Committee, with an external member, fill the GPS advisory committee role. Another issue is the distinction of the administrative chair, which we believe is absolutely necessary, from the research (thesis) mentor, who should receive the recognition as such but the current GPS “forms” do not allow this. We are in conversation with GPS to resolve these small but inconvenient incongruities.

FIGURE 3. Typical schedule of Advisory Committee meetings. Year 1 (Y1) and year 2 (Y2) are divided into Fall (FA), Spring (SP) and Summer (SU) academic semesters.

The Admissions Committee evaluates prospective graduate student applications, nominates incoming students for internal awards, and hosts Graduate Recruitment Weekend (GRW). In 2020, six Life Sciences doctoral programs—BCBP, Entomology, Biology, Medical Science, Genetics IDP, Toxicology IDP—joined to host the inaugural Life Sciences Symposium on the final day of GRW (see Appendix H). With more than 400 prospective students, current students, and faculty in attendance, the day-long symposium featured graduate student posters and short-talks, resource tables, and keynote talks from the Vice President for Research and the Associate Provost for Graduate and Professional Studies. Pending continued financial support from the Office of Graduate and Professional Studies (OGAPS), which is now being restructured as the Graduate and Professional School (GPS), BCBP has committed to co-hosting the annual symposium for at least two more years.

The Outreach and Recruitment Committee seeks to attract quality graduate students to our program through scientific community engagement, partnership with regional institutions, direct marketing, and web presence. Since its inception in 2019, the committee has assisted in the department website's complete overhaul, including developing individual faculty research websites, revamped department social media accounts, and initiated an assertive email and web advertising campaign. In response to recruitment limitations imposed by the COVID-19 pandemic, the committee developed the 2020 BCBP Graduate Admissions Workshop. This 10-week virtual lecture series sought to address common questions, dispel myths, and identify success strategies in the graduate admissions process. 148 students across 60 institutions registered for the workshop, more than 50% of whom identify as an underrepresented minority (URM) student or attend a federally designated URM-serving

institution. 39% of registrants cited Spring or Fall 2021 as their target semester of matriculation, while the remaining 61% cited target matriculation years of 2022 or 2023. Among those interested in a 2021 start, 48 were enrolled in majors that would reasonably translate to our program (i.e., BICH, CHEM, BIOL, etc.). 12.5% of these students applied for Fall 2021 admissions. Program Curricula The PhD degree is granted based on original research, coursework, and successful completion of required benchmarks, including the Preliminary Examination and Research Proposal. Incoming graduate students should have strong foundational knowledge in biology, chemistry, mathematics, and physics. Recommended prerequisite coursework includes: ● Two semesters of Biochemistry (equivalent to BICH 410/411) ● One semester of Physical Chemistry (equivalent to CHEM 328) ● One semester of Molecular Genetics (equivalent to BICH/GENE 431) ● Two semesters of Organic Chemistry (equivalent to CHEM 227/228) ● One semester of Physics ● One semester of Calculus Students who wish to take remedial coursework (e.g., GENE 431, CHEM 328) may discuss their options with the Advisory Committee before the Fall semester. A typical degree plan is outlined below (see also Appendix I). Year 1. During the Fall of the first year of graduate studies, students take 4 courses and participate in three 5-week laboratory rotations. Students will meet individually with the Advisory Committee during orientation week to discuss procedures and recommendations for selecting laboratory rotations. At the end of this semester, most students will choose a research group to begin their preliminary examination and research proposal. BICH 603 Principles of Biochemistry and Biophysics 3 cr. BICH 608 Critical Analysis of the Biochemical Literature 2 cr. BICH 631 Biochemical Genetics 3 cr. BICH 689 Application of Scientific Values 1 cr. Rotation 1 Rotation 2 Rotation 3

In the Spring, students take the modular course series. Designed for flexibility, students select six 5-week courses to create a schedule tailored to the student’s research interests. Modular course offerings change every year; previous offerings include Metabolism, Quantitative Analysis in Biochemistry and Biophysics, Quantitative Analysis in Genomics / Molecular Biology, Advanced Ligand Interactions, NMR Spectroscopy, and Biochemical Kinetics. Finally, all first-year students must serve as Teaching Assistants. A description of the teaching requirement and philosophy are provided in a later section. BICH 6XX Advanced Modules* 6 cr. BICH 690 Theory of Biochemistry Research 2 cr. BICH 697 Teaching 1 cr.

Students continue lab work throughout the Summer, enrolling in 6 research credits hours to maintain full-time status. They also meet with the Advisory Committee to ensure that their coursework and early research efforts remain on track. At this meeting, the committee will

offer elective coursework and Journal Club recommendations based on student research interests. BICH 691 Research 6 cr.

Year 2. Students typically take six elective course credits during the second year of studies. A non-comprehensive list of electives can be found in Appendix J. They also complete their final required semester of Teaching Assistantship. Electives (2) 6 cr. BICH 6XX Journal Club 1 cr. BICH 697 Teaching 1 cr. BICH 691 Research 1 cr. In the Spring, students continue to take Journal Club and Research credits. In preparation for the upcoming Preliminary Examination, students enroll in Oral and Written Scientific Communication courses. All Preliminary Examinations are held in April. After completing the Preliminary Examination, students submit a formal Degree Plan and select a Thesis Committee. The Degree Plan formalizes a student’s intent to earn a doctoral degree and establishes the required coursework with the Office of Graduate and Professional Studies. BICH 681 Written Communication 2 cr. BICH 689 Oral Communication 1 cr. BICH 6XX Journal Club 1 cr. BICH 690 Theory of Biochemistry Research 2 cr. BICH 691 Research 3 cr.

As in Year 1, students continue lab work throughout the Summer, enrolling in 6 research credits hours to maintain full-time status. BICH 691 Research 6 cr.

Year 3 and Beyond. Once all required core coursework is complete, students continue to enroll in Journal Club, Theory of Biochemistry Research, and Research credits during the Fall and Spring semesters. For the Summer semester, students continue to enroll in Research credits. Beyond the required coursework, students may take additional courses, if the sponsoring PI is willing to cover the additional cost. Students are required to hold at least one committee meeting every academic year. Meeting protocols are outlined in Appendix K. BICH 6XX Journal Club XX cr. BICH 691 Research XX cr.

Rotations and Laboratory Selection In the fall semester of Year 1, students participate in three 5-week laboratory rotations. Students meet with the Advisory Committee before each rotation period; the committee guides students in selecting rotation groups based on evolving research interests. After the meeting, students submit a ranked-order list of three faculty names to the GPC. Rotation assignments are made according to the preference list, pending faculty approval.

Before the end of the semester, students meet with prospective mentors to determine whether they are willing and able to accept a new student into the group. In the rare case that a student is unable to find a satisfactory placement, they may opt to complete a fourth rotation. This option is only available to students who remain in good academic standing. At the end of each rotation period, participating faculty are asked to submit a performance evaluation (see Appendix K). Courses Students must maintain full-time registration status (9 credit hours in Fall/Spring, 6 credit hours in Summer). As described above, the first two years of study are primarily core, modular, Journal Club, and elective coursework. In post-candidacy years, students typically meet the registration requirement through a combination of Research credits (BICH 691), Theory of Research credits (BICH 690), and Journal Club credits (BICH 67X). A detailed description of the core, modular, Journal Club, and elective courses can be found in Appendix J. Teaching Assistantship and Relationship to the Undergraduate Programs The intersection of the graduate and undergraduate programs largely occurs through the demands of the latter for teaching assistants in recitations and laboratory courses. The philosophy of the graduate program is that teaching experience is a necessary component of a well-rounded preparation for entering the profession, whether academic or otherwise. On the other hand, the sheer size of the undergraduate programs run by BCBP places a heavy demand on the graduate program (see Table 1). The need for teaching assistants has instilled an inherent conflict between recruitment of graduate students and maintaining an increasing standard of quality of matriculants. As we enforce a higher bar for admission to the graduate program, we will need to experiment with online “help desks” and recitations and/or allow the recitation class size to increase. The former has proven viable during the COVID pandemic while the latter is less desirable. An alternative that will also be explored is the use of “professional” teaching assistants. Budgetary reductions for graduate student support also impact the ability to fully fund graduate student teaching. TABLE 1. Semester demand on Teaching Assistantships since 2018. The decrease observed since Summer 2020 reflects adjustments made for online teaching in response to Covid-19. SEMESTER TA POSITIONS TOTAL/YR Spring 2018 39 Summer 2018 10 Fall 2018 46 95 Spring 2019 40 Summer 2019 10 Fall 2019 48 98 Spring 2020 40 Summer 2020 6 Fall 2020 28 74 Spring 2021 30

Research Proposal and Preliminary Examination The transition to candidacy has been significantly modified over the past year and is comprised of a short NIH-style written proposal that is defended by oral examination in the Spring of the second year of study. These constitute the “Preliminary Examination” and mark the transition of the student to status as a candidate for the PhD degree. The philosophy of

the Preliminary Examination is not to filter students but, rather, to assist them in the challenge of changing the orientation of the student from a “book study” perspective to that of an independent thinker in an experimental (i.e. unknown) setting. Two mini-courses have been developed to assist the student. One focuses on the strategies and skills of the written proposal (currently taught by Dr. Cecilia Tommos) and oral presentation (currently taught by Dr. Jean-Philippe Pellois). The written proposal is organized according to the National Institutes of Health (NIH) Grant Guidelines and includes the sections outlined in Table 2. Descriptions are adapted from “Detailed Guidelines for the NIH Proposal” (Main Medical Center Research Institute).

TABLE 2. Preliminary examination proposal components.

Specific Aims (1 page) Identifies the primary objectives of the project, including the problem to be addressed, the current state of knowledge, and the potential contributions to the research field.

Research Strategy (5 pages) Comprises three sections: Significance, Innovation, and Approach.

Significance Provides a terse and scholarly background, including only literature review that pertains directly to the topic and demonstrates a modern understanding of the field.

Innovation Explains how the proposal challenges current research or seeks to establish novel concepts, approaches, or methods. Advantages over known methods should be detailed.

Approach Delineates the strategy, methodology, and analytical techniques to be used and includes preliminary results.

Bibliography (No limit) References formatted according to the NIH standards.

Preliminary Examinations are held in April and evaluated by an Ad hoc. examination committee selected by the Graduate Office. Recent experience has shown that flexibility in the timing of the Preliminary Examination may contribute negatively to time-to-degree and we are now enforcing a strict timeline. The Research Proposal is submitted to each committee member 14 days before the meeting. At the examination, the Committee first meets without the student present for a preliminary discussion of the proposal. Should the written proposal be found lacking, the meeting is rescheduled. The student gives an oral presentation aided by no more than 8 slides (approximately 15 minutes). The Committee is asked to refrain from interruptions. Following the presentation, the Chair opens the meeting to questions, which may range from proposal specifics or broader questions underlying the proposal's theme. The Preliminary Examination is not meant to be a comprehensive examination. Following the question period's conclusion, the Committee meets in the student's absence to vote pass or fail on the written proposal and the presentation. A failing grade on the written proposal requires remediation within two weeks. A failing grade on the oral presentation requires a repeat oral examination within 3 months. During this period, the student is placed on academic probation and is subject to dismissal from the program if a passing grade is not achieved on a second attempt. Forms and detailed meeting protocols can be found in Appendix K. Where appropriate, the presentation should demonstrate mastery of each skill identified on the form.

Per OGAPS/GPS, the results of the Preliminary Examination expire after 4 calendar years. Students requiring an extension may submit a Petition for Extension of Time Limits. Annual Committee Meetings and Thesis Committee The structure and operational features of the thesis committee has been revised this past year in an effort to remove potential conflicts-of-interest between mentor and student and to increase the efficiency and effectiveness of the committee with the overall goal of reducing time-to-degree and enhancing the training experience of the student. The University has a rather awkward committee structure where the mentor is also recognized as the chair of the thesis committee. This creates an inherent conflict of interest, which is ameliorated by the newly adopted committee structure as outlined in Table 3. Committee membership is determined by the Associate Head in consultation with the mentor and student with the aim of having one member who identifies as a biophysical researcher and one who identifies as a biochemical researcher. OGAPS requires that one member have a primary appointment outside of BCBP. This latter requirement is often problematic.

TABLE 3. Thesis working committee composition and structure. Title Affiliation Responsibilities Chair BCBP Largely administrative, with an emphasis on balancing the needs of the mentor and student; provides scientific guidance Member BCBP Serve in a scientific and professional development advisory capacity Member Non-BCBP Serve in a scientific and professional development advisory capacity Ex officio BCBP Thesis advisor & direct mentorship

Students must hold at least one committee meeting every academic year following successful completion of the Preliminary Examination. The meetings may be more frequent in the early and late stages of dissertation research as determined by the Chair of the committee. The meetings are meant to be concise and commence with a discussion between the committee and thesis advisor(s) in the student's absence. The goal is to have a frank conversation about the advisor's view of the student's progress and any issues that may impede progress towards completing dissertation work. The student then presents a short overview of progress since the last meeting. A draft of the presentation is provided to the committee at least two weeks before the meeting. The Chair then opens the meeting for discussion, usually no more than 40 minutes. The Thesis Advisor is then excused and the committee and student discuss any issues that may impede progress towards completing dissertation research. The Chair files the Thesis Committee Meeting Report and Thesis Advisor Report with the Graduate Office. The forms must include recommendations for the timing of future meetings, the anticipated date of completion of dissertation research, and whether there are issues that warrant intervention by the AHGP. Forms and detailed meeting protocols can be found in Appendix K. Seminar Series The Department hosts nationally and internationally renowned scientists across a range of disciplines for our regular seminar series (see Appendix L). The graduate students are encouraged to host at least two speakers per year. This is coordinated by the BGA (see below). Graduate students are expected to attend these lectures throughout their time in the program. Seminars are typically held each Wednesday (Fall and Spring) at 4:00 pm in BICH 108. Until further notice, all seminars are held virtually. Students are invited to engage

individually with speakers at a meet-and-greet session following the talk. Travel funds to meetings are contingent, in part, upon regular attendance at both the seminars and meet- and-greets. Dissertation and Thesis Defense Students may petition their thesis committee for formal permission to begin composing their dissertation at any time following advancement to candidacy. The thesis committee, not the Thesis Advisor, are the primary wardens and will assess a student’s readiness collectively. In very rare cases, the AHGP may overrule a denial by the thesis committee for permission to write and defend a dissertation. Once permission to write and defend has been granted, the defense must occur within three months or the committee must be recanvased for permission. TAMU has extensive requirements for preparation of the dissertation. To initiate the defense process, students must first receive approval from OGAPS. The written dissertation must be given to each committee member at least 14 days before the scheduled defense. The timeline and forms required are delineated in Appendix K. Graduate Training Programs In 2020, six academic programs and the Office of Graduate and Professional Studies were awarded a five-year, $1.2M grant from NIH NIGMS to enhance diversity in the biomedical sciences. The TAMU Initiative for Maximizing Student Diversity (IMSD) supports one first- year graduate student from each program, while matching contributions from the University support a second-year graduate student. Participating students are offered personalized mentorship, instruction, and professional development opportunities. This is the only predoctoral T32 available to graduate students in the BCBP graduate program. The NIH has recently organized the T32 predoctoral programs and, as summarized later in this report, the PhD program in Biochemistry has several fatal weaknesses in its recent historical record of retention, time to degree and quality of matriculants. We hope that the recent steps taken to restructure the program will lead to better performance of students. Parallel efforts in recruitment are being undertaken to improve the quality of applicants and matriculants to the program. Number of Degrees Awarded Per Year The growth of the graduate program over the past 30 years is best exemplified by the number of PhD degrees awarded every year (Figure 4). Overall, 86 PhD degrees were awarded in the 90s (9+/-2 per year), 113 in the 00s (11+/-2 per year), and 126 in the 10s (13 +/-2 per year). On one hand, this trend is likely to decline in the coming decade as the size of recruited classes has been decreasing. The current efforts put in place to enhance PhD completion rates may mitigate this effect.

FIGURE 4. Number of PhD degrees awarded by year for the past 30 years. Average Time to Degree The BCBP year-to-degree average for students who entered the program since 2000 is 6.3 years (Figure 5). The large standard deviations shown for the period 2000-2010 reflect the fact that the YTD distribution is wide. In particular, a large portion of students graduated beyond year 7. This is described further below (see Figure 7) and it is something the graduate program seeks to remedy. The average YTD has been reduced in recent years (i.e., 6.0 average YTD for 2011-2013 cohorts; students who entered in 2013 have graduated except for one). This is an encouraging trend and we aim to continue improving this metric. Eight students from the 2014 cohort have already graduated (average YTD for this group is 5.8). Six students are still on the PhD track. It is likely that Covid19 has disrupted their progress. We therefore anticipate that the YTD of this group may extend beyond the 6.5 YTD mark.

FIGURE 5. Average year-to-degree for students who entered the program between 2000 and 2013. The YTD average for the whole time period is 6.3+/-1.0, and 6.0+/-0.7 for students entered between 2011 and 2013. Academic Enhancements and High-Impact Opportunities for Students Established in 1992, the Biochemistry Graduate Association (BGA) seeks to improve the welfare and educational experience of BCBP graduate students. Elected BGA representatives sit on the Admissions and Outreach & Recruitment committees to enhance communication between students and faculty. Similarly, a faculty member (selected by the BGA) is appointed to the BGA in a non-voting advisory capacity. The BGA is funded primarily by the Department through discretionary funds and through its own fund-raising efforts. The Department is re-evaluating this relationship. In the opinion of the Head, many of the functions carried out by BGA are better executed by the Graduate Program Office. Examples include management of graduate student travel awards and support of student- sponsored seminar speakers. Modest funds are provided to BGA to enhance the social activities of the graduate student population. The BGA organizes various activities, including research and professional development seminars, as well as the annual vendor show and research competition.

Town Halls To encourage student involvement and open communication, the AHGP and GPC host a BGA Town Hall every semester to discuss program initiatives, changes, and concerns. Attendance is mandatory for all students. Assessment of Student Learning Outcomes The BCBP Graduate Program identifies three primary learning outcomes, as defined by the TAMU Office of Institutional Effectiveness and Evaluation: Communicate Effectively, Critical Thinking, and Mastery of Graduate Biochemistry and/or Biophysics.

Communicate Effectively. To evaluate mastery of this learning outcome, the department employs a combination of interim and summative assessments specific to pre-candidacy students. With respect to interim assessment, measures include (1) Effective oral communication through classroom performance and (2) Effective written communication through classroom performance. As described in earlier sections, in Spring 2021, two new communication courses were developed to help prepare students for their preliminary examination. In each course, students are evaluated on classroom participation (e.g., course participation, discussion contributions, presentations, and the ability to provide constructive feedback to peers), semester-long improvements in critical analysis of scientific research proposals, and the ability to write or present a compelling research proposal. To demonstrate effective synthesis of course-acquired communication skills, all second-year graduate students are required to submit a Research Proposal and sit a Preliminary Examination. In this summative assessment of pre-candidacy students, the following metrics are considered:

Professional / Personal Development (0–10; 0 = poor, 10 = exceptional): ● Employ active listening techniques ● Speak with well-informed confidence; build slides that are visually accessible and error free ● Draft clear and concise documents; integrate informative figures ● Develop cohesive narratives ● Adapt presentations to a variety of formats / audiences

Critical Thinking. To evaluate mastery of this learning outcome, the department employs a combination of formative and summative assessments across the entire graduate tenure. With respect to formative assessment, all first-year graduate students are required to take BICH 608: Critical Analysis of the Biochemistry Literature. The course is designed to first establish a baseline understanding of incoming student-level, then rapidly develop the necessary skills to critically read, understand, and evaluate the scientific literature. The ability to effectively integrate literature background is evaluated in the Research Proposal and Preliminary Examination (pre-candidacy) and Dissertation and Thesis Defense (post- candidacy). In these summative assessments, the following metrics are considered:

Professional / Personal Development (0–10; 0 = poor, 10 = exceptional): ● Thoughtfully consider the broader impacts of their work ● Display integrity in acquisition / dissemination of scientific data [including proper literature attribution] ● Identify challenges early; critically evaluate and efficiently implement solutions

Mastery of Graduate-Level Biochemistry and/or Biophysics. To evaluate mastery of this learning outcome, the department employs a combination of interim and summative

assessments across the entire graduate tenure. With respect to interim assessment, students are evaluated on engagement in research group meetings, laboratory productivity, and conference attendance—success in all which requires a comprehensive understanding of the scientific literature, experimental design, data analysis and interpretation, and laboratory techniques. As above, the Research Proposal and Preliminary Examination and the Dissertation and Thesis Defense serve as an effective summative assessment for pre- and post-candidacy students, respectively.

Admissions and Admissions Criteria Admission criteria have included GPA (typically above 3.0), an undergraduate curriculum that adequately prepares students for their first year in the program, and undergraduate research experience. A detailed breakdown of these metrics from past applicants will be presented in the relevant student profile sections. With application numbers declining, fewer students meet these criteria. Therefore, the size of entering classes has declined over the past 10 years (Figure 6). The number of domestic applicants has been relatively constant, between 20 and 40 per year. In contrast, the number of international applicants dropped from 100 to ~40 over the period of 2010 and 2014.

FIGURE 6. Number of applicants to the PhD program since 2010. The data show the total number of applicants as well as the number of international and domestic applicants. Red lines indicate decreasing applicant pools, while green lines highlight increases in the number of total applicants. Some of the recruiting actions taken that coincide with these increases are shown.

Domestic students' application fees were historically waived (i.e. paid for) by the department, but international students had to pay $90 for their applications. Based on these declining numbers, the program expanded waiving fees to international students in 2015. This year saw an increase in international applicants, from 40 to 60. This may be coincidental, and we do not have direct evidence that waiving fees impacted applications. Nonetheless, fees for international student applications have remained waived. The Department may revisit this policy, given the associated cost, in a period when few international students are admitted. After 2015, declining trends for both domestic and international students resumed (Figure 6). In 2019, the GRE requirement for the application was eliminated. This was based on the observation that there is no apparent correlation between GRE scores and graduation with a PhD. Moreover, several universities had already

implemented this change nationwide, encouraging undergraduate students not to take GRE tests. The number of applications in 2020 increased for the second time in the past 20 years. Again, it is not possible to assess whether this change has had a direct impact on applications.

To remain attractive to prospective students (in addition to financially rewarding current students appropriately), the department voted to increase stipends regularly. The stipend of graduate students increased from $22,000 to $24,000 in (9% in increase), $26,000 in 2013 (8%), and $30,000 in 2018 (15%). However, these stipend increases do not appear to correlate with an increase in the yearly number of applicants, presumably because the BCBP stipend is not extraordinary. Response to previous APR critiques The main criticism from the previous review was the long graduation times (Appendix M). At the time of the last review, the cumulative average year to degree (YTD) was 6.7 years, while the national average was and remains at 5.5 years. Furthermore, 81 PhD candidates graduated at or beyond seven years, which represented 22% of the total number of PhD candidates (367) who graduated over the same period. Notably, preliminary exams were also often delayed beyond the 3-year (or 9 semesters) limit previously set by the department. For students who have entered the program since 2000, YTD is still high, at 6.3 years on average, although as we noted earlier, for the students that entered between 2011 and 2013, YTD was 6.0 years on average (see Figure 5).

To ensure that we reduce YTD further, several changes have been implemented since 2019. They include: ● Shortening of the rotation period for 1st-year students, from 2 semesters to 1 semester. ● Shifting of teaching assistantship duties from Fall & Spring of year 2 to Spring of year 1 and Fall of year 2. ● Shifting of the preliminary examination timing from "before the end of year 3" to a fixed and mandated date in the Spring of year 2. ● Elimination of year-1 pre-preliminary exam activities (the original research proposal or prep-E). ● Changes in the thesis committee structure, including redefining the committee chair's role as separate from that of the research advisor. ● Implementation of regular meetings with the Advisory Committee for pre-candidacy students to provide proactive advising and guidance.

The overall distribution of year to degree and time to preliminary exam are shown in Figure 7, and the implemented changes are outlined in Figure 8.

FIGURE 7. Distribution of year-to-degree (YTD) and year-to-preliminary-exam (YTPE) for BCBP PhD students who graduated during the 2000-2015 period. The average YTD was 6.3+/-1 year. Approximately 24% of the students graduated after 7 years or more in the program. The deadline for taking the preliminary exam during this time period was 3 years. Approximately 30% of the students took their preliminary exams well after this deadline.

FIGURE 8. Implemented changes to improve advising and decrease the time to degree.

The changes made in 2015 have already borne fruit. As illustrated in Figure 9, the PhD candidates currently in the program have all taken their preliminary exams before the 3-year deadline (with the exception of 2 who were delayed by one semester). Only 1 student has been in the program for more than seven years. We expect that changes implemented in 2019 will contribute further to this positive trajectory.

FIGURE 9. PhD candidates currently in the program distributed as a function of the academic year they entered the program. Blue circles represent individual PhD candidates and the y-axis represents the total number of years they have been in the program. The green circles represent the timing of when these students passed their preliminary exam. The dash line represents the preliminary exam deadline that was in place during this time period. Pre-candidacy students, or students who have graduated, are not shown.

Lastly, another concern expressed in the previous review was the shrinking size of our applicant pool. The measures we have taken were detailed above, in Admissions and Admissions Criteria. Analysis The structure of the graduate program has changed significantly since the 2014 APR. The Executive Committee of the Graduate Program (chaired by the Associate Head, Dr. Pellois) and the Graduate Recruiting and Admission Committee (GRAC) were historically separate and independent. In 2019, GRAC was split into an Outreach Committee and an Admission Committee. Both committees are chaired by a member of the department and placed under the purview of the Associate Head, for coordination.

An essential part of these restructuring efforts has been replacing the academic advisor position with an administrative postdoctoral associate/graduate program coordinator. Specifically, Dr. Justine deGruyter was hired in Fall 2019 for this position. Dr. deGruyter supervises numerous administrative tasks relating to the graduate program and has been instrumental in implementing the changes described in Figure 8. Dr. deGruyter also chairs the Outreach Committee and has been very active in reaching out to potential graduate student applicants. Notably, because of the traveling restrictions imposed by Covid-19 in Summer 2020, Dr. deGruyter developed an online 10-week workshop aimed at helping prospective students prepare their graduate school applications (200 students participated). Dr. deGruyter is also involved in developing and writing educational grants.

Most of the changes described in Figure 8 are recent and it is too early to see their impact on student YTD. Nonetheless, shifting the preliminary exam to a uniform fixed date should contribute to a downward positive trend. Thesis committee members are also now expected to define a clear graduation timeline during students’ annual committee meetings. In new

meeting reports developed in Fall 2019, an expected graduation date is specified by the committee and set independently of the student’s advisor, albeit with their input. The reports also provide feedback to students on their performance and the areas they need to work on. The goal is to define the path forward and help establish what students need to focus on to meet their graduation timeline (this feedback is generally not about scientific directions, as the research advisor more appropriately determines this).

Changes in the Preliminary Examination are made logistically possible by other changes implemented progressively since 2015. For instance, laboratory rotations have been shortened and semesters with TA duties shifted earlier. Pre-candidacy activities such as an Original Research Proposal (ORP) or Pre Proposal (PreP) were also eliminated. Overall, these changes allow students to join laboratories in Spring of year 1 (vs. Summer of year 1 in the previous format) and be relieved of TA duties by the end of Fall of year 2 (versus the end of Spring of year 2 previously). Hence, students have the opportunity to emphasize research earlier by taking ownership of their project between Spring and Summer of year 1, and prepare for their preliminary examination without significant distractions in Spring of year 2. Finally, oral and written communication courses were developed for Spring of year 2. These courses are designed to support graduate students in preparing for the written proposal and the preliminary examination's oral presentation components. Interdisciplinary Program (IDP) in Genetics For completeness, we mention the Interdisciplinary Program (IDP) in Genetics, which is directed by University Distinguished Professor David Threadgill. The Department of Biochemistry & Biophysics provides administrative support and space, but the IDP in Genetics operates independently of the BCBP Graduate Program office and the Associate Head. Dr. Threadgill is supported by an Administrative Postdoctoral Associate, Dr. Ximena Paez-Colasante, and Ms. Tamara Ospina-Vega. Dr. Paez-Colasante is responsible for academic advising, program evaluations, teaching assistant assignments, course evaluations, course assignments, scheduling, and general administration of the Genetics Program. Ms. Ospina-Vega assists with general program administration and is responsible for the program’s regular seminar series.

Undergraduate Programs Academic Programs and Curricula The Department of Biochemistry and Biophysics directs two undergraduate degrees: a BS in Biochemistry (BICH) and a BS in Genetics (GENE). The programs are directed by the Department’s Undergraduate Program Office. In September, 2019 Dr. Tim Devarenne assumed the role of Associate Department Head for the Undergraduate Programs. Devarenne is assisted by one full-time staff Program Assistant (Ms. Kaitlyn McGaff), who manages the Undergraduate Program Office. Faculty oversight for both the BICH and GENE degrees is provided by the Undergraduate Program Committee (UPC), which is chaired by Dr. Devarenne and includes Drs. Margy Glasner, Pingwei Li, David Threadgill, Vlad Panin, Paul Straight and Bryant Miles. Advisors Khara Spears and Megan Teel are ex officio members. The UPC meets monthly and as needed when specific situations arise.

Significant revisions of both the BICH and GENE degree plans were last conducted during the 2010-2011 school year and were put in place with the 2012-2013 school year as described in the last Academic Program Review. These revisions were made to:

● Maintain a clear distinction between our degrees and those of other life science majors at Texas A&M. ● Allow students to customize their degree plans in accord with their post-graduate goals. ● Provide sufficient flexibility for a student to pursue a BICH/GENE double major or a minor in another discipline without a large increase in the total semester credit hours (SCH) required for the degree. ● Reduce the number of SCH from 132 to 120. There is a mandate from the Texas State Legislature that limits SCH for a degree to a maximum of 120. Revisions to the BICH and GENE degree plans since the last Academic Program Review are discussed below. Accreditations In the 2014-2015 school year, the department decided that the Biochemistry BS degree would benefit from accreditation by the American Society for Biochemistry and Molecular Biology (ASBMB). ASBMB accredits 90 undergraduate biochemistry degree programs within the USA, including six from Texas: Texas A&M University, Texas State University, Texas Tech University, Texas Wesleyan University, Houston Baptist University, and the University of St. Thomas. Accreditation by ASBMB offers several benefits for both the students and the department. Among these are that both the students and department know their biochemistry degree meets the highest standards of quality and innovation, and students have the option of taking a degree certification exam before graduation. The department can also use the degree certification exam results to assess how well students are learning and retaining critical information related to biochemistry and molecular biology to make any needed course adjustments.

The accreditation process was handled in early 2015 by Dr. David Peterson, the Associate Head for Undergraduate Programs at the time. The application included information about the Biochemistry degree, such as a description of the courses our students are required to take, how inquiry-based learning is approached, how communication and teamwork skills are developed, and a description of the research requirements. The application was submitted in March 2015, and notification of accreditation

was given in June 2015. The accreditation is valid from June 1, 2015, through May 31, 2022.

We note that an analogous accreditation mechanism for our genetics BS degree is not currently available by any relevant scientific society (e.g., from the Genetics Society of America). Program curricula in Biochemistry The BICH program was last updated in 2010-2011. No significant changes have been made to the degree plan though one class has been added: freshman BICH 101 Perspectives in Biochemistry and Genetics. This course is also cross-listed as GENE 101 and is a requirement for GENE majors and is taught by five tenure-track faculty. BICH and GENE majors, with some exceptions, generally do not take a class in their major until their junior year. Thus, students do not get exposed to BICH/GENE topics early in their academic career, and they can lose interest in their major and switch to a different degree. BICH/GENE 101 addresses this problem by introducing students to topics in biochemistry and genetics and how they relate to the interface of science and society. For example, we discuss the current problem with orange trees and citrus greening disease and how this can be combated by producing transgenic plants resistant to the disease. Thus, students learn about what causes the disease, how transgenic plants are made, and the controversies about using transgenic plants in the food supply. Other topics covered include gene therapy, dementia/Alzheimer’s, and the microbiome. The science underlying these topics and the societal issues related to each of these topics are discussed. The class also includes several writing assignments and a group presentation project. BICH/GENE 101 began as a requirement starting in Fall 2016 for the 2016-2017 school year. Program curricula in Genetics The GENE degree plan was reviewed internally and extensively modified during the summer of 2019. Discussions among the faculty initiated this review. The GENE degree plan was out of date in relation to the type of data analyzed and techniques used in modern genetics. The impetus was to implement more classes with large data set analysis such as genomics/transcriptomics analysis and include the statistics classes needed for students to understand how to process such data while maintaining our firm commitment to provide research experiences undergraduates. It was also hoped this restructuring would attract a new subset of students and possibly boost enrollment in the GENE degree program.

A committee to reorganize the GENE degree was established at the beginning of June 2019 and consisted of Dr. Tim Devarenne (chair), Dr. Michael Polymenis, Dr. David Dr. Threadgill, and Dr. Jim Hu. The committee was tasked with reviewing the existing GENE degree plan and designing a new degree plan, taking into account the focus mentioned above. The review was guided by the genetics curriculum from other institutions, including the University of Wisconsin, Duke University, the University of California-Davis, Iowa State University, University of Kansas, Cornell University, North Carolina State University, Oregon State University, University of Alabama-Birmingham, and the University of Georgia.

The major changes to the GENE degree plan implemented by the committee were designed to give students the statistical and computational skills necessary to analyze large omics data sets. Thus, the 3 course series of statistics classes was implemented:

STAT 211 Principles of Statistics I, STAT 212 Principles of Statistics II, and STAT 404 Statistical Computing. Two courses that were formerly GENE electives were added as required courses: GENE 419 Computational Techniques for Evolutionary Analysis and BICH 450 Genomics. The new degree plan includes 6 GENE electives, and GENE students are strongly encouraged to choose courses from a list of bioinformatics/big data classes offered across campus to fill these electives. Finally, the biochemistry courses GENE students are required to take was changed. Previously, GENE students were required to take the same BICH 440 Biochemistry I and BICH 441 Biochemistry II courses as the BICH majors. GENE students are now required to take the one-semester BICH 409 Principles of Biochemistry, covering topics from both BICH 440 and BICH 441. This was so that new courses could be added to the GENE degree plan without going over the maximum 120 SCH. The university approved this degree plan in time for students entering the GENE program for the 2020-2021 school year. See below for details of the GENE degree plan.

We have implemented an additional change to the GENE degree plan that will also affect the BICH degree plan. We have developed a new genetics lab, GENE 314 Principles of Genetics Laboratory, specifically designed for students majoring in the hard sciences such as BICH, GENE, BIOL, CHEM, and molecular biology (MBIO), among others. Currently, students in those majors take the GENE 312 Genetics Laboratory course, which also has students from majors such as animal science (ANSC), nutrition (NUTR), wildlife and forestry science (WFSC), and poultry science (POSC). Thus, GENE 312 generally teaches to the ANSC, NUTR, and WFSC students' level and does not offer more rigorous course material to benefit the demanding science majors. GENE 314 will cater to the hard science majors and help these students for subsequent courses. GENE 314 has been approved to begin in Fall 2021 for the 2021-2022 school year. Courses/Degree Plans The Department is responsible for BS programs in Biochemistry (BICH) and Genetics (GENE). In the Department, 20-25% of our majors graduate with a double major in BICH and GENE. This is a prevalent option among college students with a significant number of advanced placement or dual registration credits from high school. Students who elect to double major in BICH and GENE can use their free electives to fulfill the other major's requirements. In this manner, a BICH/GENE double major only requires 127 SCH to graduate. BS in Biochemistry The current, complete degree plan for a BS in Biochemistry is shown in Table 4 and took effect in the 2016-2017 school year. Foundation courses in General and Organic Chemistry, Biology, and Calculus are generally taken during the program's first two years. Physical Chemistry is also required. Genetics, Molecular Genetics, and a two-semester Biochemistry sequence with small class size (30-40 students per section) is taught by tenure track faculty within the Department. Directed electives include choices in Genomics, Biophysics, and other selected topics. Selected courses in Chemistry, Biology, and Math can also fulfill the requirement for directed electives. Undergraduate research is completed by registration for 4 SCH of BICH 491, a requirement that is most often spread over several semesters. The fourth BICH 491 SCH for which the student registers must include a writing- intensive component.

TABLE 4. Biochemistry BS Curriculum.

Core Curriculum SCH Courses in Communication; Creative Arts; Language, Philosophy and Culture; Social and Behavioral Sciences; American History and Government/Politics 27

Biology BIOL 111 Introductory Biology I/Laboratory 4 BIOL 112 Introductory Biology II/Laboratory 4 BIOL 351 Fundamental of Microbiology/Laboratory 4

Chemistry CHEM 119 Fundamentals of Chemistry I/Laboratory 4 CHEM 120 Fundamentals of Chemistry II/Laboratory 4 CHEM 227/237 Organic Chemistry I/Laboratory 4 CHEM 228/238 Organic Chemistry II/Laboratory 4 CHEM 327 Physical Chemistry I 3 CHEM 328 Physical Chemistry II 3

Physics PHYS 206/226 Newtonian Mechanics/Laboratory 4 PHYS 207 Electricity & Magnetism/Laboratory 4

Math MATH 151 or MATH 171 Engineering Math I or Calculus I 4 MATH 152 or MATH 172 Engineering Math II or Calculus II 4 MATH 251 Engineering Math III 3

Genetics GENE 302/314 Principles of Genetics/Laboratory 4

Biochemistry BICH 101 Perspectives in Biochemistry 1 BICH 404 Biochemical Calculations 2 BICH 440 Biochemistry I 3 BICH 441 Biochemistry II 3 BICH 431 Molecular Genetics 3 BICH 414 or BICH 432 BIochemical Techniques or Laboratory in Molecular Genetics 2 BICH 491 Research 4 BICH Directed Electives Choose from non-lab 400-level (or higher) BICH courses 6

Free Electives Students intending to pursue an advanced degree in Biochemistry are strongly encouraged to use some of their free electives to enroll in additional upper division courses in GENE, BICH, BIOL, CHEM, or MATH. 12

TOTAL 120

BS in Genetics

The current, complete degree plan for a BS in Genetics (GENE) is shown in Table 5 and took effect for the 2020-2021 school year. Foundation courses in Chemistry and Biology are identical to those for BICH, and GENE students must complete 4 SCH of undergraduate research. But a series of Statistics courses, STAT 211/212/404, are required for GENE majors in place of the BICH requirement for Calculus III to prepare students for the analysis of large data sets. Additionally, GENE students take the one-semester biochemistry course BICH 409 instead of the two semesters BICH 440/441 required for BICH majors. The required GENE courses are very distinct from those of BICH. Thus, the BICH and GENE majors are more distinct from each other than ever before. The GENE major is also different from other majors, such as the degrees offered in Biology. For example, GENE majors must

take a rigorous MATH series, MATH 151/152, that the Department of Mathematics accepts as a prerequisite for advanced MATH courses. Biology majors are only required to take one mathematics course, which the students can select from three possible courses; the lower level MATH 147, MATH 151, or the higher level MATH 171.

TABLE 5. Genetics BS Curriculum.

Core Curriculum SCH Courses in Communication; Creative Arts; Language, Philosophy and Culture; Social and Behavioral Sciences; American History and Government/Politics 27

Biology BIOL 111 Introductory Biology I/Laboratory 4 BIOL 112 Introductory Biology II/Laboratory 4 BIOL 351 Fundamental of Microbiology/Laboratory 4

Physics PHYS 201 College Physics I/Laboratory 4 PHYS 202 College Physics II/Laboratory 4

Math MATH 151 Engineering Math I 4 MATH 152 Engineering Math II 4

Statistics STAT 211 Principles of Statistics I 3 STAT 212 Principles of Statistics II 3 STAT 404 Statistical Computing 3

Genetics GENE 101 Perspectives in Genetics 1 GENE 302/314 Principles of Genetics/Laboratory 4 GENE 412 Population, Quantitative, and Ecological Genetics 3 GENE 419 Computational Techniques for Evolutionary Analysis 3 GENE 431 Molecular Genetics 3 GENE 432 Laboratory in Molecular Genetics 2 GENE 491 Research 4 GENE Directed Electives Choose from non-lab 400-level (or higher) GENE courses 6

Biochemistry BICH 409 Principles of Biochemistry 3 BICH 450 Genomics 4

TOTAL 120

Admission Criteria The Texas A&M Office of Admissions handles admission into the BICH and GENE

undergraduate programs for first-year students. All incoming freshmen that meet the Texas A&M minimum requirements are allowed to declare BICH or GENE as their major. The department does not have a role in accepting or denying admission to first-year students.

The department does have a role in accepting or denying admission for BICH and GENE transfer students. Texas A&M encourages all departments to be open to admitting qualified transfer students who have begun their academic careers at one of Texas' many junior colleges. Texas A&M requirements to be considered for admission as a transfer student are completion of 24 SCH of graded, transferable coursework and a GPA of at least 2.5. The Texas A&M Office of Admissions provides the application materials to the department for transfer students meeting these requirements. The department advisors and the Associate Head for Undergraduate Programs then evaluate the applications based on grades in foundation courses such as chemistry, biology, calculus, and the student's application essay and recommendation letters. The department requires transfer students to have completed two semesters each of calculus, introductory chemistry, and introductory biology with a grade of at least a C to be accepted into the BICH or GENE programs. Final decisions on acceptance or denial are made by the department only. Figure 10 shows the number of transfer students accepted into the BICH and GENE programs over the past five academic years.

FIGURE 10. Number of BICH and GENE transfer students admitted for AY 2015-2019. Number of Degrees Awarded per year The number of BICH and GENE degrees awarded by the department in the years since the last APR, academic years (AY) 2015-2019, are shown in Table 6. This data includes degrees given to students that entered as a freshman and transfer students. The number of degrees awarded has steadily increased over these five years. This reflects the steady increase in freshman BICH and GENE enrollment that was seen in the AY 2009-20013. During this period, the BICH freshmen enrollment increased 47% to reach a combined BICH and GENE enrollment of approximately 140 students. BICH and GENE enrollment

has been maintained at about 150 students since then; see Figure 31, in a later section. This increase in student enrollment would account for the increase in degrees awarded.

TABLE 6. Number of BICH and GENE degrees awarded for AY 2015-2019.

AY 2015 AY 2016 AY 2017 AY 2018 AY 2019 BICH 42 38 51 47 44 GENE 25 35 34 51 39 AY Total 67 73 85 98 83

Average Time to Degree The number of degrees and the average time to degree for BICH and GENE majors for AY 205-2019 is shown in Table 7. This data includes only students that entered the programs as a freshman and does not include transfer students and therefore differs from Table 6. While the number of degrees awarded by the department has increased over this period, the average time to degree has remained relatively constant. This suggests that the quality of students entering the BICH and GENE programs has not declined while the number of students has increased.

TABLE 7. Graduation statistics for BICH and GENE majors for AY 2015-2109.

AY 2015 AY 2016 AY 2017 AY 2018 AY 2019 # # # # # BICH 31 4.19 31 4.00 44 4.14 38 4.16 39 3.99 GENE 21 3.69 30 4.03 31 4.02 41 4.18 33 4.14 Total 52 3.94 61 4.02 75 4.08 79 4.17 72 4.07

Academic Enhancements For over 35 years, the department has maintained a strong culture of undergraduate involvement in research and has required a significant research experience for all its undergraduate majors, including transfer students. The requirement is for 4 SCH of BICH/GENE 491 research. Students are encouraged to get involved in research early, and many students spend significantly more time than the required minimum in research labs. For about the past 16 years, the research requirement mandates that one of the 4 SCH must be writing intensive where students write a short undergraduate thesis. This also meets the university requirement for "writing intensive" courses within the student's major. This is intended to be a real-life writing exercise with cycles of feedback and editing between the student and the PI. The format of the thesis should be in the style of a published journal article. The requirement for participation in research is one of the signature aspects of our BICH and GENE undergraduate programs.

The department does several things to facilitate and promote undergraduate research. It provides funding to print posters of student research to enable participation in meetings and symposia, such as the University Student Research Week. The Biochemistry and Genetics Society, an undergraduate student organization, sponsors an annual poster session to highlight undergraduate research. The department also receives funding from the College of Agriculture and Life Sciences to fund 4-6 Texas A&M undergraduates as additions to the NSF-funded department REU program. This has been a special experience for students

considering research careers, as a summer of total immersion in research provides a real taste of life as a research scientist.

Getting first-year students off to a good start to increase retention of students within the BICH and GENE programs is a high priority for our department. Therefore, in Fall 2016, the department initiated the Genetics and Biochemistry Enrichment Experience (GaBEE) program. GaBEE is a series of late afternoon meetings for freshman BICH, and GENE majors, and attendance is required for all freshman BICH and GENE students enrolled in BICH/GENE 101. At the GaBEE meeting, we discuss academic success, money management, and various services offered by Texas A&M, including the Career Center and the Office of Professional School Advising. The meetings end with a social time with pizza, during which the faculty teaching BICH/GENE 101 mingle and talk with the new freshmen.

Each first-year student is assigned a faculty mentor, and students are strongly encouraged to make an appointment to chat with their mentor. We want students to discover that faculty can be helpful and friendly.

Assessment of Student Learning Outcomes Assessment of Biochemistry Program One tool we use for the assessment of our BICH undergraduate majors is the ASBMB degree certification exam. Our biochemistry undergraduate students began taking the degree certification exam in 2016 and have taken the exam every year since. A total of 145 students have taken the exam from 2016-2020. The exam consists of 11 questions, with seven at a high Bloom’s level and four at a low Bloom’s level. The biochemistry/molecular biology topics covered on the exam include structure/function, energy transfer, information storage, and quantitative reasoning. Each question is scored on a three-level scale: highly proficient (3), proficient (2), not yet proficient (1). Answers that were left blank or whose content is deemed grossly incorrect or irrelevant are scored as 0. Students can achieve degree certification, degree certification with distinction, or no certification based on the scores.

To achieve certification, students must score proficient or above on either five higher- order and three lower-order Bloom’s questions or six higher-order and two lower-order Bloom’s questions. To achieve certification with distinction, students must score proficient or above on either seven higher-order and three lower-order Bloom’s questions or six higher- order and four lower-order Bloom’s questions. The results from our students are shown in Figure 11 compared to the average of all schools taking the exam.

FIGURE 11. Performance of TAMU BICH students on ASBMB Degree Certification Exam.

Our BICH students generally do well on the ASBMB degree certification exam. In years 2017, 2018, and 2019 our students achieved degree certification on par or better than the national average. Our students did better in 2018 and 2019 than the national average for degree certification with distinction (Figure 11). This suggests that our students comprehend and retain the material they are taught in biochemistry and molecular biology.

We also track how our BICH students perform on individual questions, but a clear pattern has not emerged. For example, in 2019, our BICH students did worse than the national average on information storage questions. However, our students matched or did better in all other years than the national average on information storage questions. With additional data gathered over the years, clearer trends may develop that show the biochemistry topics our students are having difficulty comprehending. Those topics can then be reinforced in the relevant courses.

Anecdotal evidence from our main biochemistry class, BICH 440 Biochemistry I, suggests that our students are having difficulty with the calculations associated with this course. We have noticed this in the past and implemented the course BICH 404 Biochemical Calculations, which was designed for students to take before or concurrently with BICH 440 so instructors in BICH 440 can spend less time teaching how to do certain calculations and more time covering the details of the subject matter. In recent years BICH 440 instructors have noticed that students are still struggling with the calculations. Thus, we

are exploring ways to adjust BICH 404 to improve student retention of the needed material to enhance their performance in BICH 440. See the Analysis section below for details.

Assessment of Genetics Program For the GENE program, we have been using the GENE 491W theses as an assessment tool. As stated above, all the department's undergraduate students are required to take 4 SCH of research, and the final credit should be writing-intensive, where the students write a short thesis on their research. To evaluate the theses, we use the written communication VALUE rubric (see Appendix N) published by the American Association of Colleges and Universities (AAC&U). For the most recent assessment (2019-2020 school year), ten theses were selected randomly by the department undergraduate office staff. Each thesis was evaluated by two faculty on the department undergraduate program committee (UPC) using the AAC&U rubric. The goal was to have students score at least 13 (out of 20) points based on the AAC&U rubric and have at least 80% of the students meet this goal. The results show that only 70% of the theses were graded at 13 points or better. While that is close to the goal it matches what has been seen in the assessment analysis for other recent years. Additionally, the UPC members noticed that many of the theses are lacking in detail and proper organization. Obviously, the students and their research advisors do not participate in rounds of editing and review to improve the thesis. Thus, we are using this information to improve the thesis writing process, as detailed in the Analysis section below. Response to previous APR critiques The main suggestion from the previous review was pursuing ASBMB accreditation for the BS in Biochemistry, which has now been accomplished. Analysis of Biochemistry Program Based on the anecdotal evidence discussed above, it seems our biochemistry students are not as well prepared as they could be for the department's first biochemistry class, BICH 440 Biochemistry I. We have been discussing several options on how to address this issue. Several of them are briefly discussed here. One option is to have students take the BICH 404 Biochemical Calculations course before BICH 440. Currently, most students take these two courses concurrently. At a minimum, if students remain allowed to take BICH 404 and BICH 440 concurrently, the two courses need to be better synchronized so that students learn specific calculations in BICH 404 at least a week before that topic is covered in BICH 440. Another issue with BICH 440 appears to be that too much basic biochemistry is covered in BICH 440, which does not allow time for in depth analysis on specific topics. Thus, the department is considering developing a course that covers some basic biochemistry topics such as the structures of amino acids, lipids, sugars, and nucleic acids, and the reactions they undergo to be offered in the spring semester of the second year. This course could be developed and taught by the department. Alternatively, the department could partner with the Department of Chemistry to offer a section of organic chemistry that is more biochemically related and covers these topics. This would also allow students to maintain an interest in biochemistry since they currently do not have a biochemistry course until the third year of the degree plan. In the coming year, these options will be analyzed by the UPC, and the best options presented to the department for more discussion before implementation.

A major deficiency of the department’s undergraduate offerings is the lack of an undergraduate biophysics degree. Currently, in Texas, there are no universities, public or private, that offer a stand-alone biophysics degree for undergraduates. However, several universities offer a biophysics track within the physics department, an interdisciplinary

biophysics program, or a medical biophysics program (e.g. University of Texas, Austin; Southern Methodist University; Texas Christian University; Texas A&M, Commerce; Tarleton State University; Sam Houston State University; Rice University; St. Mary's University).

Thus, within Texas, there is a lack of a dedicated, stand-alone undergraduate biophysics degree program. The planning for this undergraduate biophysics degree is in the very early stages. In October 2020, the department UPC formed a biophysics degree subcommittee consisting of Drs. Pingwei Li (chair), Tim Devarenne, Margy Glasner, Lanying Zeng, and Jae-Hyun Cho. The committee has researched biophysics degree programs at other universities, including the University of Michigan, Brown University, Iowa State University, Johns Hopkins University, and Columbia University. Using information from these programs and the department's interests, the committee is now developing a biophysics degree plan. The goal is to have this new degree finalized and available to students within five years from now. This is a comparable timeline in comparison to other departments that have implemented new degree plans. To get a head start on the biophysics degree, the department is considering developing a biophysical chemistry class before the entire degree program's final approval.

Analysis of Genetics Program With the recent significant changes implemented in the GENE degree plan, it is difficult to say what should be addressed to improve student performance, if anything. It will take several years of assessment and observation to evaluate how the students respond to the new direction of the GENE degree. We hope that the shift to focusing on statistical and computational skills for use in the analysis of large data sets attracts a new type of student that is not only interested in the classical and molecular aspects of genetics but also wants to learn how to apply computational skills to genetics.

The assessment of the GENE 491W theses made it clear to the UPC that students are not writing their thesis as intended: organized like a published research paper and going through rounds of editing and revision with their research advisors. To address these issues, we will require all students registered for GENE 491W to attend a short presentation at the beginning of the semester that will be given by a UPC member and explain what is expected from the student for writing their thesis. It will be reinforced that the student is supposed to take responsibility for all aspects of the writing process, such as initiating the writing and meeting deadlines set by the department and those set between the student and research advisor. The goal is to improve the students’ ability to communicate information about research in a written format. This process will also be applied to BICH students writing their 491W thesis.

Faculty Profile Tenured and tenure-track Ad loc. faculty There are 30 tenured and tenure-track, research-active Ad loc. faculty in BCBP (Table 8). In addition, since 2010, Dr. Suma Datta has been serving full-time as Assistant Provost for Undergraduate Studies. TABLE 8. Ad loc. faculty. Other Grad Name Rank Hired Tenured Promoted Affiliations Location Bryk, Mary Associate 2002 2008 GENE BCBP Cho, Jae-Hyun Assistant 2012 NMR Cruz-Reyes, Jorge Full 2001 2007 2017 GENE BCBP Devarenne, Tim Associate 2006 2012 MEPS NMR Glasner, Margy Associate 2008 2015 BCBP Gohil, Vishal Associate 2012 2018 BCBP He, Ping6 Full 2009 2013 2017 MEPS, GENE Borlaug Herman, Jennifer Associate 2011 2017 CPT BCBP Igumenova, Tatyana Associate 2008 2014 NMR Kurouski, Dmitry Assistant 2017 BCBP Li, Pingwei Full 2005 2011 2017 ILSB Meek, Tom Full 2014 2014 2014 ILSB Mullet, John1 Full 1983 1986 1991 GENE, MEPS BCBP Panin, Vlad Full 2002 2008 2015 NEUR, GENE BCBP Park, Bill Full 1984 1984 1991 MEPS BCBP Pellois, Jean-Philippe Full 2006 2012 2016 CHEM BCBP Polymenis, Michael Full 1999 2005 2015 GENE BCBP Rye, Hays Associate 2009 2015 BCBP Sacchettini, Jim2 Full 1996 1996 1996 CHEM, CSB ILSB Shan, Libo3,6 Full 2020 2009 2016 Borlaug Shippen, Dorothy Distinguished 1991 1997 2002/2019 GENE BCBP Straight, Paul Associate 2008 2014 GENE BCBP Sze, Sing-Hoi Associate 2002 2008 CPSL HRBB Threadgill, David4 Distinguished 2013 2000 2013 MCM, TOX, GENE Reynolds Tommos, Cecilia Full 2019 2019 2019 NMR Wand, Josh Full 2019 MCM, CHEM NMR Young, Ry5 Distinguished 1987 1983 1987/2018 BIOL, CPT BCBP Zeng, Lanying Associate 2012 2018 CPT BCBP Zhang, Junjie Associate 2014 2020 CPT ILSB Zhang, Xiuren6 Full 2008 2014 2018 MEPS Borlaug

1Perry L. Adkisson Chair in Agricultural Biology; 2Rodger J. Wolfe-Welch Foundation Chair, Science; 3Christine Richardson Dr. in Agriculture; 4Tom and Jean McMullin Chair, Genetics; 5Sadie Hatfield Dr. of Agriculture; 6will relocate to BCBP in 2021

FIGURE 12. Age and rank distribution of Ad loc. faculty over the review period. The crossbars in each box are the medians, and the whiskers are drawn at 1.5 times the interquartile range. Demographics of Ad loc. faculty The faculty's rank distribution is: Three Distinguished Professors (2 with endowed chairs or Professorships), 14 Full Professors (two with endowed chairs or Professorships), 11 Associate Professor, and two Assistant Professors. The rank and age distributions have changed significantly over the review period, in favor of senior faculty (Figure 12). The distinguished, full, associate, and assistant members have a median age of 60, 56, 48, and 42 years, respectively. Since the last departmental review, all faculty members' median age increased from 48 to 53 years. The shifts in age and rank distribution primarily reflect faculty members present during the previous review and less turnover. Of the 30 Ad loc. faculty in the last review, one retired in 2019 (Dr. David Peterson), two in 2020 (Drs. Greg Reinhart and Gary Kunkel), one passed away in 2020 (Dr. Jim Hu), and one was recruited elsewhere in 2018 (Dr. Craig Kaplan). At the same time, Dr. Dmitry Kurouski (2017) was hired as Assistant Professor, Drs. Josh Wand (2019) and Cecilia Tommos (2019) as Full Professors, and Drs. David Threadgill (2018) and Libo Shan (2020) became Ad loc. to BCBP from other Departments in the University. Overall, the current number of 30 Ad loc. faculty is the same as in 2014, but higher than in the more distant past (25 members in 1998 and 2006). The faculty's rank distribution shows a clear top-heavy pattern, which will be exacerbated further as the two Assistant Professors progress in their promotion. Faculty diversity The gender ratio of the Ad loc. faculty is 22 male (20 tenured, 2 tenure-track) and 8 female (all tenured). The trend is favorable compared to past reviews (24:6 in 2014, 21:4 in 2006, and 22:3 in 1998). According to categories specified by the Texas Higher Education Board, the faculty ethnicity breaks down to 20 White (19 tenured, 1 tenure-track), 1 Hispanic (tenured), and 9 Other (8 tenured, 1 tenure-track). This compares to 23 White and 2 Other in 1998; 18 White,1 Hispanic, and 6 Other in 2006. The Department has not had an African-

American faculty member since the 1980s. Nonetheless, the faculty's gender and ethnic diversity have increased, becoming more female and less White over the past review periods. Faculty qualifications The Academic Program Review is mandated to include a statement defining a candidate's qualifications for a tenure-track faculty position. The Department is extremely broad in technical expertise and research orientation, with faculty populating almost every wavelength of a spectrum of research from physical biochemistry to cell biology and genetics. This precludes rigid disciplinary definitions for vetting candidates. Because it has had responsibility for both the Biochemistry and Genetics undergraduate curricula, one traditional criterion for assessing the fit of a candidate for faculty membership has been the ability to teach either the large core courses in Biochemistry (BICH410-411) or Molecular Genetics (GENE302 and GENE431). To accommodate such a broad mission, the following language has been used for formal job search advertisements:

General Duties and Responsibilities: The successful applicant will ● conduct research in the area of biochemistry or molecular biology of microbial, plant, or animal systems. Such a program will relate to the overall objectives of Texas A&M Agriculture. ● participate in the graduate and undergraduate teaching programs of the Department of Biochemistry and Biophysics. ● relate to ongoing programs in the Colleges of Agriculture and Life Sciences, Science, Medicine in the Health Sciences Center, and of Veterinary Medicine, and generally enhance research programs in the life sciences across campus. ● establish a research team that would include graduate students, postdoctoral fellows, and other technical support. ● obtain substantial extramural grant support.

Administrative Relationships: This faculty member will be under the direct supervision of the Head of the Department of Biochemistry and Biophysics and would, in turn, supervise the work of his/her research group.

Qualifications: (preferred/required) It is required that the successful candidate will have a PhD in biochemistry or a related field. Postdoctoral research experience, the demonstrated ability to conduct independent research, and the demonstrated ability to teach effectively in the classroom are highly preferred.

The above language was used in the searches that resulted in most of the hires since 2006, and similar position descriptions go back much earlier. This language has been modified when the search was narrowly focused (i.e., for structural biology and NMR) or was part of a multi-departmental search (e.g., CPT searches).

The Department adopted formal statements of faculty evaluations and expectations for tenure and promotion in 2018 and last amended them in 2020 (Appendix B), per the promotion and tenure guidelines from the College and the Dean of Faculties. The Department has by-laws, last updated in 2019, which define faculty status and voting rights (see Appendix A).

To help all faculty succeed, the Department created in 2020 a mock Study Section committee. Faculty planning grant submissions are encouraged to submit to the committee a complete draft of their proposal about one month before the actual submission deadline.

Comments of the panel are then communicated to the faculty by the panel's chairs (currently Drs. Pellois and Bankaitis). It is also not unusual for a faculty member to ask other faculty to review a grant proposal before it is submitted. Recently, a Junior Faculty Mentoring Committee was also put in place.

At Texas A&M University, Assistant Professors have a seven-year probationary period after hiring. A single application for tenure is allowed, generally in the summer of the fifth academic year. In the Department of Biochemistry and Biophysics, the Promotion and Tenure Committee (PATC) administers the tenure application process, including a formal mid-term review reported to the college. The PATC reports its recommendation, based on a review of the candidates' achievements in research, teaching, service, letters from external reviewers, and a public seminar, to the faculty and Head, generally by October of the sixth year. The vote of the Departmental members of the appropriate rank and the recommendation of the Head is reported up the academic ladder to the AgriLife Promotion and Tenure Committee, the Dean of COALS, the Provost, the President, and the Texas A&M System Board of Regents, which makes the final decision. Participation in interdepartmental and interdisciplinary programs Several of the Ad loc. faculty have joint appointments in other departments, in the Departments of Biology (BIOL), Chemistry (CHEM), Molecular and Cellular Medicine (MCM), and Computer Sciences (CPSL). Many faculty members also participate in interdisciplinary campus-wide graduate programs that promote collaborations or are an alternative source of graduate students (Table 8, under Affiliations). Texas A&M has several degree-granting interdisciplinary faculties. Genetics (GENE), Molecular and Environmental Plant Sciences (MEPS), Toxicology (TOX), and Neurosciences (NEUR) are all PhD granting programs approved by the Texas Higher Education Coordinating Board. Participating faculty members are all Ad loc. members of different departments. The Interdisciplinary Faculties usually have an elected chair and committees and report to a Council of Participating Deans.

Joint faculty In addition to the Ad loc. faculty, there are 9 Full Professors with active research groups who are joint members and thus entitled to supervise Biochemistry doctoral students (Table 9). Of these faculty, six are Distinguished Professors, and seven, including five of the Distinguished Professors, hold endowed chairs or Professorships. Dr. Patrick Stover is the Vice-Chancellor and Dean of our College and a member of the National Academy of Sciences. One joint faculty, Dr. Magnus Höök, is located at the Institute for Biosciences and Technology (IBT) campus in Houston; the others are at the College Station campus. In terms of voting on policy and tenure and supervising doctoral students in the Biochemistry PhD program, joint faculty have full faculty rights. Of the 8 joint members on the College Station campus, a few regularly attend the weekly departmental seminar, and usually, two or three attend the monthly faculty meeting. However, most participate in the activities, discussions, and voting for faculty recruitment, which, as noted above, typically occupies a significant fraction of each academic year. Currently, 13 graduate students pursue their PhD in laboratories of joint BCBP faculty members (Drs. Liu, Raushel, Bankaitis, Lindahl, Hook, Safe), compared to 63 students in laboratories of Ad. loc faculty. Several joint faculty present courses that BCBP graduate students choose as electives (see Appendix J).

TABLE 9. Joint faculty. Name Rank Joined Primary Bankaitis, Vytas1 Distinguished 2013 MCM Chapkin, Robert2 Distinguished 1988 Nutrition and Food Science Höök, Magnus3 Distinguished 1992 IBT Kapler, Geoffrey4 Full 1994 MCM Lindahl, Paul Full 1988 CHEM Liu, Wenshe5 Full 2019 CHEM Raushel, Frank6 Distinguished 1980 CHEM Safe, Steve7 Distinguished 1981 Veterinary Physiology & Pharmacology (VPP) Stover, Patrick Distinguished 2018 AgriLife, Vice Chancellor and Dean 1 Wehner-Welch Foundation Chair; 2 William W. Allen Chair; 3 Neva & Wesley West Chair; 4 Tom and Jean McMullin Chair; 5 Gradipore Chair; 6 Powell Chair; 7 Syd Kyle Chair Non-tenure track Research Faculty Research Assistant or Associate Professor positions are associated with a tenured/tenure- track faculty sponsor, and their role and responsibilities are defined in the departmental bylaws. There are currently two Research Assistant Professors in the Department (Table 10), which are active in research, having each authored multiple publications since 2018. TABLE 10. Non-tenure track research faculty. Name Rank Hired Sponsor Papers since 2018 Caro, José A. Assistant 2019 J. Wand 3 Krieger, Inna Assistant 2018 J. Sacchettini 7 Academic Professional Track Faculty The Department has 7 non-tenure track Academic Professional Track Faculty (Table 11), including 5 Senior Lecturers (1 male, 4 female) and 2 Lecturers (2 female, including one Hispanic). All but one of those faculty had active research careers before taking these instructional positions. For example, Dr. Chavela Carr held a faculty position at Robert Wood Johnson Medical School before coming here and has taught a wide variety of courses from cell biology and genetics to biochemistry. Having a corps of instructional faculty who are vitally connected to on-going science and possessing great experience and broad expertise is a strong positive for the Department, especially keeping our large service courses up to date and rigorous. TABLE 11. Academic Professional Track Faculty. Name Rank Hired Year of PhD Field Institution Ayres, Nickie Sr. Lecturer 2007 1987 Genetics; Cell & Mol. Biol. U Nebraska Carr, Chavela Sr. Lecturer 2014 1995 Biology MIT Miles, Bryant Sr. Lecturer 2001 1998 Chemistry TAMU Perez, Stephanie Lecturer 2018 2012 Biochemistry TAMU Pishko, Jane Lecturer 2016 1993 Biochemistry UT Austin Pozzi, Michelle Sr. Lecturer 2009 Biochemistry TAMU Reynolds, Megan Sr. Lecturer 2009 2009 Genetics TAMU

Fields of study of research-active faculty The Department is in a robust overall research environment. Texas A&M University ranks in the top 25 public institutions (11th in total research expenditures and 24th in federal research funding), according to the latest (2017) data from the Center for Measuring University Performance (https://mup.umass.edu/sites/default/files/annual_report_2019.pdf). A large part of this research activity is associated with modern life sciences. BCBP is widely recognized as a focal point in the life science research enterprise within the College and the

University. The Department of Biochemistry and Biophysics is positioned at the interface between the biological and physical sciences and has a very broad-based faculty involved in research in many different areas. Table 12 groups the research-active faculty into general areas of emphasis. These categories are somewhat arbitrary, based on sorting people by their primary training and methodologies. There are both substantial overlaps between groups and large differences within them. TABLE 12. Research areas of the Department.

Interactions among research-active faculty One measure of the collaborative climate and synergistic research activities in the Department is the output of publications co-authored by faculty members. The network shown in Figure 13 includes all such publications since 2015. A large number of faculty have co-published with one or more members in the review period. A few faculty appear to be key nodes (Drs. Jim Sacchettini, Junjie Zhang, Ry Young, Vytas Bankaitis), nucleating the most interactions. Note that several faculty members only recently joined the Department (e.g., Drs. Josh Wand, Cecilia Tommos, David Threadgill, Libo Shan). Hence, it is reasonable to expect that the interactions will expand in the future.

FIGURE 13. Network of co-authorships among research-active faculty since 2015. Research productivity of the Ad loc. faculty With such a diverse faculty, there are numerous challenges to assessing overall productivity. The number of sources and average funding levels of federal grants varies greatly by field. The intrinsic publication rate is different in some scientific areas if for no other reason than differences in the time it takes to prepare experimental “reagents” (a knock-out mouse takes longer to construct than a mutant enzyme). “Impact factors” of the leading journals in some fields are much higher than in others. Nevertheless, publications and funding are the primary quantitative measures available for the assessment of productivity. Publications In Biochemistry, Biophysics, and Molecular Genetics, the major and simplest measure of scholarly output is the faculty's publication record, both in terms of numbers and impact. Although numbers of publications are not a linear indicator of either activity or quality, they are a useful metric, especially in terms of judging trends. It is helpful to separate publications to ones where the faculty had a leading role (e.g., 1st, corresponding, or co-corresponding author) from the total number of authorships. On both counts, the Department as a whole seems to be on an upward trajectory (Table 13). On average (median), each Ad loc. faculty published 1-2 papers as lead author per year and 1 more as a co-author, for a total of 2-3 articles per year; for individual publication records, see Appendix Q. The overall average in the last review period was 2.1 publications per faculty per year, which was exceeded in each of the previous five years. 67

TABLE 13. Publication output of Ad loc. faculty. Publications 2015 2016 2017 2018 2019 2020 lead author 32 44 53 41 49 68 total (co-author) 58 67 90 72 91 109 lead/faculty 1.1 1.5 1.7 1.3 1.5 2 total/faculty 1.9 2.2 2.9 2.3 2.8 3.2

FIGURE 14. Publications of Ad loc. faculty over the review period. A more granular view is offered in Figure 14 by breaking down faculty output for each rank, year, and publication authorship (lead and total output). Some general patterns emerge: ● The median output of lead publications per faculty varies little among the different ranks (Figure 14, top panels). ● Full and Distinguished Professors have higher output (Figure 14, bottom panels), likely reflecting their increased involvement in collaborations. ● The variance in the publication output among more senior faculty increases, reflecting different career trajectories for some. ● An Assistant Professor (Dr. Kurouski) had an extraordinary publication output in the last 2 years. The impact of research publications by individual members of the Ad loc. and adjunct faculty shows the broad distribution expected for the range of the time in their independent careers (Figure 15). However, it is notable that the range of impact, as indicated by these simple measures, is quite large for Associate Professors. Closer examination suggests that some Associate Professors are struggling to establish a firm footing in their field of inquiry.

FIGURE 15. Cumulative literature impact of Ad loc. and Joint faculty. Raw measures of impact of faculty research (left) Web-of-Science Citations and (right) H-factor. As of January 2021. Funding If the scholarly output is the end product of research productivity, the means to that end is securing research funding. The simplest measure of funding for the faculty is total expenditures from external sources (Table 14; raw data in Appendix P). These numbers include direct and indirect costs, for any grant that an Ad loc. member serves as a PI (including multi-PI projects), and adjusted accordingly for members with partial Ad loc. appointments. By this measure, the Ad loc. faculty as a whole maintained a healthy funding record on par or higher from the previous review period. TABLE 14. External Grand Research Expenditures from Ad loc. faculty. 2015 2016 2017 2018 2019 2020 Total $11,060,478 $11,160,795 $10,325,409 $11,326,830 $11,085,515 $13,566,897 Faculty Median $194,497 $209,324 $193,997 $292,099 $258,481 $287,941

FIGURE 16. Funding of Ad loc. faculty over the review period. The numbers were further broken down for funds per individual and rank for each of the years in the review period (Figure 16). The picture, in some ways, mirrors the total publication output seen in Figure 14, as follows: ● Distinguished and, to some extent, Full Professors are overall more successful in attracting external funding. ● The variance in the funding levels among more senior faculty increases, reflecting again different career trajectories for some. ● A single individual (Dr. Sacchettini) has been exceptionally successful in securing external funding over the review period (amounting to ~30-40% of total Departmental funding from external sources in most years), a pattern that is consistent with the previous review period. With a diverse faculty, the funding sources also vary quite a bit. In addition to the usual federal sources (e.g., NIH, NSF), state sources include CPRIT, The Welch Foundation. Other sources include corporate sponsors and other foundations (e.g., Bill and Melinda Gates foundation). Several faculty also serve as PIs on training grants from NSF (Drs. Dorothy Shippen, Ry Young) and NIH (Drs. David Threadgill, Dorothy Shippen). Table 15 summarizes the source of research funding for each Ad loc. faculty over the review period. It includes grants for which the faculty member was PI or co-PI. TABLE 15. Sources of research funding (n = Ad. loc faculty) for the 2015-2020 period. Rank NIH (R) NIH (P/U) NSF USDA DOE DOD STATE TAMU OTHER Assistant 1 1 2 1 Associate 6 1 7 1 1 1 5 4 2 Full 12 1 6 2 1 1 5 7 4 Distinguished 3 1 1 3

Teaching Productivity of Ad loc. and non-tenure track faculty Student:Faculty ratio The Office of Data and Research Services at TAMU calculates the student/faculty ratio for each fiscal year. The Department's largest teaching components are the 2-semester undergraduate Biochemistry survey courses and the 1-semester introductory Genetics courses. The Department also does a significant amount of service teaching at the graduate level. Figure 17 shows the Student FTE to Faculty FTE Ratio (Excludes GATs FTE), along with the equivalent values for the College and University for each of the fiscal years (FY), as reported by the University (http://dars.tamu.edu/Data-and-Reports/Faculty#star).

FIGURE 17. Student:Faculty ratio over the review period. Overall, in the last couple of years, and the University-wide increase in enrollment, the Student:Faculty ratio has increased markedly, especially for undergraduate students. It is worth pointing out that based on the latest available data (Fall 2019; http://dars.tamu.edu/Faculty/files/Faculty-Profile-Fall-2019.aspx), in the College the ratio of tenured+tenure-track faculty (n=291) over non-tenure-track faculty (n=153) is 1.9, which includes agency faculty with TAMU titles to teach a course. In BCBP, the same ratio is 3.33 (30/9). Hence, based on those numbers, compared to the other departments in the College, the number of students taught by tenured or tenure-track faculty in BCBP is disproportionately higher (~2-fold). This disproportionality is also reflected in the weighted student credit hours (WSCH), which is equal to semester credit hours (SCH) adjusted by a weighting factor to produce a value used by the State of Texas in determining the formula- based funding portion of the University’s state appropriations. For example, for the last semester, for which data is available (Spring 2020, http://dars.tamu.edu/Faculty/files/STAR- FY-2019-2020_V3.aspx), BCBP had 93,381 WSCHs. This is the highest number among all departments in the College. It has been so throughout the review period and for many years before that. Against a $3,701,461 total faculty teaching salary and $547,836 of GAT salary (with GATs accounting for just 12.9% of teaching salaries in BCBP), these numbers amount to a cost per WSCH of $46.8. Only 3 of the 15 departments in the College had a lower cost per WSCH in 2020. As mentioned above, the lower cost in those departments likely arises from the higher involvement of non-tenure-track faculty and graduate teaching assistants.

Teaching load

TABLE 16. Lecture/Lab sections taught for AY2020-21. Instructor FA2020 Title CR SP2021 CR Ayers BICH 412 Biochemistry Lab I 1 BICH 414 1 Bankaitis BICH 671 Macromolecular Folding and Design 1 BICH 671 1 Bryk Carr BICH 410 x1 Comprehensive Biochemistry I 3 BICH 410 x2 3 Carr BICH 409 (online) Principles of Biochemistry 3 Cho BICH 601/602 Fundamentals of Biochemistry 3 module NMR 1 Cruz-Reyes BICH/GENE 431 Molecular Genetics 3 Cruz-Reyes BICH 456/656 RNA World 3 Devarenne BICH/GENE 101 Perspectives in Biochemistry and Genetics 1 BICH 303 2/3 3 Devarenne BICH 675 Plant Biochemistry & Genomics 1 BICH 675 1 Glasner BICH/GENE 101 Perspectives in Biochemistry and Genetics 1 BICH 441(H) 3 Gohil BICH 411 Comprehensive Biochemistry II 3 module Metabolism 1 He BICH631 1/3 Biochemical Genetics 3 BICH/GENE 431 3 Herman BICH 689 Application of Scientific Values 1 BICH/GENE 431 3 Igumenova BICH 608 Critical Analysis of Biochemical Literature 2 BICH 303 1/3 1 Igumenova BICH/GENE 101 Perspectives in Biochemistry and Genetics 1 Kunkel 302 (H) 3 Kurouski BICH 410 Comprehensive Biochemistry I 3 module Spectroscopy 1 Li BICH 410 Comprehensive Biochemistry I 3 module X-ray 1 Meek BICH 404 Biochemical Calculations 2 BICH 440 3 Miles BICH 410 x 2 Comprehensive Biochemistry I 3 BICH 411 x2 3 Miles BICH 409 x 1 Principles of Biochemistry 3 3 Mullet BICH 675 Plant Biochemistry & Genomics 1 GENE 420 (H) 3 Mullet Module 1 Mullet BICH 675 1 Panin GENE 302 (H) Principles of Genetics BICH 406 3 Park BICH/GENE 101 Perspectives in Biochemistry and Genetics BICH 441(H) 3 Park GENE 302 3 Pellois BICH 440 (H) 2/3 Biochemistry I 3 Oral Comm 1 Perez BICH/GENE 432 Molecular Genetics Lab 2 BICH 410 x 1 3 Perez BICH 411 x 1 Comprehensive Biochemistry II 3 BICH/GENE 432 2 Pishko GENE 312 Comprehensive Genetics Lab 1 GENE 312 1 Polymenis BICH 411 3 Polymenis Module 1 Pozzi BICH 410 x 2 Comprehensive Biochemistry I 3 BICH 411 x2 3 Reynolds GENE 301 x 2 (H) Comprehensive Genetics 3 GENE 301 x2 (H) 3 Rye BICH 603 Principles of Biochemistry & Biophysics 3 Module single mol1 Rye BICH 674 Protein Folding & Stability 1 BICH 674 1 Sacchettini BICH 677 Chemical Genetics & Drug Discovery 1 BICH 654 3 Sacchettini Module Drug Discovery 1 Sacchettini BICH 677 1 Shippen BICH631 1/3 Perspectives in Biochemistry and Genetics 3 GENE 302 3 Straight BICH 440 (H) Biochemistry I 3 BICH 406 3 Sze BICH/GENE 419 Computational Techniques for Evolutionary Analysis 3 Threadgill BICH 631 1/3 Biochemical Genetics Module 1 Tommos BICH 441 Biochemistry II 3 Written Comm 2 Wand BICH 440 1/3 Biochemistry I 3 1 Young BICH 608 Critical Analysis of Biochemical Literature 2 BICH 464 3 Young BICH 676 Bacteriophage Biology 1 BICH 676 1 Zeng BICH403 Cellular Biophysics 3 BICH 404 2 Zhang, J BICH/GENE 101 Perspectives in Biochemistry and Genetics 1 module Cryo-EM 1 Zhang, J BICH 404 Biochemical Calculations 2 Zhang, X GENE 302 (H) Principles of Genetics 3 Zhang, X BICH 456/656 RNA Biology 1

The typical teaching load for tenured or tenure-track Ad loc. faculty with full appointment to BCBP is one 3CR lecture or lab course and one 1CR course, plus supervision for credit of undergraduate and/or graduate research. Non-tenure track faculty typically teach two 3CR courses per semester or multiple lab sections. Table 16 shows the current departmental classroom teaching load for a complete academic year.

Service productivity Faculty are expected to perform service activities at the departmental, university, and national/international level. The BCBP committee membership is shown on Table 17. The list includes faculty and staff. TABLE 17. Current departmental committee membership.

COMMITTEE MEMBERS

PERMANENT Executive Committee (EXCOM) Wand (Chair), Devarenne, Pellois, Herman, Rye, Shippen, McLaughlin/Cotton (ex officio) Promotion and Tenure (PATC) Sacchettini (Chair), Polymenis, Liu, He, Zhang X., Shippen, Park Post Tenure Review (PTRC) Mullet, Panin, Polymenis, Zeng

STANDING Awards Committee Glasner (Chair), Cho, He, Kurouski, Zeng, Threadgill, Tommos Wand, Cotton (ex officio) Climate Committee Gohil Development Wand (Chair), Shippen Facilities-CUE Park, Meek Graduate Admissions (GRAC) Igumenova (Chair), Bankaitis, Zeng, Meek, Zhang J., Cho, Park, Herman (BGA), deGruyter (ex officio) Graduate Advising Zeng, Tommos, Polymenis, deGruyter (ex officio) Graduate Outreach & Recruitment deGruyter (Chair), Cho, Zhang J., Caro, Cruz-Reyes Graduate Executive Committee Rye, Herman, Pellois, Igumenova, deGruyter (ex officio) NMR Users Committee Cho, Wand, Igumenova Seminar/Virtual Seminar Li (Co-Chair), Meek (Co-Chair), Herman, Zhang X., Young, Patton (ex officio), Wilbert (ex officio) Undergraduate Program Committee Devarenne (Chair), Li, Kunkel, Glasner, Miles, Threadgill, Panin, Straight, Teel/Spears (ex officio) Website Wand (Chair), deGruyter, Savage, Cotton AD HOC APR self-study Polymenis, He, Pellois, Devarenne, deGruyter, McGaff, Cotton, Wand Safety Committee Park, Wand, Pellois, Devarenne, Ayres, Rye, Cotton, Coronado, Lovingshimer Departmental Study Section Pellois (Co-Chair), Bankaitis (Co-Chair), Young, Mullet Facilities Renovation Committee Wand (Chair), Mullet, Shippen, Rye, Lovingshimer Faculty Search Committee Shippen (Chair), Kapler, Panin, Tommos, Igumenova, Zhang J., Raushel Junior Faculty Mentoring Wand, Mullet, Pellois Non-Thesis Masters Committee Pellois (Chair), Panin, Cho

BCBP faculty also serve on a variety of College, University, and System level committees, including on committees associated with IDPs (see faculty CVs, Appendix Q). Lastly, BCBP faculty regularly perform national service as members of study sections, journal editors and reviewers, and meeting organizers (see faculty CVs, Appendix Q). 73

Awards

TABLE 18. BCBP Ad loc. faculty intramural awards since 2015.

FACULTY AWARD Bryk Texas Academic Advising Network, Margaret Annette Peters Advising Award, Faculty Recognition Award Carr Distinguished Achievement in Teaching, Dean’s Outstanding Achievement Award for Excellence in Early Career Teaching, Vice Chancellor’s Award for Excellence in Teaching Gohil Dean’s Outstanding Achievement Award for Teaching, Montague Center for Teaching Excellence Scholar He Presidential Impact Fellow Herman Vice Chancellor’s Award in Excellence for Teaching Park Faculty Recognition Award Sacchettini Dean’s Outstanding Achievement Award for Research Shan Chancellor EDGES Fellow Shippen Regents Dr. Award, Dean’s Outstanding Achievement Award in Administration, Association of Former Students Distinguished Achievement Award for Graduate Mentoring Threadgill Outstanding Research Leader Award, Excellence in Mentorship and Support Award Young Regents Dr. Award, Dean’s Outstanding Achievement Award for Excellence in Faculty Mentoring, Faculty Recognition Award - Biochemistry Graduate Association Zhang, X Chancellor EDGES Fellow, AgriLife Faculty Fellow, Norman Borlaug Outstanding Faculty

TABLE 19. BCBP Ad loc. faculty extramural awards since 2015.

NAME AWARD Shippen William Rose Award for Outstanding Contributions to Biochemical Research and Commitment to Training Younger Scientists (ASBMB) Park Distinguished Rice Research and Education Team Award Threadgill Toxicological Sciences Paper of the Year Award, Barbara Bowman Distinguished Texas Geneticist Award Wand Elected Fellow of the American Physical Society

Response to previous APR critiques The following recommendations with respect to the faculty were made in the previous review (2014): 1. Involve the entire faculty in self-examining the Department and its programs. 2. A steady stream of new faculty hires. 3. Improve faculty mentoring. 4. Increase efforts of the Awards Committee.

In response to these recommendations: 1. The Department had a short retreat in early 2017, the first at least since 1999, and a strategic plan was developed. Soon after Dr. Josh Wand became Department Head, a 2- day retreat was also organized in the fall of 2019, where a more in-depth examination of the Department took place. In addition, since 2018, several operational documents were either adopted for the first time (e.g., evaluation, and promotion and tenure criteria) or revised after many years (e.g., by-laws). All the above developments improved the clarity about departmental operations.

2. New hires were made since 2015, albeit more by happenstance and taking advantage of opportunities as they arose, and less through targeted approaches. As it turned out, these hires were in areas identified in the strategic plan of 2017, in biological NMR and protein biophysics (Drs. Josh Wand and Cecilia Tommos), plant molecular genetics (Dr.

Libo Shan), genome biology (Dr. David Threadgill), live-cell imaging with modern biophysical approaches (Dr. Dmitry Kurouski). A targeted senior hire in cryoEM is currently in progress.

3. Regarding faculty mentoring (an issue raised firmly in the 2017 retreat) after Dr. Josh Wand became Department Head, a formal process was put in place, with the mock study section committee and a junior faculty mentoring committee.

4. Our awards committee is now very active, and the positive outcomes are clear (Tables 18,19), certainly for the intramural awards. Analysis Ad loc. faculty with primary appointments in the Department of Biochemistry and Biophysics are evaluated based on a nominal 60% scholarly activity – usually research in our discipline, 30% teaching, and 10% service. In 2020 the Department adopted detailed performance evaluation criteria (see Appendix B).

With regards to productivity in research, the trends are encouraging. Both the number and quality of the faculty's scholarly output are on a positive trajectory. There are now high- profile publications (e.g., in Nature, Science, etc.) with lead authors from BCBP Ad loc. faculty almost every year. The frequency of such quality output was lower in the previous review period or earlier. As a whole, the faculty has maintained a substantial level of extramural funding over the review period. To grow, more extramural funding would be needed. How and whether this goal can be achieved with the continuously growing teaching output of the Ad loc. faculty remains to be seen. Although several faculty collaborate and publish together (see Figure 13), many are not. Collaborations improve research output and, consequently, funding success. Collaborations may also lay the foundation for multi-PI project grants, which are and have been limited in BCBP. A comparison with consensus top Biochemistry Departments from peer public Universities shows that they have more large collaborative funding (P or U projects) from NIH for the current fiscal year (see Table 20; data from NIH RePorter).

TABLE 20. Number of large collaborative proposals to NIH at peer departments.

INSTITUTION P,U-type Grants University of California at Los Angeles 4 University of Wisconsin, Madison 3 University of Washington 3 University of Illinois at Urbana-Champaign 2 University of California at Davis 2 Texas A&M University (BCBP) 1 University of California at Boulder 1 Pennsylvania State University, College Park 0

The faculty's output is continuously increasing in teaching. Reforms to improve the graduate program are ongoing, and they are described in detail in the relevant sections of this report. An obvious concern is an increase in undergraduate student enrollment, which puts more pressure on the faculty. A substantial rise in Ad loc. tenure-track faculty could alleviate this pressure. In previous reviews, in 2006 and earlier, it was recommended that 35 Ad loc. faculty would be needed to meet the Department’s teaching obligations. Overall, it will be

challenging to align the rising teaching obligations of the faculty with the rising expectations for external research funding.

Faculty members' willingness to serve conscientiously on departmental committees and special assignments when called upon to do so now plays a more significant role in assessing faculty performance. In the 2017 retreat, unequal service contributions among the faculty was a topic of vigorous discussion.

More faculty now serve on grant review panels or editorial boards, raising the Department's visibility. The recognition of faculty through intramural awards has also increased. Recognition through extramural awards is an area for improvement. This has been a persistent problem, not only for BCBP but for TAMU in general. Based on scholarly output and overall research funding, TAMU and BCBP 'punch below their weight' when it comes to external awards. The University now has an office dedicated to promoting the external recognition of the faculty (https://facultyawards.tamu.edu/). Comparison to peer institutions by Academic Analytics Since 2011, Texas A&M has contracted with Academic Analytics (http://www.academicanalytics.com), a provider of comparative scholarly performance data, to provide benchmark services to compare departmental performance to peer institutions. Figure 18 was generated by comparing TAMU BCBP among a list of 55 departments across 47 public land-grant institutions identified by Academic Analytics.

FIGURE 18. Radar chart of BCBP performance among peer biochemistry departments identified by Academic Analytics. In terms of the variables described above (publications, funding, awards), it appears that BCBP is in the top quarter on most metrics among departments identified by Academic Analytics. However, the faculty percentage with articles and citations ranked better than only 30% of peer departments, for the 2015/16-2019 period covered in the analysis.

Furthermore, the $ per federal grant and federal grant $ per faculty ranked in the middle among peer departments. We note that the roster used in this analysis was for the 2019-20 academic year, and it is not clear that only tenured and tenure-track faculty were used as a query input. The publication output and impact seem unreasonably low since the total article output was in the top 20th percentile. On the other hand, regarding the low $ per federal grant, the graph may indeed reflect the relatively fewer large project grants in BCBP among peer departments. Student Profiles Graduate Students Student Profile (Current) Our current PhD cohort comprises 86 students, of which 42% identify as female, and 58% identify as male (Figure 19). Hailing from across the globe, our students claim citizenship in 13 countries, with 46.5% domestic and 53.5% international students. 29% of our students are in year 6 or beyond (matriculation 2011–2015). Among these senior students, 68% identify as male, and 60% are federally designated as international. As of December 2020, our current students are conducting research across 26 Ad loc. and joint faculty, as well as seven students who are in groups with no direct BCBP affiliation. A relic of the previous program administration, the placement of students in non-BCBP research groups is no longer permissible.

FIGURE 19. Distribution of gender for students currently enrolled in the program by matriculation year. Our current cohort has an average cumulative GPA of 3.6. The first year of core coursework is arguably the most rigorous, resulting in a greater distribution of first-year GPAs and a lower cohort average. The values tend to normalize over time as students earn letter grades in participation-based (e.g., Journal Clubs) and elective courses. The distribution of GPA by matriculation year is shown in Figure 20.

FIGURE 20. Box and whisker plot for the graduate GPA of students currently in the program and enrolled since 2015. Students are distributed by matriculation year. A cross represents the average GPA for each student group.

Student Profile (20-Year Trends) The data described in the following section classifies students by matriculation year. Application information (i.e., GRE scores, GPR) refers specifically to enrolled students and is not reflective of the total applicant pool in a given year. Class size Before 2019, the number of students offered admission, and accordingly, the number of students eventually enrolled (Figure 21) was primarily dictated by the required number of teaching assistants. With the arrival of new program leadership, a reassessment of admissions standards led to the decoupling of teaching assistant positions and the number of admissions offers. As of 2019, offers are made solely based on merit and potential. With a limited dataset, an analysis of this decoupling effect on the perceived quality of enrolled graduate students is not yet possible. Notably, 2020 saw an especially small matriculating cohort, as 75% (9 of 12) of our international students could not secure student visas due to COVID-19 embassy delays and closures. These students were offered deferred admissions to Fall 2021, though only three have confirmed acceptance as of December 2020.

FIGURE 21. Class size by matriculation year. GRE and GPR/A scores Incoming cohorts typically arrive with an undergraduate GPR/A greater than 3.0 and Verbal and Quantitative GRE scores above the 45th and 46th percentile, respectively (Figure 21). Notably, despite eliminating the GRE requirement in the 2019 admissions cycle (2020 matriculating cohort), some students opted still to submit official or self-reported scores. The values shown in Figure 22 capture only those students who reported scores and are not necessarily reflective of the full cohort.

FIGURE 22. GRE verbal (V) and GPR of PhD cohorts. Race and ethnicity The self-reporting of race and ethnicity is typically voluntary and optional. Indeed, between 2014–2019, this demographic information was either not reported by students or not recorded by the previous administration. Additionally, between 2008–2013 students were given the option of selecting “international” in lieu of race or ethnicity. In 2020, OGAPS and the Office of Admissions opted to remove the question entirely from the application. As such, our dataset is incomplete. Data for the periods of 2002–2007, 2008–2013, and 2020 are provided in Figure 23.

FIGURE 23. Ethnicity distribution of students entering the BCBP graduate program. Ethnicities have been recorded by the University using different mechanisms and different designations over several time periods. The data are shown to reflect these changes. The reporting of ethnicities has also been voluntary since 2014, yielding incomplete data not reported here.

FIGURE 24. Distribution of matriculating cohorts by gender and federal designation. FD = Female domestic, FI = Female international, MD = Male domestic, MI = Male international.

Federal designation and gender distributions Between 2000–2010, only 30–45% of matriculating classes were designated international. Over the last decade, this number has increased to more than 50% on average. As described above, delays brought about by COVID-19 closures resulted in an unusually high percentage of domestic students in our incoming class. Figure 24 describes the gender and federal designation of matriculating cohorts. Geographic diversity of domestic students Historically, most of our domestic students (52%) claim Texas residency at the time of application (Figure 25). Over time, our reach has increased to include at least one student from most states in the contiguous US. While direct attribution of this phenomenon is difficult, TAMU has a strong record of in-state enrollment.

FIGURE 25. Geographic diversity of admitted domestic students. Attrition For each incoming cohort of PhD students, only a fraction will graduate with a PhD. The rest, defined here as “attrition”, will eventually earn an MS degree (thesis (THO) or non- thesis (NTO)), withdraw (W), or transfer (T) from the PhD program (Table 21).

TABLE 21. Total department attrition rates for students matriculating between 2000–2020.

Degree PhD MS MS-NTO MS-THO T W MS/T/W Total 274 83 52 31 28 58 169 Percent 62% 19% 12% 7% 6% 13% 38%

On a year-by-year basis, these numbers are shown in Figure 26.

FIGURE 26. (Left) Attrition and PhD completion rates in real numbers. (Right) Percent attrition and PhD completion. The students currently in the program are marked as “PhD” to reflect the fact that they are currently on track to graduate. This leads however to an analysis skewed towards low attrition rates for students enrolled in 2015 and beyond. Analysis We focus on parameters that may affect the rates of PhD completion, time to degree, and our students' publication output. We discuss a shift in the composition of the departmental research personnel towards postdocs and staff scientists and away from graduate students, and the consequences of that shift for the graduate program. PhD completion rates The overall attrition rate for students enrolling in 2000 or later is 38% (see Table 21). This is considered unacceptable and has promoted drastic alterations of the graduate program as described elsewhere. A year-by-year analysis of attrition trends by gender (Figure 27, left) and federal designation (Figure 27, right) is shown below. Breaking down the students admitted since 2009 by sex and citizenship, and whether they graduated with a PhD or not, is shown in Figure 28. Although it may seem that female domestic (FD) students are more likely to leave the program without a PhD, this is likely a random anomaly and not a systemic feature of our program, for the reasons we detail below. To find predictors that significantly associate with success in our program (defined as PhD completion), we looked further back at all available data. Excluding current students and students that transferred with departing professors, of the 566 students we admitted since 1980, 375 obtained their PhD (i.e., only two out of three students ‘succeeded’ in our program over that period). Among the 566 students we admitted, for 564 we had data on their sex (male or female) and citizenship status (domestic or international), and applied a logit regression model to see if either of these variables is significantly associated with PhD completion. They are not (p = 0.177 and p = 0.116, for sex and citizenship, respectively). For 245 of the students we admitted, we had complete data about their undergraduate GPA and GRE scores (Verbal and Quantitative), along with their citizenship status, and sex. We then applied again a logit regression model for this set, to see if any of these variables is significantly associated with PhD completion. Only GPA was a strong predictor (p = 6.54e-05), while none of the other variables showed any statistically significant association (p >0.05). From odds-ratios analysis, from one unit increase in GPA, the odds of graduating with a PhD increase by a factor of 4.91.

FIGURE 27. (Left) Percent graduation rates by gender. (Right) Percent graduate rates by federal designation.

FIGURE 28. Distribution of students recruited into the program for the period 2009-2019 and corresponding distribution of the students who graduated or who remain on the PhD track within the same time period. FD = Female domestic, FI = Female international, MD = Male domestic, MI = Male international. Student productivity The majority of our students graduate with two papers or more (Figure 29A). Unsurprisingly, productive students tend to graduate in 5 to 6 years, while students with a lower productivity output tend to stay in the program for seven or more years (Figure 29B). Approximately 11% of students have graduated without a publication since 2000. There is no apparent correlation between the output of these students and YTD. Graduating without publication is largely recognized as problematic by the program. In 2015, the faculty voted to implement a publication prerequisite for graduation. This rule was meant to provide students with additional motivation and provide a clear consensus for thesis committees' expectations. The new format in the graduate committee structure and yearly evaluation in 2019 should

further contribute to solving this problem. Notably, a close examination of the student group without publication shows that these students graduated from a few laboratories (analysis not shown), most of which are not in the program any longer. Overall, we expect that progress will be seen in this metric for current and future cohorts.

FIGURE 29. Student publications. A. Percentage of PhD graduates who contribute to the indicated number of publications. These data are for students who have graduated since 2000 (n=185). B. Distribution of total publications as a function of YTD. Each data point represents one of the 185 students who have graduated from BCBP since 2000. Distribution of graduate students within the department and in research laboratories With smaller cohorts of students being recruited over the past few years, it appears that the distribution of active research personnel has shifted towards postdoctoral associates and research staff (Figure 30). It is worth noting that the research personnel's size on payroll has not changed significantly, from 175 in 2015 to 176 in 2020. Student workers are not counted in this analysis. Some undergraduate students are paid for their research work, while many work in laboratories to earn credit. BCBP graduate students in the laboratories of faculty members with a primary appointment outside BCBP are not presented in Figure 30. The diversification of the research personnel and uncoupling the departmental TA 'needs' from graduate student admissions enables BCBP to focus on the graduate program's quality. By recruiting fewer but higher quality graduate students, BCBP moves toward building a stronger graduate program.

FIGURE 30. Proportion of graduate students within research personnel.

Undergraduate Students Enrollment During the last departmental APR, the BICH and GENE freshman enrollment increased by approximately 47% From 2007 to 2013 and reached a maximum of about 140 total students (not shown). Since that time, the total number of BICH and GENE freshman has leveled off at about 150 students for each academic year 2015-2019 (Figure 31). While the freshman class size has been relatively constant, the total number of BICH and GENE majors has shown a small but steady increase in the number of students (Figure 32). This is mostly due to the rise in the number of BICH transfer students (Figure 32). With our new, more modern GENE degree plan, we expect this will attract more students, and the number of GENE first-year students entering the program may begin to increase. For example, the GENE freshman class for Fall 2020, the first year of the new GENE degree plan, has 41 students (not shown). The average number of GENE first-year students for AY 2015-2019 was 25.

FIGURE 31. Freshman BICH and GENE Enrollment for AY 2015-2019.

FIGURE 32. Total BICH and GENE Undergraduate Enrollment for AY 2015-2019.

A major part of the department's teaching load is for students outside the BICH and GENE majors. These courses include BICH 410/411 Comprehensive Biochemistry I/II and GENE 301/302 Comprehensive Genetics/Principles of Genetics. Our academic professional track faculty instructors largely teach these courses. However, several tenure track faculty also teach these courses. The number of non-BICH and GENE students taught in these courses has been around 5,000 for AY 2015-2019 (Figure 33). Combined with the number of BICH and GENE students we teach, the total number of students taught by our department over AY 2015-2019 ranged from 6,000 to 6,600 Figure 33). In this analysis, some students are counted more than once since they often take more than one course offered by our department in an academic year. Thus, the analysis counts seats occupied in classes.

FIGURE 33. Non-Major vs. Total Department Undergraduates Taught for AY 2015-2019. Student Diversity/Demographics The ethnic and gender distribution of BICH and GENE students at all levels for AY 2016- 2019 is shown in Table 22. Data for AY 2015 was not available at the time this data was gathered. The data shows that the department undergraduates are a very diverse group with higher percentages of female, Asian, black and Hispanic students than the campus average. Interestingly, both the BICH and GENE programs attract more female students than male students. The genetics program attracts many female students, with 71.0% of all GENE students being female. This is compared to only 47.7% of females campus- wide.

TABLE 22. Demographics of BICH and GENE Majors for AY 2016-2019.

BICH GENE Campus Avg Gender Number Percent Number Percent Number Percent Female 720 53.3% 422 71.0% 102026 47.7% Male 630 46.7% 172 29.0% 111859 52.3% Ethnicity Number Percent Number Percent Number Percent Asian only 262 19.4% 76 12.8% 15589 7.3% Black 84 6.2% 30 5.1% 7312 3.4% Hispanic/Latino 352 26.1% 125 21.0% 50252 23.5% Intl 14 1.0% 6 1.0% 4966 2.3% Multiracial 38 2.8% 25 4.2% 5484 2.6% Native American 2 0.1% 2 0.3% 503 0.2% Unknown 2 0.1% 0 0.0% 401 0.2% White only 596 44.1% 330 55.6% 129178 60.5% Total 1350 100.0% 594 100.0% 213685 100.0% *AY 2015 was removed from the Accountability website at time of data retrieval

Retention Rates The departmental retention rate of first-year BICH and GENE students after their first year of studies compared to other science majors at Texas A&M is shown in Figure 34. On average, the BICH retention rate is higher than that of BIOL, CHEM, and PHYS. However, the GENE retention rate has declined in recent years. The reason for this is not apparent. With the new GENE degree plan, we will track this data to see if the trend continues to decline or increases.

Of the students that leave the department, most students move to other colleges such as Veterinary Medicine, Liberal Arts, and general studies (not shown). These students are retained within the university at a very high rate that is consistently above 90% (Figure 34). Note that university-wide retention rate data for AY 2019 is not yet available.

FIGURE 34. Percent of Freshman BICH and GENE students retained in the department after the first year. Number of Degrees Awarded per Year This information was shown above, in Number of Degrees Awarded per year. Graduation Rates The number of students that enter the department as freshman, stay within the department, and graduate with a BICH or GENE degree within 6 years is shown in Figure 35 with comparison to other science majors at Texas A&M for AY 2015-2019. While the departmental graduation rates are not high, low of 27.8% and high of 47.5%, these rates are very similar to BIOL and CHEM, and in some years are higher. These numbers may reflect the challenging nature of these degrees and may be a common issue for science majors.

FIGURE 35. BICH and GENE graduation rates in comparison to other science majors for AY 2015-2019. Graduation rate calculated by percentage of FTIC students who complete their 4 yr degree within 6yrs. Average Time to Degree (most recent 5 years) This information was shown above, in Average Time to Degree. Analysis The department undergraduate student population for the BICH and GENE programs is an ethnically diverse group. These students complete their degrees in an expected time that generally does not exceed four years. While the graduation rate for BICH and GENE students is low, it is on par with other science majors at the university. The BICH program's recent accreditation by ASBMB indicates that the BICH degree meets the field's highest standards. Thus, both BICH and GENE students are well prepared for the next step in their career, whether that be professional school, graduate school, or industry. Anecdotal evidence suggests this is the case. With the recent change in the GENE degree program, we hope to attract more students to this program and a new subset of students with computational interests. Time will tell if this will pan out.

One of the most challenging issues for the department related to our undergraduate programs is the number of non-major students taught by the department. This is and likely will continue to be a large burden on the departmental teaching staff. With the university continually increasing enrollment, the number of non-major students taught by the department will likely increase. Currently, the department cannot accommodate every student each semester that requires classes such as BICH 410/411, potentially causing delays in graduation. For example, each semester, the department receives between 700- 800 requests from students to be forced into BICH 410/411. Students must fill out a force request when classes fill during open registration. We can only accommodate a small number of these force requests, and students graduating in the current semester are given priority. In other words, hundreds of force requests by students go unsatisfied every year. This is a huge opportunity cost. The department's main limitation is the number of faculty available to teach these classes required by an ever-increasing number of students.

Conclusions and Action Plan Overall, within a complex institutional environment (see Appendix O), the Department is emerging successfully from several tumultuous challenges and is looking forward to positioning itself to take on the challenges of the future. The research enterprise continues to strengthen and the productivity of the faculty is impressive under the circumstances, but can nevertheless be improved. The Department and its various programs are in transition under new leadership. As with many large academic enterprises, the various functions of BCBP are intertwined and interdependent. A burgeoning undergraduate population places increasing demands for teaching assistants. The increased demand for TAs has led to compromises in admission of graduate students. We have taken initial steps to decouple the demand for TAs from the need for a more limited number of quality graduate students. This will be achieved through remote recitations, which proved highly successful during the pandemic, and the recruitment of “professional TAs.” The professional TA is an experiment and will be hired after graduation with a limited horizon employment. It is anticipated that a single professional TA will be able to handle the work of 3-4 classical graduate student teaching assistants. Through these two strategies, we hope to relieve the convolution of the practical demand for graduate students to be teaching assistants and the need for well- prepared students to contribute to our research enterprise and flourish in our graduate programs.

We will continue to improve on our graduate education programs. It is clear that inadequate guidance through an inconsistent labyrinth of graduate education by poorly prepared students has likely contributed significantly to an unacceptable rate of attrition and to a discouraging time-to-degree statistic. As a first priority, Drs. Pellois and deGruyter have made significant headway in revitalizing the graduate program with the goal of eliminating the underlying issues and setting it on a path to excellence and stability. Only time will tell if these actions have corrected the underlying problems, but it is also clear that the philosophy of mentorship of many members of the faculty will also need to change. Nevertheless, we believe that a strong foundation has been created with which to improve the number and quality of applicants to the program and to provide those that matriculate with an efficient, rewarding and exciting path to academic excellence. Further curriculum changes are anticipated with a general enrichment in advanced topics offerings through the modular system already in place.

In spite of its vastness, the Department does not provide a place where graduate students can experience the intimacy of scientific collaboration and the exchange of ideas. By this we mean a place where students can gather to present unpolished results to students and faculty alike. Furthermore, incoming first year students are effectively orphaned in not having a place to call their own to study and think. In a very real sense, there is not an academic community. We intend to remedy this deficiency by renovating a first-floor room of ~1,500 sq ft to provide a working space for informal seminars, group meetings, spontaneous discussions and the occasional party. An interior room within this space will be set aside for first year students who have not yet identified a home research group to call their own. We hope that this space will instill a sense of community and enhance the graduate experience to well-beyond “just a job” aura.

It is somewhat unsettling that despite its formal name, the Department lacks a PhD degree that recognizes biophysics. A third of the Department works in some region of the molecular biophysics space. By not formally offering an emphasis in biophysics we are likely missing out on a desirable cohort of quantitative students. Initial steps will be taken to either create a 90

separate degree or incorporate and recognize by name biophysics in a single PhD degree program. Similar comments apply to the undergraduate program of the Department. There is no undergraduate biophysics major. Such majors have been quite successful elsewhere and attract a different cohort of students than, say, a biochemistry major. The creation of a new major is involved and takes years to complete, but we have begun the process.

The faculty of the Department of Biochemistry & Biophysics is relatively small for its teaching mandate. This is reflected in the literally hundreds of failed forced requests for our service courses that occur each (non-pandemic) year because our courses are over-subscribed. We need a larger teaching faculty. Furthermore, the teaching commitment for research active faculty remains too large. It is within the purview of the Head to redistribute effort for teaching, research and service for individual faculty. This facility will have to be invoked in order to rebalance commitments towards more teaching for less research active faculty. Nevertheless, while steps can be taken to redistribute teaching from research productive faculty to those less research-active faculty, this strategy has limited dynamic range. Indeed, we have been greatly weakened by the recent departure of genetics-oriented faculty, one through recruitment (Kaplan), another by retirement (Kunkel) and one through an untimely passing (Hu). This has destabilized the genetics major and leaves the research profile of the Department degraded in molecular genetics and genomics. Recruitment of junior faculty to fill this and other voids in the Department’s research profile is critical to its long-term success.

Financially, the recent and severe reduction in indirect cost return to the Department and the insufficiency of the state “base” budget to carry out the teaching mandate limits our nimbleness in every area of activity, but particularly with respect to supporting the research mandate. It is not clear that a significantly increased grant revenue is possible, in light of the teaching load, or effective in relieving this financial drag on the research enterprise. Biochemistry and biophysics are inherently both space intensive and expensive. There is little capacity for the Department to expand or upgrade its space or assist in the construction of competitive startup packages for those in targeted fields. Some relief is anticipated from the revitalized stockroom enterprise, however.

The near future represents a considerable challenge with respect to the quality and availability of space for research and teaching. We are faced with a significant challenge of installing two clusters of plant growth chambers to augment an existing cluster on the third floor of the BCBP building. The goal is to transport the three outstanding faculty evacuating their Borlaug “home,” in a way that enhances their research environment and brings them close to like-minded plant biochemists in the Department. Following closely on the heels of that renovation will be a refurbishment of space on the fourth floor recently released by two retirements. Junjie Zhang will relocate from the ILSB to be closer to the Titan Krios cryoEM. Adjacent space will be targeted for the mid-career senior hire in cryoEM as discussed above. The proposed redistribution of space is summarized in Appendix D. A rising concern is an announced change in the philosophy governing allocation of space in ILSB where a significant fraction of BCBP faculty reside. A contraction appears likely and with it a reduction in our prowess.

Over the next decade it is anticipated that perhaps one third of the faculty will retire. Notwithstanding the very real need to recruit an established mid-career investigator in cryoEM, it is important for its long-term health that the Department position itself to hire junior faculty. To do so with a new building not on the horizon, we need to modernize space

as it becomes available in the main BCBP building. This will require a serious commitment on the part of COALS. It will also require augmentation of the Facilities staff of the Department to handle the logistics of continual refurbishment throughout the building over a period of perhaps a decade. All these challenges require significant financial resources and it is apparent that the Department cannot “carry the water” alone and that a major investment by COALS is required to help us achieve the mandated target of rising to the top layer of our peer group.

In summary, over the next review period we hope to complete our revitalization of the graduate program in Biochemistry and establish a foundation for a successful predoctoral training grant (T32) from the NIH. During this time, we will create a companion graduate PhD degree in molecular biophysics, based on the recently installed structure and philosophy of the program in biochemistry. A review and subsequent refinement of the undergraduate program in biochemistry will be undertaken and a revision as indicated completed. The undergraduate research ties will be strengthened. As for the graduate program, an undergraduate major in molecular biophysics will be designed and installed thereby completing the education mandate of the Department of Biochemistry & Biophysics.

The teaching distributions will be optimized to provide less research faculty greater opportunity to contribute to the overall success of the Department. Fracture of undergraduate courses, such as we have experimented with Drs. Pellois and Wand in BICH 440, will likely be required to allow for fine-tuning of instructional loads.

The research profile of the Department will be deepened and expanded through recruitment of junior faculty in areas relevant to molecular genetics and epigenetics, metabolic biochemistry, signaling and protein translational modification, structural biology of large and transient complexes particularly by cryoEM, and in-cell biochemistry including cryoelectron tomography and other imaging strategies. An emphasis on plant biochemistry will be maintained with an eye on biotechnology and applications towards climate change and conservation. We will continue to install mentoring structures for junior faculty, particularly in proposal preparation and delivery of educational material at both the undergraduate and graduate levels.

Appendices

Appendix A. Departmental Bylaws

Appendix B. Faculty Evaluation

Appendix C. BCBP Remodel Plan

Appendix D. BCBP Floor Plan

Appendix E. NMR Floor Plan

Appendix F. Common Use Equipment (CUE)

Appendix G. Graduate Program Handbook

Appendix H. Graduate Recruitment Weekend and Life Sciences Symposium

Appendix I. Graduate Program | Degree Plan

Appendix J. Graduate Program | Elective Course Options

Appendix K. Graduate Program | Committee Meeting Protocols and Evaluation Forms

Appendix L. BCBP Seminar Presentations

Appendix M. 2014 External Review | Report and Departmental Response

Appendix N. BICH/GENE 491W Rubric for Assessment of Undergraduate Classes

Appendix O. Institutional Profile

Appendix P. Annual Extramural Research Grant Expenditures

Appendix Q. Faculty CVs

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Appendix A - BYLAWS OF THE DEPARTMENT OF BIOCHEMISTRY AND BIOPHYSICS

Table of contents Table of contents Introduction Article I. Definitions of Faculty Membership A. Tenured or tenure-track member Non-tenure track member Article II. Leadership of the Department Article III. Committees of the Department Definitions B. Permanent Committees The Executive Committee 2. The Promotion and Tenure Committee 3. The Post Tenure Review Committee Article IV. Adoption and Amendment of the Bylaws and Appendices A. Amendments to the Bylaws B. Adoption Article V. Faculty meetings A. Rules of order B. Meeting Agendas C. Actions on Motions D. Interpretation of Constitutionality and Related Questions E. Meetings 1. Regular Meetings 2. Special Meetings

Introduction Preamble: The Bylaws of the Department of Biochemistry and Biophysics (hereafter, the Department) are subject to compliance with the rules of the College of Agriculture and Life Sciences (COALS), Texas AgriLife Research, Texas A&M University (TAMU) and the Texas A&M University System (TAMUS). The Bylaws include Appendices, which have equal weight as the main body of the Bylaws. The Bylaws and Appendices can be changed only by the amendment procedures defined within the Bylaws. These procedures are intentionally more

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flexible for the Appendices than the core Bylaws. Appendix A. Faculty Rank, Responsibilities and Procedure for Consideration Appendix B. Departmental protocols for promotion, tenure, and post-tenure considerations Appendix C. Annual Evaluation Policy Appendix D. Standing committees of the Department

Statement of Departmental Academic Mission For its academic mission, the Department has the responsibility for offering the curricula leading to Bachelor of Science degrees in Biochemistry and in Genetics, to the Master of Science degree in Biochemistry, and to the Ph.D. in Biochemistry. In accordance with this mission, the Department serves as the primary university home department for teaching and research in biochemistry, biophysics, and molecular genetics. The mission of the graduate program of the Department is to enable students to understand, plan, execute and communicate rigorous scientific research in biochemistry, biophysics, and molecular genetics.

Article I. Definitions of Faculty Membership

A. Tenured or tenure-track member 1. Full faculty members are tenured and tenure-track faculty members with ad loc appointments in the Department. Full faculty ranks are: Assistant Professor, Associate Professor, Professor, and Distinguished Professor. Full members have unrestricted voting rights. 2. Joint faculty are faculty members who are tenured and do not have an ad loc appointment in the Department of Biochemistry and Biophysics. All Joint faculty are voting members, although they may not vote for Department Head appointment, on Bylaws adoptions or amendments, or on offers of Joint membership. 3. Expectations, rights, and duties of Full and Joint faculty, and the procedures for consideration for Full or Joint faculty membership are described in Appendix A. 4. Procedures for attainment and retention of tenured or tenure-track faculty status, as well as promotion from one rank to another, are defined in Appendix B. 5. Emeritus faculty are faculty members who have retired after tenure. Emeritus faculty may attend and participate fully in faculty meetings, except that they are non-voting. The procedures for consideration for Emeritus faculty are defined in Appendix A. 6. Senior faculty are tenure-track academic faculty who have opted for a form of voluntary separation but are not yet retired. Senior faculty may attend and participate fully in faculty meetings and have full voting privileges corresponding to the rank at which time voluntary separation was arranged.

B. Non-tenure track member 1. Lecturer, Instructional, Research or Visiting faculty are non-tenure-track faculty. 2. Lecturer faculty ranks are: a. Lecturer

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b. Senior Lecturer 3. Instructional or Research faculty ranks are: a. Instructional or Research Assistant Professor b. Instructional or Research Associate Professor c. Instructional or Research Professor 4. Expectations, rights, and duties of Lecturer, Instructional, Research or Visiting faculty are described in Appendix A. 5. Procedures for attainment and retention of Lecturer, Instructional or Research faculty status, as well as promotion from one rank to another, are defined in Appendix A. 6. Non-tenure track faculty may serve on all faculty committees except the Executive Committee, Promotion and Tenure Committee, and the Post Tenure Review Committee. Non-tenure track faculty may attend and participate fully in faculty meetings, except that they are non-voting. 7. Lecturer, Instructional or Research faculty appointments or re-appointments are limited to terms defined by the relevant guidelines as published on the Office of Dean of Faculties website: https://dof.tamu.edu/Hiring. Article II. Leadership of the Department A. The Head of the Department is appointed by the Dean of the College of Agriculture and Life Sciences (COALS). The term and conditions of office, including review, is as prescribed by the policies of COALS. B. The Head appoints Associate Heads for Undergraduate Programs and for Graduate

Programs. Article III. Committees of the Department

A. Definitions Three types are defined: Permanent Committees, Standing Committees, and ad hoc committees. 1. The Permanent committees of the faculty shall be the Executive Committee, the Promotion and Tenure Committee (PATC), and the Post Tenure Review Committee (PTRC). 2. Standing committees are appointed for ongoing long-term needs of the Department and are defined in Appendix D. 3. Ad hoc committees are appointed for short-term needs of the Department. 4. Except as otherwise provided by these Bylaws and Appendices, the Head of the Department will determine the size, membership, and Chair of each Standing or ad hoc Committee.

B. Permanent Committees

1. The Executive Committee a. The Executive Committee of the Department shall be responsible for the development and implementation of departmental policies. The Executive Committee shall specifically be responsible for advising the Head on the

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major substantive issues of departmental governance, including the availability and utilization of resources (human, space, and budgetary); graduate, undergraduate, and post-doctoral academic programs; as well as research activity and infrastructure. Minutes reflecting the substance of Executive Committee activities will be prepared, approved by the membership, and reported to the faculty in a timely manner. b. The Executive Committee shall have at least five members, consisting of the Head of Department, the Associate Heads for Graduate and Undergraduate Programs, and two tenured faculty members elected at-large. (If an Associate Head position is vacant, the Executive Committee seat will be filled by the Chair of the appropriate Graduate or Undergraduate Programs Committee). Senior Departmental Administrative Assistants shall serve as non-voting ex-officio members. c. The quorum of the Executive Committee shall consist of three voting members, one of whom must be an elected member. d. Election Procedures. 1). Nominations for each unfilled elected position shall be solicited by mail from the faculty. Voting shall be by mail-ballot. Voting shall close one week after distribution of ballots. Nominees with the most votes in each position shall be elected. 2). Terms shall be for two academic years, and the terms shall be staggered. 3). Elections shall be held in May, and the election results shall be effective on September 1.

2. The Promotion and Tenure Committee a. The Committee will evaluate candidates for promotion or tenure, according to the guidelines specified by the Department, the College, and the University. The recommendation of the Committee with regard to tenure or promotion will be made to the Head of the Department. b. The Committee will consider all nominees for joint appointments and make a written recommendation to the whole Faculty for a rank appropriate vote: i.e. for Joint Associate Professor, all tenured faculty may vote. For Joint Professor and Distinguished Professor, only tenured faculty members with these ranks may vote. All types of joint membership require two-thirds support of the votes cast for approval. c. The Committee shall consist of seven Full Professors; one member appointed by the Head of Department and six members elected by the Faculty of Biochemistry. The Head of Department and other Members of any Faculty at Texas A&M holding administrative positions of Head or higher shall not be members of this committee. No more than one Joint faculty shall serve on the Promotion and Tenure Committee at any one time. d. The period of service on the Committee shall be six years. The period of service on the Committee for the appointed member shall be three years. The appointed member may be reappointed for a consecutive three-year term. The Chair of the Committee will be elected by the membership of the Committee and serve as Chair for a period of two years. An individual serving as Chair may be reelected for one consecutive two-year term as Chair as long as the reappointment does not extend the individual’s

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period of service on the Committee beyond six years. Individual tenures on the Committee shall be staggered so that one new member is elected each year to ensure continuity. After completion of a six-year term (or two consecutive three-year terms), members will be eligible for election or appointment to a new term on the Committee after two years. e. Nominations for the unfilled elected position each year shall be solicited by mail from the faculty. Voting shall be by mail-ballot. Voting shall close one week after distribution of ballots. The nominee receiving a majority of the votes cast will be elected. If no one receives a majority, the two nominees receiving the most votes will stand for a runoff election. Voting in the runoff election shall be by mail ballot, and voting shall close one week after distribution of the ballots. The nominee receiving the most votes in the runoff election will be elected. The term of the appointment shall begin on January 1, following the election. f. In the event a member is forced to resign from the Committee before the expiration of his/her term, the position will be refilled as follows: g. Replacements will be selected by the same process that was used to fill the term originally. In the case of an elected member, an election should be held according to the procedures outlined above as soon as is practicable after the Department Head declares the vacancy. h. A replacement once elected or appointed will begin service on the Committee immediately. h. The replacement will serve out the original term (i.e., not start a new 6-year or 3-year term). i. Replacements that serve longer than 3 years will not be eligible for re-election or reappointment for 2 years after the expiration of the term.

3. The Post Tenure Review Committee a. The Committee shall conduct periodic peer evaluation for tenured faculty. The timing of the evaluation shall be no more than 6-years since the awarding of tenure; receipt of an honor based on peer evaluation of accomplishments, such as University Distinguished Professor or Regent’s Professor; or a previous Post Tenure Peer Evaluation; whichever has occurred most recently. b. The Committee shall consist of two elected [Full] Professors and one [Full] Professor appointed by the Department Head, except as indicated in Article III.B.3.d, below. c. The period of service on the Committee shall be three years, staggered so that one new member is either elected or appointed each year. d. The appointed member will be a [Full] Professor except for the following circumstance: when a tenured Associate Professor is due to be evaluated by the Committee, the Department Head shall appoint an ad hoc tenured Associate Professor to serve on the evaluation committee in place of the regularly appointed member when reviewing that case. e. The selection process for the elected members of the Post Tenure Review Committee shall be the same as described for the Promotion and Tenure Committee, in Article III.B.2. f. A member of the Committee cannot serve longer than 3 consecutive years and will not be eligible for re-election or reappointment for 2 years after the expiration of the term.

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g. The appointed member shall serve as Chair except for consideration of Associate Professors, in which case the elected member with the longest time in tenure shall serve.

Article IV. Adoption and Amendment of the Bylaws and Appendices

A. Amendments to the Bylaws Permanent or Standing committees, or full faculty members supported by 20 percent of the full Faculty, may propose amendments to the Bylaws and the Appendices. The proposed amendment(s) shall be submitted to the Executive Committee, and subject to the approval of that committee, shall be included on the agenda of a Faculty meeting for debate only. Unlike regular issues, all proposed amendments to the Bylaws or Appendices must be provided to the faculty at least two weeks before the meeting at which the first discussion is to be held. At the close of the debate, the proposal shall be referred to an ad hoc committee appointed by the Head for a report and recommendation. At the next regularly scheduled Faculty Meeting, the Faculty shall consider the report and recommendation of the ad hoc committee. A standard vote by secret ballot will then be conducted.

B. Adoption 1. Upon final adoption, the amended Bylaws and Appendices shall become effective at the next meeting. 2. All amendments and changes in the Bylaws shall be adopted by a two-thirds majority of the full Faculty and shall take effect at the next meeting except as noted in Article V.C. 3. All amendments and changes in the Appendices shall be adopted by simple majority of the full Faculty and shall take effect at the next meeting except as noted in Article V.C. 4. Amendments which have been defeated may not be reintroduced for one full academic year. The Head shall determine if a proposed amendment falls under this restriction.

Article V. Faculty meetings

A. Rules of order The rules contained in the current edition of Robert's Rules of Order shall govern in all cases to which they apply and in which they are not inconsistent with the Bylaws or any special rules of order the Faculty may adopt.

B. Meeting Agendas 1. For inclusion on the regular meeting agenda, items must be submitted to

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any member of the Executive Committee at least three working days before the meeting. The proposed agenda item shall be in writing and shall contain any motions on which action is desired at the meeting. Such items shall either be placed on the agenda or sent to an appropriate committee for consideration, at the discretion of the Executive Committee. 2. The Executive Committee shall set the agenda for all faculty meetings and report to the Faculty on the status of unscheduled items. 3. The Secretary shall submit the agenda, including motions and supporting materials, to all Faculty Members at least two working days before the meeting. 4. The Head of the Department, or his or her designee, shall serve as Chair of departmental meetings. 5. Faculty members may move to include a specific item on the next meeting's agenda at any meeting.

C. Actions on Motions 1. The Faculty, by majority vote, may take final action on items on the published agenda. 2. Emergency items: a. The Faculty, by majority vote, may declare a motion on an item that was not on the agenda as an emergency item for immediate deliberation. b. Emergency items placed on the agenda shall require a three-fourths majority of the Faculty present and voting for passage. 3. Final action may not be taken on other, non-emergency motions until the next regularly scheduled meeting. This includes all items not listed on the published agenda, including items raised by standing committee reports. 4. A single voting faculty member may demand a secret ballot for any motion. 5. Twenty-five percent of the voting faculty present may demand that a motion be determined by mail ballot. Such a motion shall be mailed to the voting faculty the next working day by the Secretary. Voting shall close after an additional six days. 6. Motions which have been defeated may not be reintroduced for one full academic year. The Head shall determine if a motion falls under this restriction

D. Interpretation of Constitutionality and Related Questions Rulings on constitutionality and conformance to bylaws and relevant legal documents shall be made by the Chair of the meeting, or his or her designee.

E. Meetings

1. Regular Meetings a. The default schedule for regular faculty meetings is the last Monday of each month at 3:30 pm. The Chair may adjust the meeting time and date to accommodate exigencies as required. b. The meeting shall adjourn by 5:00 pm, but the time limit may be extended

M-7

Approved May 2019

by a two-thirds vote of the voting members present. c. At any regular meeting, the time and/or date of any ensuing regular meeting may be changed by a two-thirds vote. d. A quorum shall be any number greater than 50% of full Faculty members of the Department of Biochemistry and Biophysics.

2. Special Meetings a. Special meetings may be called: 1). by the Head of the Department; 2). by any two members of the Executive Committee; or 3). by petition from twenty percent of the Faculty to the Head of the Department. b. Calls for a special meeting shall be mailed to all members of the Faculty at least five working days before the date of the special meeting.. c. The call for a special meeting shall specify: 1). the agenda; 2). the time, date, place, and duration. d. Only those items on the agenda shall be considered. e. Amendments to the ByLaws or its Appendices may not be considered in special meetings

M-8

Appendix B – Guidelines for Faculty Evaluations

Department of Biochemistry and Biophysics Guidelines for Faculty Evaluation Approved by the Office of the Dean of Faculties on {date} Approved by the Dean, College of Agriculture and Life Sciences on September 8, 2020 Guidelines approved by faculty vote on August 31, 2020 and revisions approved Jan. 14, 2021

Department of Biochemistry and Biophysics Guidelines for Faculty Evaluation Page 1 of 27 Table of Contents 1. INTRODUCTION 3 2. FACULTY TRACKS AND RANKS 3 3. AREAS OF FACULTY PERFORMANCE 5 3.1. Teaching 5 3.2. Research, scholarly activity or creative work 6 3.3. Service 7 3.4. Administration 8

4. INDICATORS OF FACULTY EXCELLENCE AND EFFECTIVENESS 9 4.1. Indicators of Excellence in Teaching 9 4.2. Indicators of Effectiveness in Teaching 10 4.3. Indicators of Excellence in Research/Scholarly Activity/Creative Work 10 4.4. Indicators of Effectiveness in Research/Scholarly Activity/Creative Work 11 4.5. Indicators of Excellence in Service 11 4.6. Indicators of Effectiveness in Service 11

5. CRITERIA FOR PROMOTION AND/OR TENURE 12 5.1. Evaluation Criteria for Tenured/Tenure Track Faculty 12 5.2. Evaluation Criteria for Academic Professional Track Faculty (Non-Tenure Track) 13

6. ANNUAL REVIEW 14 6.1. Purpose 15 6.2. Focus 15 6.3. Time Period of Review 15 6.4. Criteria for Rating Faculty Performance 16 6.5. Required Components 16 6.6. Assessment outcomes that require action 17 6.7. Timeline 17 6.8. Complaint procedure if annual review fails to follow published guidelines: 17

7. MID-TERM REVIEW 18 7.1. Purpose 18 7.2. Process 18 7.3. Feedback from midterm review 19 7.4. Mid-term review for Academic Professional Track and agency Assistant Professors 19

8. PROMOTION AND TENURE REVIEW 19 8.1. Purpose 19 8.2. Process 19

9. POST-TENURE REVIEW 21 9.1. Purpose 21 9.2. Peer Review Committee 21 9.3 Process 21 9.4 Professional Development Review 22 9.3. The Professional Development Plan 23

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9.4.1 Appeal 24 9.4.2 Voluntary Post-Tenure Review 24

10. GRANTING FACULTY EMERITUS STATUS 24 10.1. Procedure for consideration for Emeritus Faculty 24

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1. Introduction The mission of the Texas A&M University College of Agriculture and Life Sciences is to create and disseminate science-based solutions at the nexus of agriculture, human health, and environmental sustainability to positively impact lives and to provides hands-on, first-hand learning opportunities and experiences to each student, preparing them to go beyond College Station to reach every Texan and to develop solutions for urgent global and local challenges in agriculture, health, education, public policy, economics, and the environment. The Department of Biochemistry and Biophysics of Texas A&M University seeks to offer curricula leading to Bachelor of Science degrees in Biochemistry, Biophysics and Genetics, to the Master of Science degree in Biochemistry and Biophysics, and to the Ph.D. in Biochemistry and Biophysics. In accordance with this mission, the Department serves as the primary university home department for teaching and research in biochemistry, biophysics, and molecular genetics. The mission of the graduate program of the Department is to enable students to understand, plan, execute and communicate the results of scientific research in biochemistry, biophysics, and molecular genetics. Appropriate evaluation guidelines and reward mechanisms for faculty members to support the mission are essential. This document is designed to provide a means to promote and thus retain faculty members whose excellence makes them beneficial members of the academy, while providing them with stability of employment.

The expectations of the College of Agriculture and Life Sciences and the Department of Biochemistry and Biophysics for its faculty are that they develop a scholarly and balanced approach among teaching, research, and service to achieve effectiveness and excellence in their field of endeavor. The nature of scholarly innovation requires both flexibility and freedom, thus, the expectation of applying a single formula for evaluating performance is unattainable. That is, it is neither desirable nor feasible to specify a rigid set of evaluation guidelines (University Rule 12.01.99.M2, Section 4.4.2.2). Therefore, this document provides a general set of guidelines and criteria congruent with the mission of the University and the Unit; and such guidelines and criteria are used as indicators of effectiveness and excellence.

This document articulates general Unit guidelines for faculty, annual review, tenure and promotion, promotion and post-tenure review, consistent with the requirements and guidelines found in the following University documents: TITLE LINK 12.01.01- Institutional Rules for Implementing Tenure http://policies.tamus.edu/12-01-01.pdfs

12.01.99.M2 - University Statement on Academic http://dof.tamu.edu/Rules/Faculty-Rules Freedom, Responsibility, Tenure, and Promotion – Appendix I 12.06.99.M0.01 - Post-Tenure Review http://dof.tamu.edu/Rules/Faculty-Rules

Dean of Faculties Guidelines for Annual & Mid-Term http://dof.tamu.edu/Rules/Faculty-Rules Review Dean of Faculties Promotion and Tenure Guidelines http://dof.tamu.edu/Faculty-Resources/CURRENT-FA (published annually) CULTY/ Promotion-and-Tenure

In the event of inadvertent discrepancies between this document and Texas A&M University or Texas A&M University System policies, rules, and procedures, the University or System statements take precedence.

2. Faculty Tracks and Ranks Definition of faculty ranks and tracks can be found at University Rule 12.01.99.M2 and University Guidelines to Faculty titles. Departments and Colleges may describe here categories of performance (section 4.4.1 of UR 12.01.99.M2) associated with each title within their unit.

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Tenured Professor. A tenured Professor should lead a research program in an agricultural/life science specialization incorporating biochemistry or biophysics including molecular genetics; achieve and maintain national and international recognition and leadership through publication in refereed journals, presentations at regional, national and international meetings and participation in peer review; maintain sustained external funding for research; provide leadership to interdisciplinary and interagency regional, state, national and international programs; and, when appropriate, collaborate with research programs at AgriLife research and extension center(s). The tenured Professor will contribute productively to the undergraduate and graduate programs of the Department through development and teaching of courses of high-quality; through advisement and mentoring of students; and by participation in the activities sponsored by the undergraduate program outside the classroom; and by participating in graduate dissertation committees and related activities. The tenured Professor will serve on committees in the Department and other college, university, and interdisciplinary programs as appropriate; provide service to professional societies that support the discipline; and provide a forum for networking among colleagues. Through these and other efforts the tenured Professor will contribute to an environment of collegiality and collaboration within the Department.

Tenured Associate Professor. A tenured Associate Professor should lead a research program in an agricultural/life science specialization incorporating biochemistry or biophysics including molecular genetics; achieve and maintain national recognition and emerging leadership through publication in refereed journals, presentations at regional, national and international meetings and participation in peer review; strive to maintain continuity of external funding for research; provide leadership to interdisciplinary and interagency regional, state, national and international programs; and, when appropriate, collaborate with research programs at AgriLife research and extension center(s). The tenured Associate Professor will contribute productively to the undergraduate and graduate programs of the Department through development and teaching of courses of high-quality; through advisement and mentoring of students; and by participation in the activities sponsored by the undergraduate program outside the classroom; and by participating in graduate dissertation committees and related activities. The tenured Associate Professor will serve on committees in the Department and other college, university, and interdisciplinary programs as appropriate; provide service to professional societies that support the discipline; and provide a forum for networking among colleagues. Through these and other efforts the tenured Associate Professor will contribute to an environment of collegiality and collaboration within the Department.

Tenure-Track Assistant Professor. The tenure-track Assistant Professor will develop and lead a research program in an agricultural/life science specialization incorporating biochemistry or biophysics including molecular genetics; achieve national recognition through publication in refereed journals, presentations at regional, national and international meetings and participation in peer review; and develop research grant proposals and acquire external funding for research. The tenure-track Assistant Professor will, as appropriate, collaborate with research programs at AgriLife research and extension center(s). The tenure-track Assistant Professor will develop and teach undergraduate and graduate courses in related area of specialization, consistent with needs for the general departmental curriculum and the graduate program. Through these and related activities and by limited limited service on committees, the tenure-track Assistant Professor will contribute to an environment of collegiality and collaboration within the Department.

Senior Lecturer. The Senior Lecturer will participate in classroom teaching, primarily at the undergraduate level, in support of the educational goals of the Department for both departmental majors and non-majors in topics related to biochemistry, biophysics and genetics; supervise and train graduate teaching assistants; contribute to student mentorship through office hours and other outside-the-classroom teaching opportunities as appropriate. Participate in occasional committee service both in the department and in the larger university community.

Lecturer. Present lecture and/or laboratory courses in biochemistry, biophysics or molecular genetics as appropriate. For lecture courses, specific duties and responsibilities include preparing and presenting lectures, holding review sessions, writing and grading homework and examinations and assigning final grades. For laboratory courses, duties and responsibilities include planning experiments, ordering supplies, presenting pre-laboratory

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lectures, assuring proper safety procedures are followed, grading lab notebooks and lab reports, and assigning final grades. Both lecture and lab courses involve training and supervision of teaching assistants.

Instructional Assistant Professor, Instructional Associate Professor and Instructional Professor. Historically, the Department has not utilized the Instructional Professor Track but will consider appropriate appointments. Duties, responsibilities and expectations parallel the Lecturer and Senior Lecturer appointments, but entail some administrative responsibilities as defined by the Department Head.

Research Assistant Professor, Research Associate Professor and Research Professor. Historically, the Department has only utilized the Research Assistant Professor title but under appropriate situations would consider appointments at the Research Associate Professor and Research Professor levels. As a non-tenured member of the faculty, the Research Assistant Professor assists in the development and execution of research programs in an agricultural/life science specialization relevant to the Department in collaboration with a sponsoring member of the tenured faculty. The terms of appointment and promotion to Research Associate Professor are defined by AgriLife policy and may include acquisition of independent funding. Research Assistant Professors are expected to contribute to an environment of collegiality and collaboration within the Department through limited service on committees and related activities.

3. Areas of Faculty Performance (Reference University Rule 12.01.99.M2, Section 4.4.1) Decisions on tenure, promotion, and merit compensation will be based upon the faculty member’s performance in the assigned categories of performance (teaching; research, scholarly activity, and/or creative work; service; administration). Descriptions of faculty expectations in their assigned areas of faculty performance are presented below. Alternate work assignments (such as administration, etc.) may replace one or more areas in certain situations, but only with the written approval of the Department Head and Dean. Faculty with alternate work assignment will be reviewed based on assigned duties (including administrative assignments).

3.1. Teaching Teaching is central to the mission of the College, and effectiveness in teaching is required of all faculty. All faculty members are expected to: 1) contribute to instruction and student development; 2) continuously strive to improve their teaching effectiveness; and 3) promote and diversify the development of the College’s instructional programs. Effectiveness and excellence in teaching affect decisions on merit compensation, tenure, and promotion. Evaluation of teaching does not lend itself solely to quantitative measurement. Multiple sources of information and methods must be considered when assessing teaching. Student evaluations are required but not sufficient to evaluate teaching. Other measures/sources of information may include: 1) self-evaluation; 2) peer-evaluation; 3) student feedback; and 4) student learning. The criteria for effectiveness that shall be considered in evaluating teaching performance are as follows:

A rating of ‘Excellent’ can be achieved with broad instances of evidence such as: ● Outstanding teaching performance as evidenced by such measures as peer-evaluation, student evaluations, and/or student outcomes ● Outstanding direction of undergraduate and/or graduate research or creative activity that is validated by peers ● Selection for a University or professional society outstanding teacher award ● Evidence of courses taught at a rigorous and challenging level, with recognized excellence. ● Development and utilization of effective pedagogical methods and materials ● Publication of widely adopted or acclaimed instructional material ● Developing a new course that fills an identifiable need in the curriculum ● Receiving external grant support for teaching/learning projects ● Invitation to teach at domestic or international institution of recognized excellence ● Receipt of awards for research or academic performance by the faculty member’s students

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● Placement of graduate students or post-doctoral fellows into significant academic, scholarly or professional positions ● Significantly contributing to the professional development of students (e.g. working with the University honors program; advising student organizations) ● Outstanding performance as a departmental undergraduate or graduate advisor

A rating of ‘Satisfactory’ can be achieved with evidence such as:

● Effective teaching performance as evidenced by peer evaluation, student satisfaction, and student outcomes ● Effective direction of undergraduate and/or graduate research or creative activity, as evidenced by student satisfaction and student outcomes ● Selection for a college or departmental outstanding teacher award ● Development and utilization of effective pedagogical methods and materials as evidenced by peer evaluation, student satisfaction and student outcomes ● Development of new courses or major revision of existing courses ● Receiving competitive internal grant support for teaching/learning projects ● Reflective critique and continuous improvement of teaching as evidenced by self- evaluation ● Direction of graduate student thesis or dissertation research ● Member of graduate student advisory committees ● Evidence of high quality in class preparation, interaction, and accomplishments ● Effectively coordinating a multi-section course. ● Service as departmental undergraduate or graduate advisor (may also be included as a service activity where appropriate) ● Significant self-development activities leading to enhanced teaching effectiveness ● Participation in University Honors and/or other programs for mentoring the professional development of students ● Chair of doctoral research committees

A rating of ‘Needs Improvement’ can be achieved with evidence such as: ● Little evidence of improvement of low classroom performance despite efforts to do so ● Students in laboratory not making normal progress ● Little participation in graduate or undergraduate programs and/or student advisory committees

A rating of ‘Unsatisfactory’ can be achieved with evidence such as: ● Poor classroom performance with no effort to improve ● No students being trained in the laboratory ● No service on graduate student advisory committees 3.2. Research, scholarly activity or creative work Research/scholarly/creative activity is central to the mission of the College, and effectiveness in activities associated with research/scholarly work is required of all faculty. All faculty members are expected to; 1) conduct research/scholarly activity, 2) continuously strive to improve research effectiveness and impact, and 3) produce, publish and communicate the results of research/scholarly/creative work. This involves sustained external research funding.

Evaluation of research/scholarly/creative activity using metrics such as publication output, research funding, presentations at national and international meetings, intellectual property disclosures and awarded patents, membership on editorial boards and grant review panels, and research awards.

A rating of ‘Excellent’ can be achieved with broad instances of evidence such as:

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● High impact publications as evidenced by citation, profile of journal within and outside the specific discipline • Sustained and superior levels of funding to fully support a leading research program • Receiving major award recognition • Oral presentations of research results at National or International meetings • Invited research seminars at other institutions • Faculty whose research program does not lend itself to these conventional means for dissemination of research results should present alternative evidence

A rating of ‘Satisfactory’ can be achieved with evidence such as: • Continued progress towards developing or sustaining peer recognition and leadership through peer-reviewed publications, reviews, presentation of research results at a regional or national or international meetings • External research funding sufficient to maintain a core research program • Appropriate career-development activities, such as a Faculty Development Leave, designed to increase research productivity • Presentation of seminars at academic or industrial institutions

A rating of ‘Needs Improvement’ can be achieved with evidence such as: • Core research funding is lacking • Proposals to sustain core research funding are in preparation but have not been submitted or repeated unsuccessful applications for funding • Peer-reviewed publications are insufficient to maintain a national profile within the discipline • Attendance at research conferences or national meetings, but without presentation of research results

A rating of ‘Unsatisfactory’ can be achieved with evidence such as: • No peer reviewed publications • Prolonged absence of external research funding • Very little if any research or scholarship actively being conducted • No research grant proposals under development • Minimal or no attendance at research conferences or national meetings

3.3. Service Service is central to the mission of the College and University. All faculty are expected to serve on departmental committees as requested by the Department Head as well as to provide service as appropriate at the College, University levels and National levels. Evidence of service is expected of all faculty and senior faculty are expected to seek leadership roles.

Evaluation of service does not lend itself to simple quantitative measurement since effective and excellent service can take many forms. Examples include serving as a reviewer for journals or funding agencies, service in professional organizations, service on committees, task forces, or as a consultant, being an advisor to student organizations, and serving in administrative roles in the Department, College or University.

A rating of ‘Excellent’ can be achieved by evidence such as: • Serving as editor or member of editorial board of a major journal • Serving as a standing or frequent ad hoc member of a peer-review committee for a national granting agency such as NIH or NSF • Being an officer in a national or international professional organization • Serving on a major governmental commission, task force, or board (e.g. NIH study section) • Serving an administrative leadership role at Texas A&M University

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• Serving as program chair or in a similar position at a national or international meeting • Serving as an officer in the faculty Senate • Chairing a major standing or ad hoc Texas A&M University committee • Evidence of excellence in professional service to the local community and public at large, including required clinical work or extension service. • Performing in multiple service roles or providing significant leadership in one or more roles in the Department, University, and Profession. These expectations are normalized to academic rank; i.e. less service is expected for assistant professors, etc.

A rating of ‘Satisfactory’ can be achieved by evidence such as: • Service as a reviewer for major journals • Service as an ad hoc reviewer for national granting agency such as NIH or NSF • Being an officer in national or international professional organization • Being an officer in regional or state professional organization • Serving as program chair or similar position for regional or state professional organizational meeting • Serving in an elected role in a national, regional, or international professional organization • Serving as an active member of the Faculty Senate • Serving on University, college, and departmental committees and task forces • Serving as a consultant • Being an advisor to student organizations • Serving in administrative roles within the department • Evidence of professional service to the local community and public at large, including required clinical work or extension service • Significant self-development activities that lead to enhanced service effectiveness

A rating of ‘Needs Improvement’ can be achieved by evidence such as: • Minimal service on Departmental and University committees • Limited involvement with reviewing manuscripts or grant proposals • Limited professional involvement

A rating of ‘Unsatisfactory’ can be achieved with evidence such as: • Absence of significant service on departmental committees • Paucity of manuscripts or grant proposal reviews • Paucity of service in professional organizations

3.4. Administration 3.4.1. Department Head The Professor and Head will serve as the chief administrative officer of the Department and as an advocate for the disciplines that it represents. The Head reports to the Vice Chancellor and Dean of the College of Agriculture and Life Sciences, Texas A&M University, College Station. The position provides leadership and support for numerous faculty initiatives including: enhancing and expanding undergraduate and graduate education; increasing contributions to knowledge and science through extramurally funded research; fostering collegiality and interdisciplinary collaboration among faculty; conducting outreach programs; securing additional resources through development; strengthening relationships with diverse stakeholder groups; and promoting communication of science-based findings to inform public policy and private decision makers.

Evaluation and Retention

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An evaluation of the Department Head that includes faculty input should be conducted at or before the midpoint of the first term of appointment and prior to any decision to reappoint the Department Head, but can be initiated by the college Dean at other times. This review does not replace the annual review which the college Dean conducts concerning the Department Head’s performance but will inform the annual evaluation.

The evaluation of the Department Head should serve to improve performance and engage professional development. In addition, it should promote a sense of shared values between the faculty, Department Heads, Deans, and the University administration.

● The Dean, with notification to the Dean of Faculties, shall initiate a preliminary review of a new Department Head at or before the midpoint of the first term of appointment that includes faculty input. Thereafter formal reviews to solicit faculty input should occur at least every fifth year of the Department Head’s term in office and a summary of the review shall be shared with the faculty. ● All reappointment reviews shall include a comprehensive opportunity for college faculty members and other stakeholders to present their views to the college Dean regarding the strengths and weaknesses of the Department Head. ● Faculty participation in reviews for the evaluation and retention of Department Heads will be carried out as described in the Standard Administrative Procedure 12.99.00.M0.03, Appendix A. ● A recommendation for approval of the reappointment by the Dean shall be made to the Provost and Executive Vice President through the Dean of Faculties.

3.4.2 Associate Head for Undergraduate Programs The Head appoints the Associate Head for Undergraduate Programs. The Associate Head for Undergraduate Programs will oversee the administrative and academic operations of the Biochemistry and Genetics undergraduate programs, including serving as Chair of the Undergraduate Program Committee. In consultation with the Head, provides leadership for the continuous improvement of the undergraduate program. Notwithstanding these duties, the Associate Head is expected to fulfill the obligations, duties and expectations of his or her rank with respect to teaching and research.

3.4.3 Associate Head for Graduate Programs The Head appoints the Associate Head for Graduate Programs. The Associate Head for Graduate Programs will oversee the administrative and academic operations of the Biochemistry Graduate Program, including serving as Chair of the Graduate Program Committee. In consultation with the Head, provide leadership for the continuous improvement of the graduate program. Notwithstanding these duties, the Associate Head is expected to fulfill the obligations, duties and expectations of his or her rank with respect to teaching and research. 4. Indicators of Faculty Excellence and Effectiveness The Unit recognizes that there are multiple indicators of various levels of performance. Additionally, performance and their respective indicators will vary over time for any individual at different career stages. This document does not provide a specific formula for evaluating faculty performance. However, it is possible to describe accomplishments that are most likely to lead to career development and to favorable evaluations.

4.1. Indicators of Excellence in Teaching Indicators of Excellence in Teaching include, but are not limited to: ● Outstanding teaching performance as evidenced by such measures as peer-evaluation, student evaluations, and/or student outcomes.

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● Outstanding direction of undergraduate and/or graduate research or creative activity that is validated by peers and communicated. ● Selection for a University or professional society outstanding teacher award ● Evidence of courses taught at a rigorous and challenging level, with recognized excellence. ● Development and utilization of effective pedagogical methods and materials ● Publication of widely adopted or acclaimed instructional material ● Developing a new course that fills an identifiable need in the curriculum ● Receiving external grant support for teaching/learning projects ● Invitation to teach at domestic or international institution of recognized excellence ● Receipt of awards for research or academic performance by the faculty member’s students ● Placement of graduate students or post-doctoral fellows into significant academic, scholarly or professional positions ● Significantly contributing to the professional development of students (e.g. working with the University honors program) ● Outstanding performance as a departmental undergraduate or graduate advisor

4.2. Indicators of Effectiveness in Teaching Indicators of Effectiveness in Teaching include, but are not limited to: ● Effective teaching performance, as evidenced by peer evaluation, student satisfaction and student outcomes ● Effective direction of graduate research or creative activity, as evidenced by student satisfaction and student outcomes ● Selection for a college or departmental outstanding teacher award ● Development and utilization of effective pedagogical methods and materials as evidenced by peer evaluation, student satisfaction and student outcomes ● Development of new courses or major revision of existing courses ● Receiving competitive internal grant support for teaching/learning projects ● Reflective critique and continuous improvement of teaching, as evidenced by self-evaluation ● Direction of graduate student thesis or dissertation research ● Member of graduate student advisory committees ● Evidence of high quality in class preparation, interaction, and accomplishments ● Effectively coordinating a multi-section course ● Service as departmental undergraduate or graduate advisor (may also be included as a service activity where appropriate) ● Significant self-development activities leading to enhanced teaching effectiveness ● Receiving on a competitive basis internal funding for teaching ● Participation in University Honors and/or other programs for mentoring the professional development of students ● Chair of doctoral research committees

4.3. Indicators of Excellence in Research/Scholarly Activity/Creative Work Indicators of Excellence in Research/Scholarly Activity/Creative Work include, but are not limited to: • High impact publications as evidenced by citation, profile of journal within and outside the specific discipline ● Sustained and superior levels of funding to fully support a leading research program • Receiving major fellowship or research award • Frequent citation of publications • Publication of scholarly book(s) by reputable publisher(s) • Awards for, or publication of, peer reviewed creative activities

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• Serving as a member of review panel for national research organization • Presentation of invited papers at international and national meetings • Sustained and significant external peer-reviewed funding for research • Significant publication and/or funding resulting from collaborative efforts with researchers in other fields where the faculty member occupies a substantial role in research) • Publications with teaching focus in leading refereed journals • Evidence of creative professional practice (including patents and disclosures)

4.4. Indicators of Effectiveness in Research/Scholarly Activity/Creative Work Indicators of Effectiveness in Research/Scholarly Activity/Creative Work include, but are not limited to: ● Publication of scholarly book(s) ● Publications in refereed journals ● Publication of a chapter in a scholarly book ● Editing a scholarly book ● Presentation of papers at national or international meetings of appropriate disciplines ● Publications in non-refereed but widely recognized journals ● A record of successful doctoral dissertations ● Significant self-development activities, such as a Faculty Development Leave, that lead to increased research and publication effectiveness ● Publications in refereed journals resulting from collaborative efforts with researchers in other fields ● Publications with teaching focus in refereed journals ● Sustained external funding to maintain a core research program 4.5. Indicators of Excellence in Service Indicators of Excellence in Service include, but are not limited to: ● Serving as editor or member of editorial board of a major journal ● Serving as a standing or frequent ad hoc member of a peer-review committee for a national granting agency such as NIH or NSF ● Being an officer in a national or international professional organization ● Serving on a major governmental commission, task force, or board ● Serving an administrative leadership role at Texas A&M University ● Serving as program chair or in a similar position at a national or international meeting ● Serving as an officer in the Faculty Senate ● Chairing a major standing or ad hoc Texas A&M University committee ● Performing in multiple service roles or providing significant leadership in one or more roles in the Department, University, and Profession. These expectations are normalized to academic rank; i.e. less service is expected for assistant professors, etc. ● Evidence of excellence in professional service to the local community and public at large, including required clinical work or extension service

4.6. Indicators of Effectiveness in Service Indicators of Effectiveness in Service include, but are not limited to: ● Service as a reviewer for major refereed journals or as an ad hoc reviewer for national research organizations. ● Being a committee chair in national or international professional organization ● Being an officer in regional or state professional organization ● Serving as program chair or similar position for regional or state professional organizational meeting ● Serving as an active member of the Faculty Senate ● Serving on University, college, and department committees and task forces

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● Serving as consultant ● Being an advisor to student organizations ● Serving in administrative roles within the department ● Evidence of professional service to the local community and public at large, including required clinical work or extension service ● Significant self-development activities that lead to enhanced service effectiveness 5. Criteria for Promotion and/or Tenure 5.1. Evaluation Criteria for Tenured/Tenure Track Faculty Faculty members should be evaluated for promotion and tenure on accomplishments in each of their areas of faculty performance (teaching, research/scholarly activity/creative work, patient care, and service), with primary emphasis on the quality, significance, and impact of their work. For promotion and/or tenure, in addition to meritorious accomplishments, a high potential for continued excellence is required. Documentation of excellence is best provided by peer review. The criteria for the unit are as follows:

5.1.1.Assistant Professor Assistant Professors are recruited into our department based on the following criteria: ● Number and quality of research papers published ● Evaluations provided by letters of recommendation received ● Quality of written materials including a proposed research plan provided by the candidate ● Communication and organizational skills ● Potential contribution to the research programs and profile of the department ● Potential to obtain federally funded research grants ● Potential for teaching excellence ● Likelihood of collegiality and contribution to the general well-being of the Department and to its goals

5.1.2.Associate Professor Except in unusual circumstances, the decisions to recommend the awarding of tenure and the promotion to the rank of Associate Professor are made concurrently. The decision to recommend the award of tenure and promotion to Associate Professor derives from whether, in the separate judgment of the Promotion and Tenure Committee, the Department as a whole, and that of the Head, the candidate has established a record that allows for the confident prediction that academic success and positive contributions to the broad and complex mission of the Department will continue and grow. This determination is made by referencing measures of success in research, teaching, and service. The terms of appointment of Assistant Professors reflect a balance of research, teaching and service. Research holds the predominant weight while service has the least. Given that initiative, creativity and independence are essential characteristics for success as a faculty member, no fixed rubric to define the terms of promotion is possible, but the following guidelines are established.

The quality and strength of the candidate’s research program will receive the greatest consideration. Criteria include: a. Creation of a leading-edge research program relevant to biochemistry or biophysics b. Acquisition of adequate external research funding including from federal agencies by peer review c. An increasing trajectory of peer-reviewed publications and invited reviews of work undertaken while at Texas A&M d. An increasing trajectory of national recognition as evidenced by citation metrics, invitations to present at local, regional and national meetings e. Successful mentoring of graduate and undergraduate student research f. Strong confidential evaluations by leaders in the relevant disciplines at peer and aspiring institutions

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The quality of the candidate’s teaching is a critical element of the decision to recommend tenure and promotion to the rank of Associate Professor. Criteria include: a. Effectiveness as established by the results of student evaluations, which must be conducted for every course taught b. Peer examination of coursework materials c. Peer evaluation of lectures as viewed by recording or in person d. A positive trajectory of improvement in all of these criteria over the term of appointment

Expectations for service to the Department, AgriLife and the University will initially be kept to a minimum for Assistant Professors. Some service through thesis committees, research mentoring at the graduate and undergraduate levels and occasional committee assignments or other instances of service will be expected and evaluated. Service to the candidate’s discipline through peer review is anticipated but more extensive service to societies and journals is not.

5.1.3.Professor In consideration of promotion to the rank of Professor, all the expectations cited above are enhanced and broadened, as indicated below. Research accomplishments continue to be central, with particular attention paid to accomplishments following promotion to Associate Professor. Importantly, these accomplishments should lead to international as well as national recognition and leadership. a. Creation of a leading-edge research program relevant to biochemistry and/or biophysics b. Sustained and significant external research funding including from federal agencies through peer-review c. A history of evolving research interests, collaboration and interdisciplinary research that broadens the research profile of the candidate and the Department d. Clear evidence of national and international leadership through broad participation in journal peer review, editorial positions on journals, or participation in national or international peer review panels e. A trajectory of increasing impact on the candidate’s research area as measured, for example, by the breadth and depth of citations in the peer-reviewed literature f. Evidence of impact by numerous presentations at national and international meetings g. A strong and extensive record of didactic and laboratory teaching at Texas A&M at both the undergraduate and graduate levels. Evidence of self-criticality, creativity, adaptability, innovation and diversity in pedagogy is essential. h. A strong and broad history of leadership and service to the Department through committees and administrative tasks particularly to the graduate program. Service to professional societies and organizations at the regional and national levels is also anticipated

5.2. Evaluation Criteria for Academic Professional Track Faculty (Non-Tenure Track) For appointment and promotion in the academic professional track (non-tenure track), faculty members should be evaluated in their assigned areas of faculty performance. Faculty with Professor in their title are expected to make significant contributions in one area of teaching, research/scholarly activity/creative work, service or administration. Lecturers and faculty with Instructional in their title will be evaluated for promotion with a primary emphasis on the quality and impact of their teaching. Lecturers can be laterally reclassified as Instructional Assistant Professors and Senior Lecturers can be laterally reclassified as Instructional Associate Professors if their appointment responsibilities are expanded beyond just the area of teaching. Faculty with Research in their title will be evaluated with a primary emphasis on the quality and impact of their research/scholarly/creative work activities. For promotion, in addition to meritorious accomplishments, a high potential for continued excellence is expected for Academic Professional Track Faculty. During the annual evaluation, performance in their assigned areas of teaching, research/scholarly activity/creative work, service or administration will be rated as described in Section 3 and Section

5.2.1. For Promotion from Lecturer to Senior Lecturer

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Teaching: Effectiveness in teaching and a high potential for excellence in teaching are expected of ● Lecturers seeking promotion to Senior Lecturer. Teaching excellence can be demonstrated with outstanding teaching performance as evidenced by peer reviews, student satisfaction, and student outcomes; innovations in pedagogical/course design; development and effective implementation of high impact learning experiences; presentations on teaching and learning at academic institutions and professional conferences; recognition of excellence by internal and external teaching awards; continued professional development in teaching, and other appropriate indicators such as those described in 4.1 and 4.2.

5.2.2. For Promotion from Instructional Assistant Professor) to Instructional Associate Professor

Teaching: Excellence and effectiveness in teaching and a high potential for continued excellence and ● effectiveness are expected of an Instructional Assistant Professor or Assistant Professor of the Practice seeking promotion to Instructional Associate Professor or Associate Professor of the Practice, respectively. Teaching excellence and effectiveness should be demonstrated based on appropriate indicators such as those described in 4.1 and 4.2.

Service: Effectiveness in service and a commitment to excellence in service (see indicators described in ● 4.5 and 4.6) are an expectation of Instructional Assistant Professors seeking promotion for whom service is the assigned secondary duty. Service efforts may involve curriculum development, program supervision, ensuring program accreditation and other service activities that are critical to the teaching mission of the department or program. Significant service contributions to the institution and profession are expected and these contributions can often have strong synergies with their efforts in teaching.

Research: Effectiveness in research and a commitment to excellence in research (see examples of ● indicators in sections 4.3 and 4.4) are an expectation of the Instructional Assistant Professors seeking promotion for whom research is the assigned secondary duty.

5.2.3. For Promotion from Instructional Associate Professor to Instructional Professor

Teaching: Excellence and effectiveness in teaching and a high potential for continued excellence and ● effectiveness are expected of an Instructional Associate Professors seeking promotion to Instructional Professor. Teaching excellence and effectiveness should be demonstrated based on appropriate indicators such as those described in 4.1 and 4.2. In addition, there should be demonstrated capacity for leadership in teaching and scholarship of teaching, with potential for growth in scope and national impact.

Service: Effectiveness in service and a commitment to excellence in service (see indicators described in ● 4.5 and 4.6) are an expectation of Instructional Associate Professors seeking promotion for whom service is the assigned secondary duty. Service efforts may involve curriculum development, program supervision, ensuring program accreditation and other service activities that are critical to the teaching mission of the department or program. Significant service contributions to the institution and profession are expected and these service contributions should have strong synergies with their efforts in teaching. In addition, there should be potential for leadership and national impact in service.

Research: Effectiveness in research and a commitment to excellence in research (see indicators ● described in 4.31 and 4.4) are an expectation of the Instructional Associate Professors seeking promotion for whom research is the assigned secondary duty. There should be potential for leadership and national impact in research.

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6. Annual Review Annual reviews of performance are to be conducted in accordance with Section (2.4) of University Rule 12.01.99.M2 (University Statement on Academic Freedom, Responsibility, Tenure, and Promotion).

All University-employed faculty members, whether tenured, tenure-track, or non-tenure track, must have an annual written review, for which the Department Heads, directors, or supervisors are responsible.

In terms of annual reviews for budgeted joint appointments, Department Heads, directors, or supervisors will need to collaborate with the heads, directors, or supervisors of the appropriate units to develop accurate reviews, (Section 2.4.4 of University Rule 12.01.99.M2 University Statement on Academic Freedom, Responsibility, Tenure and Promotion).

In the case of budgeted joint appointments, it is recommended that heads, directors and supervisors collaborate to provide one annual review letter for the faculty member.

In terms of annual reviews for faculty whose area of responsibility is administrative (e.g., associate Deans, Department Heads, or directors), annual reviews will be conducted by their immediate supervisor. For a faculty member with an administrative appointment that has faculty responsibilities such as teaching and/or research, the immediate supervisor is required to solicit feedback from the Department Head, director, or supervisor regarding the faculty member’s performance in those areas. Faculty with administrative appointments equal to or less than 25% effort are to be evaluated annually by their Department Head, director, or supervisor with input from the supervisor of the administrative appointment. A faculty member should receive only one evaluation that covers all areas of responsibility.

6.1. Purpose ● Provide evaluative feedback regarding the faculty member’s performance relative to the expectations and norms for the individual’s faculty position. ● Provide developmental feedback regarding areas where the faculty member’s contributions may be enhanced and/or improved. ● Provide feedback regarding progress toward promotion and/or tenure as relevant. See University Rule 12.01.99.M2. For tenured associate professors, the process should be used to identify o the faculty member's progress toward promotion to professor. For professors and tenured associate professors the annual review should also be part of the ongoing process of communication between the faculty member and the institution in which both institutional and individual goals and programmatic directions are clarified, the contributions of the faculty member toward meeting those goals are evaluated and the development of the faculty member and the University is enhanced. In all cases, the annual review shall serve as the primary documentation for evaluation of job performance in the areas of assigned responsibility and for merit salary increases. ● Create a sound and logical basis for merit compensation recommendations.

6.2. Focus The focus of the annual review process will vary by title and rank and the stage of the individual’s career at the time of the review. For tenured faculty, the annual review evaluates continued effective and/or excellent performance, and where relevant, progress toward the next promotion. For tenure-track faculty, the annual review serves as an assessment of progress toward tenure and promotion. For academic professional track faculty (non-tenure track), the annual review evaluates performance and serves as assessment of progress towards retention and/or promotion, as applicable, section 2.4.2 of University Rule 12.01.99.M2 (University Statement on Academic Freedom, Responsibility, Tenure and Promotion).

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6.3. Time Period of Review The Department Head will conduct faculty performance annually, usually during the Spring semester. The evaluation will be based primarily upon data and metrics pertaining to the previous calendar year, but trends extending into the recent past and/or into the current year may be considered. This data will be obtained from the faculty and a variety of other sources.

6.4. Criteria for Rating Faculty Performance During an annual evaluation, performance in each of the areas of research/scholarship, teaching and service contributions of faculty performance will be rated on four performance ratings as descried in Section 3: “Unsatisfactory,” “Needs Improvement,” “Satisfactory,” and “Excellent” based on evidence of effectiveness and excellence as described in section 4.1. Overall performance will also be described using these terms. 6.5. Required Components The annual review must contain the below components in accordance with Section 2.4.5 of University Rule 12.01.99.M2, (University Statement on Academic Freedom, Responsibility, Tenure and Promotion). 6.5.1.Faculty member's report of previous activities. The exact form of the faculty member’s report of previous activities may vary from department to department within the College, but must include the following:

● The report should be focused on the immediately previous calendar, however, trends extending past the previous year, and into the current year will also be factored in as appropriate, but should allow a faculty member to point out the status of long-term projects and set the context in which annual activities have occurred. ● The report should incorporate teaching, research/scholarly activity/creative work, patient care, and service as appropriate. ● Faculty members should state their short-term and long-term goals and/or objectives.

The faculty member will be asked to supply relevant information, including: a complete and up to date CV; germane grant proposal activity not adequately summarized in the CV; reprints of up to 5 papers published during the previous calendar year (Associate Professors can include preprints of manuscripts in press; Assistant Professors can include manuscripts submitted); teaching summary for the previous calendar year, including summary of classroom teaching, research students (including postdoctoral researchers) and any materials that might speak to the quality of teaching; and any additional activities, accomplishments, awards, etc. that the faculty member might feel is inadequately described in the other submitted materials.

6.5.2.A written document stating the Department Head's, program director’s, or supervisor’s evaluation and expectations. The Department Head will write an evaluation for the year in a memorandum or in the annual review document transmitted to the faculty member. This document also provides an opportunity for the Department Head to offer advice. The faculty member acknowledges receipt by signing a copy of the document and should be allowed to provide written comments for the file if they so choose. A faculty member refusing to sign the acknowledgment of the document will be noted in the file. This memorandum, and/or the annual review and any related documents, will be placed in the faculty member's unit personnel file. Moreover, this memorandum and/or annual review shall also include a statement on expectations for the next year in teaching, research/scholarly activity/creative work, patient care, and service. This memorandum and/or annual review should include an informed judgement by the Department Head, director, or supervisor of the extent to which the faculty member complies with applicable rules, policies, and procedures.

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No faculty member may receive an overall satisfactory rating if they have not complied with all required System and University training programs (System Regulation 33.05.02 Required Employee Training). In cases where a faculty member has been notified of a mandatory training requirement near the time of the end of the evaluation period, they shall be given 30 days to complete the requirement. To satisfy these requirements the following acknowledgements must be added to the “ACKNOWLEDGEMENT” portion of the Department Head’s, director’s, or supervisor’s written evaluation and the faculty member must initial: ● I acknowledge that I have completed all mandatory Texas A&M University System training.

6.5.3.Meeting between the Department Head, director, or supervisor and the faculty member The Department Head, director, or supervisor may meet with the faculty member to discuss the written review and expectations for the coming year. In some cases, there may be a need for more frequent meetings at the request of the Department Head/director/supervisor or faculty member.

6.5.4.Performance Assessment In assessing performance, the weights given to teaching, research/scholarly activity/creative work, patient care, and service shall be consistent with the expectations of the individual’s appointment, the annual review, and with the overall contributions of the faculty member to the multiple missions of the Department, College, and University.

6.6. Assessment outcomes that require action As per University SAP 12.06.99.M0.01 (Post-Tenure Review), the following annual evaluation and periodic peer review ratings require further action:

6.6.1.Unsatisfactory Performance An overall unsatisfactory rating is defined as being “Unsatisfactory” in any single area of faculty performance: teaching, research/scholarly activity/creative work, service, and other assigned responsibilities (e.g., administration), or a rating of “Needs Improvement” in any two areas of faculty performance.

An annual review resulting in an overall “Unsatisfactory” performance shall state the basis for the rating in accordance with the unit established criteria (see Section 7.4.). Each unsatisfactory review shall be reported to the Dean. The report to the Dean of each “Unsatisfactory” performance evaluation for a tenured faculty member shall be accompanied by a written plan developed by the faculty member and Department Head, program director, or supervisor, for near-term improvement. If deemed necessary, due to an unsatisfactory annual evaluation, the Department Head, director, or supervisor may request a “Periodic Peer Review” (see Section 9.2.) of the faculty member. A tenured faculty member who receives an overall annual rating of “Unsatisfactory” for three consecutive annual reviews or who receives an “Unsatisfactory” periodic peer review (see section 9) shall be subject to a professional development review, as provided for by University SAP 12.06.99.M0.01 (Post-Tenure Review). 6.6.2.Needs Improvement Performance If a tenured faculty member receives a “Needs Improvement” rating in any single area of faculty performance during the annual evaluation or periodic peer review (see section 9), they must work with their Department Head, director, or supervisor immediately to develop a plan for near term improvement. For teaching, this plan should take one year or less to complete successfully. In other areas (e.g., research/scholarly activity/creative work), this plan may take up to three years to complete successfully. The rating of “Needs Improvement” can stay as “Needs Improvement” as long as predetermined milestones in the improvement plan are being met, otherwise the rating will be changed to “Unsatisfactory”. The rating of “Needs Improvement” should be changed to “Satisfactory” when pre-determined milestones are met.

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6.7. Timeline The annual review process is set to conclude prior to the beginning of the budgetary process, thereby enabling Department Heads, directors, or supervisors to assess faculty performance when determining salary merit increases. The Dean of Faculties’ Guidelines for Annual & Midterm Reviews states, “These reviews must be completed before merit raises may be recommended, and never later than June 15 of each year.” 6.8. Complaint procedure if annual review fails to follow published guidelines: A faculty member who believes that his or her annual review process did not comply with the department published annual review guidelines, or in their absence those published by the college, may file a complaint in writing addressed to the Dean of the college with a copy to the Dean of Faculties. The Dean of the college will review and decide on the merits of the complaint. The decision of the Dean of the college may be appealed to the Dean of Faculties. See section 2.4.3.5 of University Rule 12.01.99.M2.

There is no formal grievance or appeal regarding the substance of an annual review. See section 2.4.3.6 of University Rule 12.01.99.M2. 7. Mid-Term Review In accordance with Section (4.3.5.2.) of University Rule 12.01.99.M2 (University Statement on Academic Freedom, Responsibility, Tenure, and Promotion), it is mandatory that a comprehensive mid-term review for tenure-track faculty subject to a probationary period (of five or more years), be conducted (normally by December of the third year) to determine the progress towards tenure.

7.1. Purpose ● A mid-term review is intended to provide a formative review of tenure-track faculty members near the mid-point of their probationary period.

● This review will familiarize the faculty member with the tenure and promotion process and ensure that the faculty member understands the expectations of those entities that will ultimately be responsible for the tenure and promotion decision.

● This review will ensure the faculty member has a clear understanding of their current status and progress.

● This review should mimic the tenure and promotion review process as closely as possible, including submission of dossier items by the faculty member; however internal letters of recommendation may be solicited by the unit rather than external letters of recommendation. As with the tenure and promotion process, the mid-term review will include review by the unit’s P&T committee, Department Head/ director/supervisor, the college P&T committee, and Dean.

● This review should result in an independent evaluation of the faculty member’s accomplishments and performance in teaching, research/scholarly activity/creative work, patient care, and service to date as well as provide constructive guidance for the remainder of the probationary period.

● This review may take the place of the annual faculty performance review. It is recommended that an annual review be done even in the year when the faculty member goes through a midterm (or tenure) review.

● If a tenure-track faculty member is not progressing adequately toward the requirements for tenure, action not to renew the contract of the individual may be appropriate.

7.2. Process The mid-term review should be conducted between March of the academic year prior to the target academic year, and December of the target year. For example, if the mid-term review is due during the academic year, the

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mid-term review may occur anytime between March 2022 and December 2022. See below example for faculty member hired in calendar year 2019.

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Hired Probationary Period Mid-Term Review will occur between Mar – Dec 2022 Calendar 7 years (due before December 2022 of AY Year 2019 2022-2023)

7.3. Feedback from midterm review Feedback is required for faculty members going through midterm review. Suggested feedback to the faculty member includes summaries of reports and recommendations for going forward from the Dean, Department Head (supervisor/unit director), and departmental faculty.

7.4. Mid-term review for Academic Professional Track and agency Assistant Professors To provide a formative review of Instructional Assistant Professors and Assistant Professors of Practice near the mid-point of the period toward promotion, a similar mid-term review process will be conducted for Academic Professional Track Assistant Professors in the third calendar year in the rank. The mid-term reviews for AgriLife Research Assistant Professors will be conducted following the policies and guidelines of the respective agencies. 8. Promotion and Tenure Review 8.1. Purpose Tenure is granted to recognize demonstrated national leadership and impact in a research field and a demonstrated commitment to teaching excellence and outreach/service. Promotion to Professor is granted for international leadership and impact in a research field and demonstrated commitment to teaching excellence and service. In exceptional and rare cases, national/international leadership and impact in teaching and service can be the basis for promotion from associate to full professor (see University Rule 12.01.99.M2).

8.2. Process Any individual hired in a tenure-track position will be required to submit his/her dossier for tenure review during the academic year prior to the year of mandatory consideration. Such reviews may be made earlier and are, in fact, encouraged whenever it appears appropriate. If an early review does not result in a favorable decision for promotion or tenure, a review will be conducted again at the mandatory time. In exceptional circumstances, a person not recommended for tenure in the mandatory year may be reconsidered in the terminal year, at the discretion of the Department Head and with the agreement of the Dean and the Provost. The sole ground on which a Department Head may propose making such an exception to general practice is that the case has substantially changed since the mandatory consideration. The Dean of Faculties will discuss procedures should such a case arise. Reconsideration does not entail an additional terminal year.

Hired Probationary Period Mandatory Review (at all levels) will occur:

Calendar Year 2014 7 years 2019-2020

Procedures for the development of the candidate’s dossier can be found on the website of the Dean of Faculties Promotion and Tenure Guidelines. The candidate should order the CV so that the primary area upon which they are being evaluated is listed first. Tenure-track faculty should put research/scholarly activity/creative work as the first section.

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For a promotion case with a negative outcome, a minimum of ONE YEAR must elapse before resubmission is allowed (e.g. if a candidate was not recommended for promotion during the academic year 2018-2019, the earliest they can submit the dossier again is academic year 2020-2021). Requests for an exception can be made to the Dean of Faculties only with concurrence of the Department Head and Dean.

8.2.1. The Promotion and Tenure Committee a. The Committee will evaluate all candidates for promotion, including APT faculty, or tenure, as applicable according, to the guidelines specified by the Department, the College, and the University. The recommendation of the Committee with regard to tenure or promotion will be made to the Head of the Department. b. The Committee will consider all nominees for joint appointments and make a written recommendation to the whole Faculty for vote. All types of joint membership require two-thirds support of the votes cast for approval. Faculty voting will be conducted in the same way as for full faculty membership except that all full members irrespective of rank may vote on candidates for joint membership as with full faculty membership. The final decision at the departmental level rests with the Head. Appointments are for a five year term and renewal will follow the same procedures. c. The Committee shall consist of seven Full Professors; one member appointed by the Head of Department and six members elected by the Faculty of Biochemistry and Biophysics. The Head of Department and other Members of any Faculty at Texas A&M holding administrative positions of Head or higher shall not be members of this committee. No more than one Joint faculty shall serve on the Promotion and Tenure Committee at any one time. d. The period of service on the Committee shall be six years. The period of service on the Committee for the appointed member shall be three years. The appointed member may be reappointed for a consecutive three-year term. The Chair of the Committee will be elected by the membership of the Committee and serve as Chair for a period of two years. An individual serving as Chair may be reelected for one consecutive two-year term as Chair as long as the reappointment does not extend the individual’s period of service on the Committee beyond six years. Individual tenures on the Committee shall be staggered so that one new member is elected each year to ensure continuity. After completion of a six-year term (or two consecutive three-year terms), members will be eligible for election or appointment to a new term on the Committee after two years. e. Nominations for the unfilled elected position each year shall be solicited by mail from the faculty. Voting shall be by mail-ballot. Voting shall close one week after distribution of ballots. The nominee receiving a majority of the votes cast will be elected. If no one receives a majority, the two nominees receiving the most votes will stand for a runoff election. Voting in the runoff election shall be by mail ballot, and voting shall close one week after distribution of the ballots. The nominee receiving the most votes in the runoff election will be elected. The term of the appointment shall begin on January 1, following the election. f. In the event a member is forced to resign from the Committee before the expiration of his/her term, the position will be refilled as follows: g. Replacements will be selected by the same process that was used to fill the term originally. In the case of an elected member, an election should be held according to the procedures outlined above as soon as is practicable after the Department Head declares the vacancy. h. A replacement once elected or appointed will begin service on the Committee immediately. h. The replacement will serve out the original term (i.e., not start a new 6-year or 3-year term). i. Replacements that serve longer than 3 years will not be eligible for re-election or reappointment for 2 years after the expiration of the term.

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8.2.2. Timeline The Dean of Faculties updates guidelines annually (usually February or March). When announced, the guidelines are distributed to all faculty and requests to be considered for promotion are solicited. Mandatory considerations also begin at this time. Candidate dossiers are assembled and submitted to the department’s Promotion and Tenure Committee (PATC) for initial review in May. PATC provides the candidate’s suggested reviewers and also suggests reviewers to the Department Head. The Department Head selects a mixture of suggested reviewers from both lists and requests letters of evaluation. This process is completed by June. The candidate gives a public research seminar, generally in late August or early September. PATC reviews the dossier, conducts a vote on a proposal to promote and/or grant tenure and announces their findings to the tenured faculty in September. A vote is taken amongst the tenured faculty of equal or higher rank than rank being sought by the candidate. The Head prepares his/her own evaluation. The Head’s evaluation and recommendation along with the evaluation and recommendation of PATC and the result of the vote of the eligible faculty are sent to the AgriLife Peer Review Committee in September. The Head meets with the candidate and informs him or her of the outcome after each step of the process going forward (e.g. the decisions of the Dean, the Provost, the President and the Board of Regents). This process can continue into the late Spring.

9. Post-Tenure Review In accordance with University SAP 12.06.99.M0.01 (Post-Tenure Review), post-tenure review applies to tenured faculty members and is intended to promote continued academic professional development and enable a faculty member who has fallen below performance norms to pursue a peer-coordinated professional development plan and return to expected levels of productivity. Post-tenure review comprises: 1) Annual performance reviews (see Section 6.) conducted by the Department Head, director, or supervisor (or individual responsible for conducting the annual evaluation). 2) Periodic review by a committee of peers (see Section 9.2.).

9.1. Purpose ● Assess whether the individual is making a contribution consistent with that expected of a tenured faculty member. ● Provide guidance for continuing and meaningful faculty development. ● Assist faculty to enhance professional skills and goals/objectives. ● Refocus academic and professional efforts, when appropriate.

9.2. Peer Review Committee th A periodic post tenure peer review will be conducted in the 6 academic year following the last comprehensive peer review conducted since the awarding of tenure. Peer review will be conducted by a committee consisting of 2 elected full professors and 1 full professor appointed by the Department Head, each serving staggered 3-year terms so that one new member is either elected or appointed each year. In those instances when an associate professor with tenure is to be reviewed, the Department Head will appoint a tenured associate professor to serve as an ad hoc member in place of the regular appointed member of the peer review committee to participate in the review.

9.3 Process A periodic peer evaluation will be conducted no more than 6-years since the awarding of tenure; promotion following the awarding of tenure; receipt of an honor based on peer evaluation of accomplishments, such as University Distinguished Professor or Regent’s Professor; or a previous Post Tenure Peer Evaluation; whichever has occurred most recently. At the beginning of each academic year the Department Head will notify the members of

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the faculty who will be subject to the Post Tenure Peer Review, as well as the members of the Post Tenure Peer Review Committee. The faculty to be reviewed will be asked to submit a full CV and any other documents that may be useful for the Committee to address whether the following expectations have been met. The Post Tenure Peer Review Committee will review the submitted materials and prepare a written evaluation of the faculty member’s performance, providing an evaluation rating in the categories of assigned responsibilities, as well as an overall evaluation. The criteria for the individual and overall performance ratings should be consistent with annual evaluations. After the Committee has performed their evaluation, they will communicate to the Department Head the rating (Satisfactory, Needs Improvement, and Unsatisfactory) they have determined for each of the 3 categories; Scholarship, Teaching, and Service; along with a brief statement regarding the reasons for their determination. The results will be communicated to the Dean and to the respective faculty member by the Department Head.

For faculty receiving a rating of “Needs Improvement” or “Unsatisfactory”, the faculty member will meet with the Department Head to develop a plan for improving the performance. This plan should be developed as much as possible by the faculty member. Should resources be required to meet the plan, the Department Head will make reasonable effort to secure those resources. The plan should articulate specific goals and a timeline for achieving those goals. The faculty member and the Department Head should meet subsequently to evaluate progress being made toward meeting the proposed goals, and the plan revised as necessary if appropriate. These subsequent meetings should take place no less frequently than once every 6-months until the goals have been achieved.

If all of the relevant review categories are satisfactory, the faculty member will be subjected to periodic peer review again in six years or fewer, as determined by college/department guidelines, or following three consecutive unsatisfactory annual evaluations by the Department Head, director, or supervisor, whichever is earlier.

A finding of “Unsatisfactory” performance in any particular category shall state the basis for that finding in accordance with the criteria described in the unit guidelines. An unsatisfactory Periodic Peer Review will trigger the initiation of a Professional Development Review.

A finding of “Needs Improvement” in any two categories shall state the basis for that finding in accordance with the criteria described in the unit guidelines. Such an outcome will also trigger the initiation of a Professional Development Review.

A rating of “Needs Improvement” in a single category must specifically elaborate the deficiencies, in writing, to better inform the immediate development of a near term improvement plan developed in collaboration between the Department Head and the faculty member.

For tenured faculty with budgeted joint appointments, Periodic Peer Review will be conducted as per the post-tenure review guidelines of the unit where the faculty holds the majority of the appointment (ad loc) unless the 1 faculty member requests to be reviewed by both units. If reviewed only by the primary unit, the Department Head, director, or supervisor will share the report with the other Department Head, director, or supervisor of the secondary unit.

st By no later than May 31 , each unit will provide to the dean and the Dean of Faculties, the list of those faculty who underwent Periodic Peer Review, the outcome of the review, and the year when each tenured faculty last underwent a review. The Peer Review Committee’s written evaluation and the faculty member's post-tenure review documents will be placed in the faculty member’s departmental personnel file.

9.4 Professional Development Review A professional development review will be initiated when a tenured faculty member receives three consecutive overall “Unsatisfactory” annual reviews (see Section 6) or an “Unsatisfactory” Peer Review (see Section 9.2) or upon

1 It is recommended that faculty who hold budgeted joint appointments complete the post-tenure review in both units.

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request of the faculty member (see Section 9.4.1). The Department Head will inform the faculty member that he or she is subject to a Professional Development Review, and of the nature and procedures of the review. A faculty member can be exempted from review upon recommendation of the Department Head and approval of the Dean when substantive mitigating, circumstances (e.g. serious illness) exist. For more information on the process of the Professional Development Review see University SAP 12.06.99.M0.01 (Post-Tenure Review). If substantial or chronic deficiencies are identified, the review committee specifically elaborates the deficiencies in writing and a copy is provided to the faculty member, Department Head, and Dean. The faculty member, review committee, and Department Head shall then work together to draw up a “Professional Development Plan” (see Section 8.3) acceptable to the Dean.

The purposes of Professional Development Review are to: identify and officially acknowledge substantial or chronic deficits in performance; develop a specific professional development plan by which to remedy deficiencies; and monitor progress toward achievement of the professional development plan.

The Professional Development Review will be conducted by an ad hoc review committee (hereafter referred to as the review committee), unless the faculty member requests that it be conducted by the Department Head. The three-member ad hoc faculty review committee will be appointed by the Dean, in consultation with the Department Head and faculty member to be reviewed. On behalf of the Dean, the Executive Associate Dean will solicit a list of names of potential committee members from the faculty member and a list of individuals that should not be contacted. The Department Head will give feedback on the submitted names and have the opportunity to provide additional names. When appropriate, the committee membership may include faculty from other departments, colleges, or universities.

The faculty member to be reviewed will prepare a review dossier by providing all documents, materials, and statements he or she deems relevant and necessary for the review within one month of notification of Professional Review. All materials submitted by the faculty member are to be included in the dossier. Although review dossiers will differ, the dossier will include at minimum current curriculum vitae, a teaching portfolio, and a statement on current research, scholarship, or creative work.

The Department Head will add to the dossier any further materials he or she deems necessary or relevant to the review of the faculty member’s academic performance. The faculty member has the right to review and respond in writing to any materials added by the Department Head with the written response included in the dossier. In addition, the faculty member has the right to add any materials at any time during the review process.

The Professional Development Review will be made in a timely fashion (normally within three months after submission of the dossier). The Professional Development Review will result in one of three possible outcomes:

● No deficiencies are identified. The faculty member, Department Head, and Dean are so informed in writing, and the outcome of the prior annual review is superseded by the ad hoc committee report,

● Some deficiencies are identified but are determined not to be substantial or chronic. The review committee specifically elaborates the deficiencies in writing and a copy is provided to the faculty member, the Department Head, and the Dean to better inform the near-term improvement plan of Section 2.4, 4.1, 5.3 Substantial or chronic deficiencies are identified. The review committee specifically elaborates the deficiencies in writing and a copy is provided to the faculty member, Department Head, and Dean. The faculty member, review committee, and Department Head shall then work together to draw up a “Professional Development Plan” (see section 5) acceptable to the Dean.

9.3. The Professional Development Plan The Professional Development Plan shall indicate how specific deficiencies in a faculty member's performance (as measured against stated criteria in the unit guidelines under the provision of this procedure) will be remedied. The plan will be developed with the collaboration among the faculty member, the review committee, the Department

Department of Biochemistry and Biophysics Guidelines for Faculty Evaluation Page 25 of 27

Head, and the Dean, and should reflect the mutual aspirations of the faculty member, the unit, and the college. The plan will be formulated with the assistance of and in consultation with the faculty member. This plan should be developed as much as possible by the faculty member. The plan should articulate specific goals and a timeline for achieving those goals. It is the faculty member's obligation to assist in the development of a meaningful and effective plan and to make a good faith effort to implement the plan adopted. Should resources be required to meet the plan, the Department Head will make every effort to secure those resources. The faculty member and the Department Head should meet subsequently to evaluate progress being made toward meeting the proposed goals, and the plan revised as necessary if appropriate. These subsequent meetings should take place no less frequently than once every 6-months until the goals have been achieved. For more details on the Professional Development Plan see Section 9 of University SAP 12.06.99.M0.01 (Post-Tenure Review). 9.4.1 Appeal If at any point during the procedure the faculty member believes the provisions of the Post-tenure review are being unfairly applied, a grievance can be filed under the provisions of University SAP 12.99.99.M0.01 (Faculty Grievances Procedures not Concerning Questions of Tenure, Dismissal, or Constitutional Rights).

If the faculty member wishes to contest the composition of the Professional Development Review committee due to specific conflict of interest with one or more of the proposed committee members, an appeal may be made to the Dean of Faculties and Associate Provost. After consultation with the faculty member, Department Head/director/supervisor, and the Dean, the decision of the Dean of Faculties and Associate Provost on the committee composition is final (section 6, University SAP 12.06.99.M0.01). If the faculty member wishes to contest the Professional Development Review committee's finding of substantial or chronic deficiencies, the faculty member may appeal the finding to the Dean, whose decision on such an appeal is final (section 6, University SAP 12.06.99.M0.01). If the faculty member, Department Head/director/supervisor, and review committee fail to agree on a Professional Development Plan acceptable to the Dean, the plan will be determined through mediation directed by the Dean of Faculties and Associate Provost (section 6, University SAP 12.06.99.M0.01). 9.4.2 Voluntary Post-Tenure Review A tenured faculty member desirous of a voluntary Post-Tenure Review may seek the counsel of peers, through a Periodic Peer Review or a Professional Development Review, by making a request to the Department Head, director, or supervisor (section 6, University SAP 12.06.99.M0.01). 10.Granting Faculty Emeritus Status University Rule 31.08.01.M2 states the following: Every individual who, at the time of separation holds a tenured appointment at Texas A&M University and has served the University at least 10 years, must be considered for emeritus status unless the faculty member requests in writing that he/she not be so considered. Non-tenured faculty, or those who have served less than 10 years, may also be considered.

For faculty without tenure or who have served the University for fewer than 10 years, see Institutional Rule 31.08.01, which indicates the process for this situation. See the Dean of Faculties website for procedures and forms for nominating a faculty member for emeritus status. 10.1. Procedure for consideration for Emeritus Faculty ● Nomination for Emeritus Faculty membership can be submitted by any tenured full faculty member to the Executive Committee. The nomination packet should consist of all materials deemed pertinent to the candidacy and, if judged to warrant detailed consideration by the Executive Committee, will be forwarded to PATC.

Department of Biochemistry and Biophysics Guidelines for Faculty Evaluation Page 26 of 27

● PATC will review the nomination packet, vote on the candidacy and report the outcome of the deliberations and vote to the faculty. The main criterion will be a previous five-year record of “satisfactory” or “excellent” annual evaluations. ● After discussion, voting will be conducted in the same way as for full faculty membership. As with full faculty membership, the final decision at the departmental level for offering an Emeritus membership rests with the Department Head.

Contact Office

Department of Biochemistry and Biophysics, Office of Dr. A. Joshua Wand, e-mail [email protected].

Department of Biochemistry and Biophysics Guidelines for Faculty Evaluation Page 27 of 27

Appendix C: Main BCBP Building (#1507) Space Allocations & Renovation Plan

Significant changes in space allocation in the main BCBP building (#1507) and attendant renovations are in progress and will be completed over the next two years. The infrastructure of much laboratory and administrative space in this building is worn out. In addition, four existing faculty that currently housed in the Borlaug Center (Shan, X. Zhang, He) and the ILSB (J. Zhang) will relocate to the main BCBP building. Nearly 14,000 sq ft is involved. Some of this space has been recently vacated through retirement (Reinhart, Kunkel) or departure (Kaplan), significant reorganization within the building has been required. Seven faculty have seen their space contracted or moved, either through voluntary gestures or by negotiation. The status of the building in September, 2020 is shown in Appendix D. The status as of March, 2021 is summarized in the following figures. Unless dated, the changes are in progress or completed. An area on the second floor was first renovated to accommodate APT faculty (Miles, Pozzi) and emeritus faculty (Peterson, Reinhart, Kunkel) obtain contiguous space on the third floor for the Shan, He and X. Zhang laboratories. Bryk and Park were relocated to smaller “spiffed up” space on the second floor. Gill (a guest from Animal Science) and a module of Young’s space were reassigned to space previously occupied by Jim Hu. Professor Hu passed away unexpectedly in 2020. Shan, He and X. Zhang need specialized plant growth chambers, which are also being installed on the third floor, and additional unregulated plant growth rooms, which are planned for a vacant area on the first floor. Accommodation of plant preparation facilities on the first floor will require renovations to the stockroom. These renovations are planned to be completed by end of 2021 if not sooner.

Renovations in the NMR annex (Building #1525) to the main BCBP building to accommodate the newly acquired Titan Krios cryoEM instrument and provide a low humidity preparation room are on-going and are planned to be completed in early 2022 if not sooner. Related to this, J. Zhang will relocate from the ILSB to space on the 4th floor of the main BCBP building that was previously assigned to Reinhart. Adjacent space, previously occupied by Kunkel, will also be renovated to accommodate a new junior hire in cryoEM/ET-based research, hopefully in an area of molecular (epi)genetics.

The main administrative space, not touched since the 1980s, will be “spiffed up” in 2021 to eliminate issues with air quality and general working conditions and accommodate relocation of Terry Lovingshimer (Operations Manager).

Coordination of the renovations have required extensive involvement by Professor Wand and Lovingshimer in coordination with Sarah Morris of Facilities and Construction and a committee of the BCBP faculty (Mullet, Rye, Shippen).

Appendix D: Main BCBP Building (#1507) Space Allocations Circa September, 2020

Appendix E – NMR Annex of BCBP Building Status and Renovation Plan

The NMR annex (Bldg #1525) houses five faculty: Cho, Devarenne, Igumenova, Tommos and Wand. It also hosts the NMR resource and the emerging cryoEM. Near term renovations include preparation of the space for the Titan Krios and creation of a BSL-2 cryoEM preparation laboratory that includes a low humidity room. The latter is requiring installation of a Munter dehumidification system on the roof (not shown). Installation of a He recovery system for the NMR magnets is also being installed in 2021.

Appendix F - Common Use Equipment

BioBio + NMR Building CUE (Sept., 2020) Instrument Location Notes Superspeeds (Old Models) RC3B 8901670 338B RC5B 8902050 N114

Superspeeds (New Models) Lynx6000 41747877 220 Installed May, 2015 Lynx6000 41747884 338B Installed May, 2015 Lynx6000 41750052 400 Installed May, 2015 Lynx6000 41747885 N120 Installed May, 2015 Lynx6000 42000225 338B Installed Oct., 2016 Lynx6000 41973987 N218 Installed Oct., 2016 Lynx6000 42124865 220 Installed Oct., 2017 ; warr. until 2020 Lynx6000 42132149 400 Installed Oct., 2017; warr. until 2020

Beckman Avanti JXN-26 (JXN16H03) 338B Installed 9/02/16

Digital Imaging Fotodyne Eclipse 414 Installed May, 2015 TAMUID#021500189781 Fotodyne Eclipse 313 Installed May, 2015 TAMUID#021500189780 FotoDyne: DED1-0710-1564 N220B

Amersham Imager 600RGB Installed July, 2015; ann. service #47230199 338 contract

GE Typhoon FLA7000 Phosphorimager Installed Sept., 2015; annual service S/N 5632520B 338 contract (see footnote 2) Upgrade installed 2/14/17; annual Zeiss Fluorescence Microscope 337 service contract (see footnote 2)

Scintillation Counter PerkinElmer TriCarb 2910TR 215 Installed Jan., 2015 TAMUID#021500177925

Film Processors QX-130A 415

Refrigerated Shakers E25R #1 300 E25R #2 400 E25R #3 400 E25R #4 229 Installed Nov., 2014 E25R #5 N220B Installed Nov., 2014 E25R #6 338 Installed Nov., 2014 E25R #7 338 Installed Nov., 2014 Lyophilizers AEX 129357 400 Labconco #160729234F 400 Installed Sept., 2016

Nanodrop Spectrophotometer 338 Installed July, 2016

BioRad CFX96Touch Real-time Thermocycler Installed Aug., 2016 S/Ns: Base CT022525, top Requires google calendar reservations 785BR15295 338 – contact CUETIP

Microfluidizer LM20-30 414 Installed Feb., 2017

Installed 5/30/18 Requires special training & google ForteBio Octet RED96 BLI calendar reservations – contact CUETIP 414 Users pay 50% of future repairs

Installed 10/30/18 Jasco J-1500 CD Requires special training & google calendar reservations – contact 414 CUETIP

Ultracentrifuges (Older Models) Location Notes L8-557 5E530 220

Ultracentrifuges (New Models) Optima XPN-80 9541176 338B Installed Feb., 2015 Optima MAX-XP 9859431 Installed Feb., 2015 (tabletop) 338

MilliQ water purification system 412

Footnotes: 1. 300, 3rd floor instrument corridor; 400, 4th floor instrument corridor 2. Maintenance 50% CUE, 50% Users 06/23/2015

Beckman Preparative Ultracentrifuge Rotors

Serial Type No. Owner / Location / Comments

Floor Model Old rotors cannot be used in new Old Rotors centrifuge (Feb. 2015) SW28 2071 Park / Young lab 1192 Cruz-Reyes SW41Ti 4249 Mullet / Young SW50.1 4677 Peterson 4998 Cruz-Reyes

Type70.1 961 Peterson 1692 Young 1405 Cruz-Reyes VTi65.2 829 Young VTi65 706 Park VTi80 1330 Kunkel Type 35 402 Pettigrew Ti50.2 1062 Young – lid very scratched

Floor Model New Rotors SW41Ti 14E2450 Dept/Young lab/In service, Feb. 2015 14E2451 Dept/Young lab/In service, Feb. 2015 Type45Ti 15U4986 Dept/Young lab/In service, Feb. 2015 Type70Ti 14U6438 Dept/Young lab/In service, Feb. 2015

Tabletop Old rotors cannot be used in new Old Rotors centrifuge (Feb. 2015) TLA100 606 Dept /Jen Herman TLA100.2 1317 Dept/Young lab TLA100.3 922 Dept/Young lab (missing gasket) TLS55 1107 Dept/Young lab 1671 Dept/Young lab TLV 583 Dept/Young lab

Tabletop New Rotors TLA100.3 14E1026 Dept/Young lab/In service, Feb. 2015 MLA-130 15U1433 Dept/Young lab/In service, Feb. 2015 TLA100 17U4320 Dept/Young lab/in service, July 2017 Appendix G – Graduate Program Handbook Introduction Welcome to the Department of Biochemistry and Biophysics at Texas A&M University! The Graduate Program Handbook describes relevant BCBP and TAMU policies and should serve as a guide throughout your graduate tenure. While every attempt has been made to ensure that the university policies outlined herein are accurate, be advised that the 2020–2021 TAMU Graduate Catalog remains the authoritative source for TAMU rules and regulations. All policies are subject to change.

1 Return to Table of Contents. Contents Introduction 1 OGAPS Calendar | 2020–2021 4 BCBP Resources 5 The Graduate Office 5 Biochemistry Graduate Association 6 General Information 7 Directory | Select Office Staff 7 University Resources 8 Office of Graduate and Professional Studies (OGAPS) 8 Student Loans 8 Student Health Insurance 8 Division of Student Affairs 8 Equal Opportunity 9 International Students 10 International Student Services 10 English Language Proficiency Certification 10 Doctor of Philosophy Degree 11 Orientation Week 11 Prerequisite Coursework 11 The Advisory Committee 11 Year 1 12 Year 2 13 Year 3 and Beyond 13 Grades 13 Rotations and Lab Selection 14 Thesis Committee | Structure and Responsibilities 14 Doctoral Research Proposal and Preliminary Examination 15 Candidacy 16 Committee Meetings | Post-Candidacy 16 Ph.D. Dissertation and Thesis Defense 16 Letter of Completion 17 BGA Town Halls 17 Teaching Assistantship 17 Full Course Waiver 17 Annual Leave 18

2 Return to Table of Contents. Seminars 18 Committee Meetings | Overview and Protocols 18 Master of Science Degree 21 Thesis Option 21 Non-Thesis Option 21 TAMU Policies 22 Petitions 22 Continuous Registration Requirement 22 Tuition and Fees 22 Paychecks 22 Right to Review Records 22 Code of Conduct 22 Ownership of Data 22 Leave of Absence 23 Fellowships and Awards 24 External Fellowships 24 Dissertation Fellowships 25 TAMU Awards and Fellowships 25 Travel Awards and Fellowships 26 Appendix | Recommended Electives and Journal Clubs 27

3 Return to Table of Contents. OGAPS Calendar | 2020–2021

Fall 2020 May 29 Friday Last day to submit Degree Plan to OGAPS for Dec 2020 graduation July 29 Wednesday Electronic Thesis / Dissertation System opens for Dec 2020 degree candidates August 12 Wednesday First day to apply for degrees to be awarded in Dec 2020 August 12 Wednesday First day to clear dissertation for Dec 2020 graduation August 18 Tuesday Last day to register for Fall classes August 19 Wednesday First day of Fall classes August 25 Tuesday Last day to clear Dissertation Services to avoid Fall registration August 25 Tuesday Last day to add/drop courses September Friday Last day to apply for Dec 2020 graduation without a late fee 18 October 2 Friday Last day to submit Request and Announcement of the Final Examination to OGAPS (or 10 working days prior to the examination) October 16 Friday Last day to take final examination / defend dissertation for Dec 2020 graduation October 23 Friday Last day to submit a signed approval form / PDF of dissertation November Tuesday Last day to drop courses with no penalty (Q-drop) 10 November Tuesday Last day to apply for Dec 2020 graduation 24

Spring 2021 October 16 Friday Last day to submit Degree Plan to OGAPS for May 2021 graduation November Wednesday Electronic Thesis / Dissertation System opens for May 2021 25 degree candidates January 6 Wednesday First day to apply for degrees to be awarded in May 2021 January 6 Wednesday First day to clear dissertation for May 2020 graduation January 15 Friday Last day to register for Spring classes January 19 Tuesday First day of Spring classes January 25 Monday Last day to clear Dissertation Services to avoid Spring registration January 25 Monday Last day to add/drop courses February Friday Last day to apply for May 2021 graduation without a late fee 19 February Friday Last day to submit Request and Announcement of the Final 26 Examination to OGAPS (or 10 working days prior to the examination) March 12 Friday Last day to take final examination / defend dissertation for May 2021 graduation

4 Return to Table of Contents. March 26 Friday Last day to submit a signed approval form / PDF of dissertation April 20 Tuesday Last day to drop courses with no penalty (Q-drop)

BCBP Resources The Graduate Office The BCBP Graduate Office is led by Prof. Jean-Philippe Pellois, Associate Head of the Graduate Program, and comprises three committees: Advisory, Admissions, and Outreach & Recruiting. Membership and committee responsibilities are described below.

Administration | All questions about program protocols should be directed to Dr. Justine deGruyter or Prof. Jean-Philippe Pellois. Associate Head – Prof. Jean-Philippe Department Head – Prof. Josh Wand Pellois BICH N315A BICH 438A [email protected] [email protected]

Program Coordinator – Dr. Justine Program Specialist – Nowlan Savage deGruyter BICH 103B BICH 103C [email protected] [email protected]

Advisory Committee | The Advisory Committee guides pre-candidacy students in rotation selections, choice of elective coursework and journal club, and formation of a thesis committee. Chair – Prof. Lanying Zeng Prof. Cecilia Tommos BICH 419A BICH N315B [email protected] [email protected]

Prof. Michael Polymenis Dr. Justine deGruyter (ex officio) BICH 333A BICH 103C [email protected] [email protected]

Admissions Committee | The Admissions Committee evaluates prospective graduate student applications, nominates incoming students for internal awards, and hosts Recruitment Weekend. Chair – Prof. Tatyana Igumenova Prof. Vytas Bankaitis BICH N118A Reynolds 108 [email protected] [email protected]

5 Return to Table of Contents.

Prof. Josh Wand Prof. Thomas Meek BICH N315A ILSB 2126 [email protected] [email protected]

Prof. Lanying Zeng Prof. Cecilia Tommos BICH 419A BICH N315B [email protected] [email protected]

Prof. Vishal Gohil (ad hoc) BGA – Ronnie Bourland ILSB 2146A Sacchettini Lab [email protected] [email protected]

Outreach & Recruitment Committee | The Outreach & Recruiting Committee seeks to attract quality graduate students to our program through scientific community engagement and partnership with regional institutions. Chair – Dr. Justine deGruyter Prof. Jae-Hyun Cho BICH 103C BICH N113A [email protected] [email protected]

Prof. Alfredo Caro Prof. Jorge Cruz-Reyes BICH NMR BICH [email protected] [email protected]

Prof. Junjie Zhang BGA – Kayla Anderson ILSB 2157A Meek Lab [email protected] [email protected]

Biochemistry Graduate Association Established in 1992, Biochemistry Graduate Association (BGA) seeks to improve the welfare and educational experience of BCBP graduate students. Elected BGA representatives sit on the Admissions and Outreach & Recruitment committees to enhance communication between students and faculty. Similarly, a faculty member (selected by the BGA) is appointed to the BGA in a non-voting advisory capacity. The BGA is primarily funded through the Graduate Enhancement Program, which is sustained through student tuition payments and private donations.

The BGA sponsors a variety of activities including research and professional development seminars, as well as the annual vendor show and research competition. The organization also offers travel grants and dissertation expense relief. Inquiries should be directed to the BGA President.

BGA Officers | 2020–2021 President – Matthew Theodore Vice President – Devon Boland Zeng Lab Devarenne Lab [email protected] [email protected]

6 Return to Table of Contents. Secretary – Kailun Zhang Treasurer – Staci Hammer Zeng Lab Polymenis Lab [email protected] [email protected]

Outreach Representative – Kayla Admissions Representative – Ronnie Anderson Bourland Meek Lab Barondeau Lab [email protected] [email protected]

Program Representative – Kayla GPSC Representative – Deanna Anderson Callerame Meek Lab Mullet Lab [email protected] [email protected]

GPSC Representative – Marina Boland Faculty Advisor – Prof. Jennifer Herman Threadgill Lab BICH 305A [email protected] [email protected]

General Information

Website: bcbp.tamu.edu Main Office: 979-845-1012 | 800-482-6246 Address: 300 Olsen Blvd. | 2128 TAMU

Directory | Select Office Staff For the full directory of office staff, please visit our website.

Betty Cotton Sherry Coronado Senior Administrative Coordinator II Business Administrator III BICH 103D | 979-458-0630 BICH 103GA | 979-845-8852 [email protected] [email protected]

Divina Page Terry Lovingshimer Technical Stockroom Supervisor Facilities Manager BICH 112 | 845-1524 BICH 209 | 979-845-3785 [email protected] | [email protected] https://stockroom.tamu.edu/

Austin Johnson Raul Rodriguez Facilities Coordinator II Laboratory Mechanic II BICH 209 | 979-845-3785 BICH 207 | 979-458-3237 [email protected] [email protected]

7 Return to Table of Contents.

University Resources Office of Graduate and Professional Studies (OGAPS)

Website: ogaps.tamu.edu Main Office: 979-845-3631 | [email protected] Address: Jack K. Williams Administration Building, Suite 112 | 1113 TAMU

The Office of Graduate and Professional Studies “serves Texas A&M graduate students as an advocate for their graduate education and houses the Ombudsperson for Graduate Education.” Please refer to the OGAPS website for academic calendars, forms, rules, and regulations.

Student Loans

Website: financialaid.tamu.edu Main Office: 979-845-3236 | [email protected]

nd Address: Pavilion 2 Floor | 1252 TAMU

TAMU offers emergency loans for tuition / fees and short-term loans for other expenses.

Student Health Insurance Students classified as Graduate Assistant – Teaching (GAT) or Graduate Assistant – Research (GAR) are considered TAMU employees and are eligible for all associated benefits. GATs and GARs will receive benefits information during orientation. International students require additional insurance for evacuation and repatriation. Please contact International Student Services for more information.

8 Return to Table of Contents. Students who are supported by individual fellowships and/or training grants are not considered TAMU employees and must acquire their own health insurance. The TAMU Student Health Plan is available for purchase. Please speak with Sherry Coronado for more information.

Information about Graduate Student Employee Benefits is available through TAMU Human Resources.

Division of Student Affairs

Website: studentaffairs.tamu.edu Main Office: 979-845-4728 | [email protected] Address: John J. Koldus Building, Suite 117 | 1256 TAMU

The Office of the Vice President for Student Affairs (VPSA) houses a wealth of resources, including: Counseling & Psychological Services (CAPS) Disability Resources Multicultural Services Student Health Services Veteran Resources and Support Center Student Assistance Services Student Legal Services

VSPA can also provide emergency funds for unexpected medical expenses on a case-by-case basis. Please contact the Director of Business Operations, Cari Tawney, for more information.

Equal Opportunity The TAMU System and BCBP are committed to equal employment opportunity, without regard to race, color, sex, religion, or age.

9 Return to Table of Contents.

International Students International Student Services International Student Services (ISS) serves as an information resource for all partners in the international education process. In addition to issuing documents used to obtain non-immigrant student visas, the office works with BCBP to ensure that our international students remain educated on Department of Homeland Security requirements. ISS also offers counseling on immigration, employment, financial issues, medical insurance, adjustment to the U.S., and income taxes.

English Language Proficiency Certification The state of Texas requires that all non-native English speakers attain English proficiency certification before serving as a teaching assistant. International graduate students can be certified prior to enrollment by achieving requisite scores on the oral component of the TOEFL or IELTS standardized tests. International graduate students who have not been certified prior to enrollment must take the English Language Proficiency Exam (ELPE) offered by TAMU Testing Services.

Level TOEFL | Speaking IELTS | Speaking ELPE Oral Exam (TAMU) 1 26–30 ≥8.0 ≥80 2 23–25 7.0–7.5 ≥75 3 <23 <7.0 <75

Level 1 Eligible for teaching assignments

Level 2 Conditionally eligible for teaching assignments for one semester only; must participate in the Center for Teaching Excellence English Language Proficiency (CTE-ELP) instruction and achieve a Level 1 scores by the end of the semester

Level 3 Not eligible for teaching assignment; must participate in the Center for Teaching Excellence English Language Proficiency (CTE-ELP) instruction 10 Return to Table of Contents.

Doctor of Philosophy Degree

The Department of Biochemistry and Biophysics seeks to foster an inquisitive and diverse community of scholars with a common interest in the chemical and physicochemical processes that occur within living systems. On successful completion of the program, our Ph.D. students are equipped to address pressing scientific challenges through cohesive application of both empirical and theoretical methods. We are committed to training students who will contribute to the advancement of knowledge in the fields of biochemistry, biophysics, and genetics, and work to improve the health and welfare of society at large. Typically, our Ph.D. students must complete at least 96 credit hours, accumulated through a combination of traditional coursework, journal clubs, and dissertation research. However, students who enter the program with a master’s degree from an accredited U.S. college or university need only complete 64 credit hours. The viability of transfer credits is determined by the Advisory Committee and the Office of Graduate and Professional Studies. Accredited universities offering the Ph.D. degree are required to examine students for suitability to be admitted as candidates for the degree. This divides your graduate experience into two parts: “pre-candidacy” and “candidacy.” The goal of the pre-candidacy phase is to prepare you for dissertation research. This is achieved through didactic coursework, laboratory rotations, and other activities. After approximately eighteen months in the program, students sit the “preliminary examination,” one of the formal requirements for ascension to Ph.D. candidacy. The remaining requirements are detailed below.

Orientation Week All incoming graduate students are required to attend Orientation Week, which is typically held the week before the first day of Fall classes. During Orientation, you will learn about TAMU policies, BCBP procedures, student resources, safety requirements, and the terms/conditions of your employment.

11 Return to Table of Contents. Prerequisite Coursework Incoming graduate students should have a strong foundational knowledge in biology, chemistry, mathematics, and physics. Recommended prerequisite coursework includes: ▪ Two semesters of Biochemistry (equivalent to BICH 410/411) ▪ One semester of Physical Chemistry (equivalent to CHEM 328) ▪ One semester of Molecular Genetics (equivalent to BICH/GENE 431) ▪ Two semesters of Organic Chemistry (equivalent to CHEM 227/228) ▪ One semester of Physics ▪ One semester of Calculus

The schedule outlined below is meant to represent a typical Degree Plan for students who entered the program after 2018. All others should refer to the “OLD” Degree Plan in the Forms section.

The Advisory Committee The Advisory Committee is comprised of three faculty members whose goal is to guide you through the pre-candidacy period of your Ph.D. studies. They will help orient you to the program and assist you in developing a curriculum that strengthens your weaknesses, buttresses your strength, and introduces you to the possibilities for advanced study and research in biochemistry and biophysics. You will meet individually with the advisory committee several times during your pre-candidacy term; a typical schedule is outlined below. The Advisory Committee will review your transcripts and make recommendations for elective coursework based on your interests and current research. You should come prepared to help guide the discussion. As you approach your preliminary examination, the committee will also offer guidance on thesis committee selection.

Rotations, Advisory Committee Meetings, and Preliminary Examination Schedule:

12 Return to Table of Contents.

Year 1 During the Fall of your first year of graduate studies, you will take 4 courses and participate in three 5-week laboratory rotations. During Orientation Week, students will meet individually with the Advisory Committee to discuss procedures and recommendations for selecting laboratory rotations. BICH 603 Principles of Biochemistry and Biophysics 3 cr. BICH 608 Critical Analysis of the Biochemical Literature 2 cr. BICH 631 Biochemical Genetics 3 cr. BICH 689 Application of Scientific Values 1 cr. Rotation 1 Rotation 2 Rotation 3

In the Spring, you will take our modular course series. Designed with flexibility in mind, you will select six 5-week courses to create a course schedule tailored to your research interests. Modular course offerings change every year; please refer to the Course Schedule for the current selection. Most students will select a laboratory in which to begin work toward their preliminary examination. Most students will pass the Preliminary Examination advance to candidacy for the Ph.D. degree. We commit a significant effort towards preparing each student. Nevertheless, it is important to recognize that formal association with a Thesis Advisor becomes official only upon advancement candidacy. Finally, all first-year students must serve as Teaching Assistants. Expectations and requirements are detailed below. BICH 6XX Advanced Modules* 6 cr. BICH 690 Theory of Biochemistry Research 2 cr. BICH 697 Teaching 1 cr. * Previous offerings include: Metabolism, Quantitative Analysis in Biochemistry and Biophysics, Quantitative Analysis in Genomics / Molecular Biology, Advanced Ligand Interactions, NMR Spectroscopy, and Biochemical Kinetics, among others.

You will continue your lab work throughout the Summer, enrolling in 6 research credits hours to maintain full-time status. You will also meet with the Advisory Committee to ensure that you remain on track – They will offer suggestions for elective coursework and Journal Club selection. BICH 691 Research 6 cr.

Year 2 You will take six elective course credits during your second year. A non-comprehensive list of electives can be found in the Appendix. Note that not all courses are offered every semester; be sure to confirm current offerings in the Course Schedule. Though you may spread the electives out over both semesters, it is strongly recommended that you take both in the Fall semester. If you opt to take only one elective in the Fall, your BICH 691 credits should be adjusted to ensure that you remain enrolled full time. You will also complete your final required semester of Teaching Assistantship. ELECTIVE Elective (2) 6 cr. BICH 6XX Journal Club 1 cr. BICH 697 Teaching 1 cr. BICH 691 Research 1 cr.

In the Spring, you will continue to take Journal Club and Research credits. In preparation for your upcoming Preliminary Examination, you will enroll in Oral and Written Scientific Communication courses. All Preliminary Examinations will be held in April. Immediately after your Preliminary Examination, you will 13 Return to Table of Contents. submit your formal Degree Plan and select a Thesis Committee. Your Degree Plan formalizes your intent to earn a doctoral degree and establishes the required coursework. You must submit the plan through the OGAPS Document Processing Submission System. The Graduate Office is available to guide you through the process. More information on thesis committee selection can be found below. BICH 681 Written Communication 2 cr. BICH 689 Oral Communication 1 cr. BICH 6XX Journal Club 1 cr. BICH 690 Theory of Biochemistry Research 2 cr. BICH 691 Research 3 cr.

Year 3 and Beyond Spring and Fall: Once all core coursework is complete, you should continue to enroll in Journal Club, Theory of Biochemistry Research, and Research credits, such that you maintain full-time registration status (9 credit hours). Summer: You should continue to enroll in Research credits, such that you maintain full-time registration status (6 credit hours). You will be required to hold at least one committee meeting every academic year. Meeting protocols are outlined at the end of this chapter.

BICH 6XX Journal Club XX cr. BICH 691 Research XX cr.

Grades While research is the primary goal of your graduate studies, academic performance is also critical to your success. Per the Office of Graduate and Professional Studies, you must maintain a GPR of 3.0 and may not receive failing grades (D or F) in any BCBP core classes. If your GPR falls below 3.0, you may be placed on academic probation; you will receive written notice that you have one year to improve your grades, or risk loss of assistantship and funding. If you your GPR falls below a 3.0 and you receive at least one failing grade in a core class, you risk loss of assistantship and funding.

Rotations and Lab Selection Prior to joining a research group, you will participate in three laboratory rotations during your first semester. These rotations are designed to be mutually beneficial to both you and the faculty member. For you, this is an opportunity to learn about a broad array of research topics and determine your preferred subdiscipline. You should also use this time to evaluate the lab environment and PI mentorship style – Can you confidently commit to completing your PhD in the group? At the same time, the PI will be assessing your motivation, technical skills, and intellectual abilities. Finally, you should consider each rotation an opportunity to contribute substantively to a research project (perhaps even gaining authorship on publications!) and cultivate relationships with faculty who may eventually provide letters of recommendation on your behalf.

You will meet with the Advisory Committee before every rotation period – They can offer advice and help you select a rotation advisor based on your evolving research interests. After each meeting, you will receive a link to submit a ranked-order list of three faculty names to the Graduate Office. Before submitting your

14 Return to Table of Contents. preferences, you must communicate your intention to all faculty members listed. Rotation assignments will be made according to the preference list, pending faculty approval.

Before the end of the Fall semester, you should meet with prospective advisors to determine whether they are willing to permanently accept you into their lab. If you are unable to find satisfactory placement, you may opt to complete a fourth rotation. This option is only available to students who remain in good academic standing.

A list of PIs that will be accepting rotation students for Fall 2020 will be provided, along with a brief description of their research program. They will also present their work during Graduate Student Orientation. If a faculty member is not listed, they will not accept rotation students unless alternative arrangements have been made.

Thesis Committee | Structure and Responsibilities Thesis committees are comprised of a Chair and three members, as outlined below. Your committee should be a broad representation of departmental expertise, including at least one member who identifies as a biophysical researcher and one who identifies as biochemical researcher. OGAPS requires that one member have a primary appointment outside of BCBP.

Title Affiliation Responsibilities Chair BCBP Moderate the committee meetings; complete all required paperwork (with input from members); ensure that the student is offered the opportunity to meet with the committee in the absence of the Thesis Advisor; serve in a scientific and professional development advisory capacity

Ex officio BCBP | Thesis Direct mentorship Member Advisor Member BCBP Serve in a scientific and professional development advisory capacity

Member Non-BCBP Serve in a scientific and professional development advisory capacity

Doctoral Research Proposal and Preliminary Examination A well-written proposal is organized according to the National Institutes of Health (NIH) Grant Guidelines and includes the following sections; all descriptions are adapted from “Detailed Guidelines for the NIH Proposal” (Main Medical Center Research Institute). The Spring Year 2 communication courses are designed to assist you in designing and describing your research proposal both in written and verbal form.

Specific Aims 1 page Identifies the primary objectives the project, including the problem to be addressed, the current state of knowledge, and the potential contributions to the research field.

15 Return to Table of Contents. Research 5 pages Comprises three sections: Significance, Innovation, and Strategy Approach.

Significance | Provides a terse and scholarly background, including only literature review that pertains directly to the topic and demonstrates a modern understanding of the field.

Innovation | Explains how the proposal challenges current research or seeks to establish novel concepts, approaches, or methods. Advantages over known methods should be detailed.

Approach | Delineates the strategy, methodology, and analytical techniques to be used. Preliminary results should be included here.

Bibliography No All references should be formatted according to the NIH limit standards.

The proposal should not exceed six pages, single-spaced in Times New Roman 11-point font with uniform 0.5” margins. The bibliography does not count toward the total page count. Figures should be integrated as appropriate. Your final proposal should be submitted to the Graduate Office no more than 14 days after your preliminary examination.

Your Preliminary Examination will be scheduled well in advance and evaluated by an ad hoc examination committee selected by the Graduate Office. Your Doctoral Research Proposal should be submitted to each committee member 14 days before the meeting. At the examination, the committee will first meet separately from the student for preliminary discussion of the proposal. Should the written proposal be found lacking, the meeting will be rescheduled. The student will give an oral presentation aided by no more than 8 slides (approximately 15 minutes). The committee will refrain from interrupting the presentation. Following the presentation, the Chair will open the meeting to questions, which may range from proposal specifics or broader questions underlying the theme of the proposal. The Preliminary Examination is not meant to be a comprehensive examination. Following conclusion of the question period, the Committee will meet in the absence of the student and vote pass or fail on the written proposal and on the presentation. A failing grade on the written proposal will require remediation within two weeks. A failing grade on the oral presentation will require a repeat oral examination within 3 months. During this period, the student is placed on academic probation and is subject to dismissal from the program if a passing grade is not achieved on a second attempt.

Evaluation forms for your Preliminary Examination can be found here. It is imperative that you carefully review and understand each point of evaluation. Where appropriate, your presentation should demonstrate mastery of each skill identified on the form.

The results of your Preliminary Examination expire after 4 calendar years. Students requiring an extension may submit a Petition for Extension of Time Limits through DPSS.

16 Return to Table of Contents. Candidacy Students must meet the following requirements before advancement to candidacy:

● Complete all graded coursework (S/U courses may remain) on the degree plan. ● Earn a GPR of at least 3.0. No grades on the degree plan may be lower than a C. ● Pass the Preliminary Examination. ● Submit an approved doctoral research proposal. ● Meet the residence requirement.* *Students who enter the doctoral program with a baccalaureate degree must spend at least two academic years in resident study to meet the residence requirement. Students who enter with a master’s degree must spend at least one academic year in resident study to meet the residence requirement.

Committee Meetings | Post-Candidacy You are required to hold at least one committee meeting every academic year. In the early and late phases of your dissertation research the meetings may be more frequent. You are responsible for coordinating the meeting; rooms can be scheduled through the main office. The meetings are meant to be concise advisory sessions and will commence with a discussion between the committee with thesis advisor(s) in the absence of the student. The goal is to have a frank discussion about the advisor’s view of the student’s progress and any issues that may impede progress towards completion of dissertation work. The student is then to present a concise overview of progress since the last meeting. This presentation should not exceed 20 minutes; a draft of the presentation should be provided to the committee 14 days before the meeting. The Chair will then open the meeting for discussion, which should be restricted to no more than 40 minutes. The Thesis Advisor should then be excused so that the committee and student can discuss any issues that may impede progress towards completion of dissertation research. The Chair will file the Thesis Committee Meeting Report and Thesis Advisor Report with the Graduate Office. The forms should include recommendations on timing of future meetings, the anticipated date of completion of dissertation research, and whether there are sufficiently serious issues to warrant intervention by the Associate Head of the Graduate Program.

Ph.D. Dissertation and Thesis Defense

You may petition your Thesis Committee for permission begin composing your dissertation at any time following advancement to candidacy. Note that the Thesis Committee, not the Thesis Advisor, are the primary wardens and will assess your readiness collectively. In very rare cases, the Associate Head for the Graduate Program may overrule a denial by the Thesis Committee for permission to write and defend a dissertation. Once permission to write and defend has been granted, the defense must occur within three months or the committee will need to be recanvased for permission. The timeline and forms required by OGAPS are delineated below. TAMU has extensive requirements for preparation of your dissertation. You should review the guidelines carefully before you begin writing. As you begin to outline your dissertation, be sure to identify sources; science is an inherently collaborative endeavor and all contributions (e.g., data, tables, figures, etc.) should be properly acknowledged.

Please consult Dr. Justine deGruyter to coordinate the oral defense of your thesis. To initiate the process, you must first receive approval from OGAPS by filing the Request and Announcement of the Final Examination. All OGAPS protocols and deadlines should be carefully reviewed. Your written dissertation must be given to each committee member at least 14 days before the scheduled defense. You will also need to provide the date, time, location, and title to Nowlan Savage at least 14 days before the scheduled defense. A detailed protocol for the public defense is provided at the end of this chapter. 17 Return to Table of Contents.

If your only remaining requirement is the defense and you will not be on TAMU payroll for the entire semester, you may register for one credit hour (BICH 691) and be reclassified as a temporary research assistant. International students must consult ISS before moving forward with reclassification.

Letter of Completion It is not uncommon for students to accept a job offer in the period between completion of the degree requirements and formal issuance of the diploma. Many universities, companies, etc. will accept a Letter of Completion as sufficient proof of degree. Students must have completed all requirements for the degree before a Letter of Completion can be issued by OGAPS. This includes dissertation clearance, university debt resolution, and an approved graduation application. Please contact Dr. Justine deGruyter if you wish to request a Letter of Completion.

BGA Town Halls In the spirit of student involvement and open communication, the Graduate Office hosts a BGA Town Hall every semester to discuss program initiatives, changes, and concerns. Attendance is mandatory.

Teaching Assistantship All graduate students are required to serve as Teaching Assistants (TAs) for two semesters, generally in the spring of their first year and the fall of their second year. To be a TA, students must be certified through the Center for Teaching Excellence (CTE) Teaching Assistant Institute (TAI) program – Details are sent before the start of each semester. BCBP graduate students are usually assigned to undergraduate lab courses or recitation sections. International students must demonstrate English language proficiency before receiving a TA assignment.

Full Course Waiver If your thesis defense and dissertation submission are the only remaining requirements, and you will not be on TAMU payroll for your final semester, you may register for 1 credit hour of BICH 691 and be reclassified as a Research Assistant on wages. This is a one-time appointment for 3.5 months. International students should contact ISS before changing employment classification.

Annual Leave Graduate students are entitled to two weeks of paid vacation per year, in addition to the standard state employee holidays. Please seek permission from your Thesis Advisor for any period of absence longer than one full work day in advance. Refer to the TAMU Student Rules for class attendance policies.

Seminars The Department hosts nationally and internationally renowned scientists across a range of disciplines for our regular seminar series. Graduate students are expected to attend these lectures throughout their time in the program. Seminars are held each Wednesday (Fall and Spring) at 4:00pm in BICH 108, unless otherwise noted. Please speak with the Graduate Office to receive notifications for out-of-department seminars.

18 Return to Table of Contents.

Committee Meetings | Overview and Protocols A summary of the required committee meetings / OGAPS action items is provided. As of September 14, 2020, OGAPS requires that all forms be approved using Docusign. Please visit the OGAPS website for more information and form initiation links. Electronic versions of the department forms can be found on the BCBP website. You must inform the Graduate Office of your intent to hold a meeting at least 14 days ahead time. Years 1 and 2 Advisory Committee Meeting Purpose: Guide pre-candidacy students through their first- and second-year coursework, rotation, and thesis committee selections. Protocol: Students will meet with a standing Advisory Committee. The Advisory Committee will recommend elective coursework and offer suggestions for rotation selections based on student research interests. After meeting 4, the student should complete an Individual Development Plan; proof of submission should be sent to the Graduate Office. Forms: Individual Development Plan (IDP) at http://myidp.sciencecareers.org.

SPRING | Year 2 Preliminary Examination Purpose: Assess student’s readiness to ascend to PhD candidacy. Protocol: Students will meet with Preliminary Examination Committee. Students should submit a written proposal 14 days before the meeting and prepare a concise research presentation of 8 slides (approx. 15 min) to be given during the meeting. After the presentation, the Chair will open the meeting to questions (approx. 45–60 min). The Chair of the Preliminary Examination Committee should complete the Committee Meeting Report with input from the other Committee Members. Recommended duration: 1.5 hours. Forms: Preliminary Examination Checklist [OGAPS] Report of the Preliminary Examination [OGAPS] Research Proposal Approval Form for Thesis, Dissertation, or Record of Study [OGAPS] Committee Meeting Report [BCBP] Laboratory Notebook(s)

OGAPS – Degree Plan Purpose: Formally establish a Degree Plan with the Office of Graduate and Professional Studies. Protocol: Students must submit a Degree Plan through https://ogsdpss.tamu.edu.

Years 3 and 4 Annual Committee Meetings Purpose: Assess research and professional development progress. Protocol: Students will meet with Thesis Committee. The Thesis Advisor should complete the Advisor Report before the meeting. Students should prepare a concise research presentation of 8 slides (approx. 15 19 Return to Table of Contents. minutes) to be given during the meeting. After the presentation, the Chair will open the meeting to questions (approx. 30 min). The Committee should meet with the student in the absence of the Thesis Advisor, and with the Thesis Advisor in the absence of the student (approx. 5–10 min each). The Chair of the Thesis Committee should complete the Committee Meeting Report with input from the Thesis Advisor and Committee Members. Recommended duration: 1 hour. At least one Committee Meeting should be held per academic year. Forms: Committee Meeting Report [BCBP, previous scores will be completed by Graduate Office prior to meeting; you must inform Dr. Justine deGruyter of your committee meeting dates] Advisor Report [BCBP] Laboratory Notebook(s) CV

Year 5 and Beyond Thesis Defense Purpose: Establish an exit strategy. Protocol: Students will meet with Thesis Committee. The Thesis Advisor should complete the Thesis Advisor Report before the meeting. Students should submit a thesis outline 14 days before the meeting and prepare a concise research presentation of 8 slides (approx. 15 minutes) to be given during the meeting. After the presentation, the Chair will open the meeting to questions. The Committee should meet with the student in the absence of the Thesis Advisor, and with the Thesis Advisor in the absence of the student. Recommended duration: 1 hour. Forms: Thesis Outline [template provided] Committee Meeting Report [BCBP, previous scores should be completed by Graduate Office prior to meeting] Advisor Report [BCBP] Laboratory Notebook(s) CV Thesis Defense Purpose: Defense of Ph.D. thesis. Protocol: Students will meet with Thesis Committee. Students should prepare a research presentation (approx. 45 minutes) to be given at a public forum. After the presentation, the Chair will open the meeting to public questions. The Chair will then close the public session. The Chair will open the private session to Committee questions. The written thesis should be given to the Committee for review. Once approved, the student should submit the thesis to OGAPS. All OGAPS guidelines for thesis submissions should be carefully reviewed.

Forms: Request and Announcement of the Final Examination [OGAPS; should be submitted at least 10 working days prior to the defense date] Written Dissertation (Ph.D., Dr. PH) or Record of Study (Ed.D, D.En.) Approval Form Thesis, Dissertation, and Record of Study Copyright and Availability Form [OGAPS] Report of the Final Examination [OGAPS, sent directly to PI; the student should not handle the signed document at any time] 20 Return to Table of Contents.

Master of Science Degree Students may elect to pursue a thesis or non-thesis Master of Science (M.S.) degree in Biochemistry, pending approval of the research advisor and Thesis Committee. M.S. students are required to successfully complete all BICH core coursework and fulfill all OGAPS requirements.

Thesis Option Students on the thesis track (MS-THO) are guaranteed full stipend support for the duration of thesis research. To fulfill departmental requirements, students must:

▪ Complete a minimum of 32 semester credit hours, including all core coursework and research hours.

21 Return to Table of Contents. ▪ Submit a degree plan for approval by the thesis committee and OGAPS. Degree plans must be submitted to OGAPS the semester before the intended graduation date. ▪ Submit a thesis proposal for approval by the thesis advisory committee and Associate Head of the Graduate Program.

▪ Schedule and pass an oral defense of the thesis.

▪ Submit a written thesis for approval by the thesis advisory committee.

▪ Provide two copies of an approved written/signed thesis to the OGAPS Thesis Office.

▪ Receive thesis approval by the OGAPS Thesis Office.

th th Domestic Students: Degree level changes must be made no later than the 20 day of class (FA/SP) or the 4 day of class (SU).

th International Students: Degree level changes must be made no later than the 12 day of class (FA/SP) or th the 4 day of class (SU). International students must have all immigration documentation corrected with the th International Student Services (ISS) office no later than the 15 day of class.

Non-Thesis Option Neither a written thesis nor an oral defense is required for the non-thesis track (MS-NTO). Once the degree change petition has been approved, students may not enroll in BICH 691 (Research); credits previously earned for BICH 691 are not applied to the total credit hour requirement. Two credit hours of BICH 690 (Theory of Research) may be applied, though any combination of credits earned for BICH 684, BICH 685, BICH 690, and BICH 695 may not exceed 25% of the total credit hour requirement. To fulfill departmental requirements, students must:

▪ Complete a minimum of 36 semester credit hours, including all core coursework. The thesis committee must approve any elective coursework.

▪ Pass a final comprehensive exam. No examination may be held prior to the mid-point of the semester in which the student will complete all remaining coursework.

TAMU Policies

Petitions All requests to change an approved Degree Plan – including thesis committee restructuring and coursework adjustments – must be submitted by electronic petition. Petitions must be approved electronically by all

22 Return to Table of Contents. members of your thesis committee, the Associate Head of the Graduate Program, and the Graduate Program Coordinator.

Continuous Registration Requirement Per University policy, all full-time graduate students supported by an assistantship must register for 9 credit hours every Fall and Spring semesters, and 6 credit hours every Summer. You must also maintain a 3.0 GPR for the duration of study. If you fail to register for the required credit hours, your graduate assistantship will be terminated, and your out-of-state tuition waiver will be revoked. Please coordinate with the Graduate Office to ensure compliance.

Tuition and Fees Graduate teaching assistants, research assistants, and non-teaching students who are employed at least one-half time at a Texas institution of higher education – with job duties that are related to teaching or research in an academic program associated with their field of study – are entitled to resident tuition and fees for themselves, their spouse, and their children. Biochemistry graduate students are limited to 7 years (or 130 doctoral hours) of resident tuition.

Paychecks Paychecks for the preceding month are posted on the first weekday of the following month (e.g., your May paycheck will arrive on the first weekday in June). Note that your first paycheck will be posted the first weekday in October; please prepare your finances accordingly.

Right to Review Records You have the right to review your education records, except those excluded by law (e.g., parents’ financial statements, physician records). Various records are maintained by BCBP, the Admissions and Records Office, Student Financial Aid, the Career Center, and the Dean of the College of Agriculture and Life Sciences.

Code of Conduct The Aggie Code of Honor affirms that an aggie does not lie, cheat or steal, or tolerate those who do. Academic dishonesty is any form, including cheating, plagiarism, deception of effort, or unauthorized assistance, may result in a failing grade and/or suspension or dismissal from the Graduate Program. Manipulation or falsification of data is grounds for immediate dismissal.

Ownership of Data All data generated in the course of your study is the property of TAMU through the Principal Investigator. NIH guidelines require that data and lab notebooks remain with TAMU and the Principal Investigator. Final decisions on publication and authorship are made by the Principal Investigator. Leave of Absence Under unusual circumstances, a student may petition for a leave of absence through DPSS. The entire thesis committee (if formed) and the Department Head or the Chair of the Intercollegiate Faculty (if appropriate) must approve and route the petition to OGAPS. If the Associate Provost for Graduate and Professional Studies approves the petition, the registration requirement will be lifted during the period of leave. Leave will be granted only under conditions that require the suspension of all activities associated with pursuing the degree.

23 Return to Table of Contents. For certain types of approved leave, such as medical, the time period for the completion of the degree will stop with the leave and begin when the student returns to the program. Other types of leave may not stop the time limit for the degree. Please refer to the OGAPS regulations for degree time limits. A leave of absence is granted for one year. In cases of extenuating circumstances, the leave of absence can be extended by the student’s committee and the Associate Provost for Graduate and Professional Studies. A student who returns to the University after an approved leave of absence will not be required to apply for readmission. International students should consult ISS to determine if/how a Leave of Absence may impact their stay or reentry into the U.S.

Fellowships and Awards While you are guaranteed funding for the duration of your studies, we encourage you to seek additional fellowships and awards. If you receive an external scholarship or fellowship, your departmental support may be renegotiated, and you may be eligible for an increased stipend.

External Fellowships All fellowships have a U.S. citizen / permanent resident requirement, unless otherwise noted. Finally, the University of Illinois Graduate College Fellowship Finder offers a comprehensive database of graduate fellowships and awards. 24 Return to Table of Contents.

Fellowship Description Deadline DOE CSGF The Department of Energy Computational Science Graduate January Fellowship provides full tuition and fees, an annual $38,000 stipend, and an annual $1000 travel allowance for up to 4 years. DoD SMART The Department of Defense Science Mathematics and Research for December Transformation includes full tuition and fees, an annual stipend of $25,000–$38,000, health insurance allowance of up to $1200, and an annual $1000 travel allowance for up to 5 years. It also includes employment by DoD upon graduation Ford Foundation The National Academy of Sciences, Engineering, and Medicine on November behalf of the Ford Foundation provides 3 years of support including an annual stipend of $27,000. NSF – GRFP NSF Graduate Research Fellowship Program provides up to 3 years October of support including $34,000 annual stipend, and $12,000 yearly tuition and fees allowance. NDSEG National Defense Science and Engineering Fellowship Program December provides up to 3 years of support including a $3,200 monthly stipend and an annual health insurance allowance of $1,200. Smithsonian Programs Smithsonian offers program in Genomics and Medical Science. They Varies also offer the Smithsonian Institution Fellowship Program, and Secretary’s Distinguished Research Fellowship. See fellowship web pages for award amounts and durations. Hertz Foundation Hertz Foundation provides up to 5 years of support, including a October Fellowship stipend of $34,000 / 9 months; this fellowship can be accepted in the same term as other fellowships. AHA Fellowship American Heart Association fellowship provides 1–2 years of support August including an annual stipend of $24,816, $4,200 a year towards health insurance, and $2,000 a year of project support. National Academy of National Academy of Sciences, Engineering, and Medicine Science March Sciences, Engineering, Policy Fellowship for students who have finished or are finishing and Medicine Science their PhD and want to transition into science policy. This fellowship Policy Fellowship includes an annual stipend of $55,000–$60,000, $5,000 towards professional development and additional funding to attend conferences. NIH Kirschstein The Ruth L. Kirschstein National Research Service Award Individual April, Fellowship Predoctoral Fellowship to Promote Diversity in Health-Related August, Research (Parent F31 – Diversity) provides up to 5 years of support December that includes an annual stipend of $24,324, tuition and fees, and project support of $3,100–$4,200. NIH GPP Graduate Professional Partnership program where part or all of No dissertation research is conducted under PI at NIH. Funding must be deadline provided by the PI you work under.

25 Return to Table of Contents. Dissertation Fellowships

Fellowship Description Deadline AAUW AAUW American/International Dissertation fellowships for November international and domestic women provide $20,000 for the year of dissertation writing. Dissertation The TAMU Office of Graduate and Professional Studies provides Nov 1 Fellowship $1,600 monthly stipend and up to $2,634 for health insurance in order to assist with the writing and organization of the dissertation

TAMU Awards and Fellowships

Fellowship Description Deadline TAMU Distinguished The TAMU Distinguished Dissertation award provides $1000 to a March 2 Dissertation Award recipient of TAMU doctoral degree whose dissertation made a significant and impactful contribution to their discipline. Distinguished Grad The Association of Former Students offers the Distinguished February Student Award Graduate Student Award to a student that exemplifies excellence in research as well excellence in teaching. Recipients are awarded with an engraved watch and framed certificate. U.S. Senator Phil The U.S. Senator Phil Gramm Doctoral Fellowship is awarded to Gramm Doctoral current grad students who exemplify the meaning of scholar/mentor Fellowship through their demonstrated abilities in teaching and research. Montgomery Award The Montgomery Award is given to a student leader whose service April has impacted the TAMU grad student body at large and includes a personalized award plaque and $1000. George W. Kunze The George W. Kunze Endowed Graduate Student Award is given to Endowed Graduate doctoral students near completion of their degree. Student Award

Travel Awards and Fellowships

Fellowship Description Deadline ASM Capstone The American Society for Microbiology Research Capstone March Fellowship Fellowship is a professional development fellowship providing up to $2,000 for underrepresented minorities to attend the ASM Microbe Meeting and the ASM Microbe Academy for Professional Development. ACS Women Chemist The Women Chemists Committee/Eli Lilly Travel Award is given to March 1 Committee and Eli female chemists to present their research at an ACS National or Lilly Travel Award Meeting. Septembe r 15

26 Return to Table of Contents. OGAPS Travel Awards The Office of Graduate and Professional Studies Travel Awards are of See varying amounts for both domestic and international travel website

Appendix | Recommended Electives and Journal Clubs A non-comprehensive list of recommended elective courses is provided; you may choose elective courses that are not listed, pending Advisory Committee approval. Note that not all classes are taught every semester. At least 3 of the 6 elective credits must be at the 600 level. In preparation for your Advisory Meetings, be sure to review the course description, prerequisite requirements, and current offerings for each elective that you are considering. BIOCHEMISTRY BICH 464 Bacteriophage Genomics 3 cr. BICH 628 Computational Biology 3 cr. BICH 650 Genomics 3 cr. BICH 654 Structural Biochemistry 3 cr. BICH 655 Crystallography Methods 3 cr. BICH 656 RNA Biology 3 cr. 27 Return to Table of Contents. BICH 657 Introduction to Structural Biology 1 cr. BICH 661 Advanced Genome Annotation with Ontologies 1 cr. BICH 662 Eukaryotic Transcription 1 cr. BICH 664 Fluorescence Spectroscopy 1 cr. BICH 665 Biochemical Kinetics 1 cr. BICH 667 Molecular Probes 1 cr. BICH 689 Special Topics X cr.

BIOLOGY BIOL 601 Biological Clocks 3 cr. BIOL 602 Transmission Electron Microscopy 3 cr. BIOL 603 Advanced TEM Methodologies in Life and Material Sciences 3 cr. BIOL 604 Fundamentals of Scanning Electron Microscopy 2 cr. BIOL 606 Microbial Genetics 3 cr. BIOL 608 Light Microscopy 3 cr. BICH 611 Developmental Genetics 3 cr. BIOL 613 Cell Biology 3 cr. BIOL 635 Plant Molecular Biology 3 cr. BIOL 636 Plant Cell Biology 3 cr. BIOL 644 Neural Development 3 cr. BIOL 647 Digital Biology 4 cr. BIOL 651 Bioinformatics 3 cr. BIOL 689 Special Topics X cr.

CHEMISTRY CHEM Organic Chemistry III X cr. 446 CHEM Modern Chromatographic Separation Methods 3 cr. 603 CHEM Organic Reactions 3 cr. 610 CHEM Organic Synthesis 3 cr. 615 CHEM NMR Spectroscopy 3 cr. 618 CHEM Analytical Spectroscopy 3 cr. 619 CHEM Chemical Kinetics 3 cr. 621 CHEM Principles of Biological Chemistry 3 cr. 627 CHEM Coordination and Bioinorganic Chemistry 3 cr. 628 CHEM Principles of Inorganic Chemistry 3 cr. 633

28 Return to Table of Contents. CHEM Introduction to X-ray Diffraction Methods 3 cr. 635 CHEM Structural Inorganic Chemistry 3 cr. 641 CHEM Physical Organic Chemistry 3 cr. 646 CHEM Molecular Modeling 3 cr. 658 CHEM Bioorganic Reaction Mechanisms 3 cr. 672 CHEM Special Topics X cr. 689

GENETICS GENE Genetics 4 cr. 603 GENE Analysis of Gene Expression 2 cr. 626 GENE Biochemical Genetics 3 cr. 631 GENE Analysis of Complex Genomes 3 cr. 654 GENE Special Topics X cr. 689

PHYSICS PHYS Thermodynamics and State Mechanics 4 cr. 408 PHYS Quantum Mechanics I 3 cr. 412 PHYS Special Topics X cr. 689

STATISTICS STAT 645 Applied Biostatistics and Data Analysis 3 cr. STAT 651 Statistics in Research I 3 cr. STAT 652 Statistics in Research II 3 cr. STAT 661 Statistical Genetics 3 cr.

VETERINARY MICROBIOLOGY VTMI 601 Pathobiology 5 cr. VTMI 663 Molecular Biology of Viruses 3 cr.

VETERINARY PHYSIOLOGY & PHARMACOLOGY

29 Return to Table of Contents. VTPP 676 Genetic and Molecular Toxicology 3 cr. VTPP 677 Fluorescence Detection: Steady State, Time Resolved, and Imaging 4 cr.

Recommended Journal Clubs are listed below. You are required to take Journal Club every Fall/Spring semester from your second year on. JOURNAL CLUBS BICH 625 Nucleic Acids–Protein Interactions 1 cr. BICH 671 Macromolecular Folding and Design 1 cr. BICH 672 Biological Membranes 1 cr. BICH 673 Gene Expression 1 cr. BICH 674 Protein Folding and Stability 1 cr. BICH 675 Plant Biochemistry and Genomics 1 cr. BICH 676 Bacteriophage Biology 1 cr. BICH 677 Chemical Genetics and Drug Discovery 1 cr. BICH 678 Metal Ions 1 cr.

Ph.D. Degree Plan (NEW) FA – Year 1 BICH 603 Principles of Biochemistry and Biophysics 3 cr. BICH 608 Critical Analysis of the Biochemistry Literature 2 cr. BICH 631 Principles of Molecular Genetics 3 cr. BICH 689 Application of Scientific Values 1 cr.

SP – Year 1 BICH 6XX Advanced Modules* 6 cr. BICH 690 Theory of Biochemistry Research 2 cr. BICH 697 Teaching 1 cr. *Students must take six 1-credit modules. SU – Year 1 BICH 691 Research 6 cr.

FA – Year 2 ELECTIVE Elective (2) 6 cr. BICH 6XX Journal Club 1 cr. BICH 691 Research 1 cr. BICH 697 Teaching 1 cr.

SP – Year 2 BICH 681 Written Communication 2 cr. BICH 689 Oral Communication 1 cr. BICH 6XX Journal Club 1 cr. 30 Return to Table of Contents. BICH 690 Theory of Biochemistry Research 2 cr. BICH 691 Research 3 cr.

SU – Year 2 and Beyond BICH 6XX Journal Club XX cr. BICH 690 Theory of Biochemistry Research XX cr. BICH 691 Research XX cr.

TOTAL = 96 credit hours (minimum)

Rotations, Advisory Committee Meetings, and Preliminary Examination Schedule:

Ph.D. Degree Plan (OLD)

FA – Year 1 grade BICH 603 Principles of Biochemistry and Biophysics 3 cr. BICH 608 Critical Analysis of the Biochemical Literature 2 cr. BICH 689 Principles of Molecular Genetics 3 cr. BICH 689 Application of Scientific Values 1 cr. Rotation 1 Rotation 2 Rotation 3

SP – Year 1 BICH 681 Seminar 1 cr. BICH 681 Seminar 1 cr. BICH 6XX Module: 1 cr. BICH 6XX Module: 1 cr. BICH 6XX Module: 1 cr. BICH 6XX Module: 1 cr. BICH 6XX Module: 1 cr. BICH 6XX Module: 1 cr. BICH 685 Directed Studies 1 cr.

31 Return to Table of Contents. SU – Year 1 BICH 691 Research 6 cr.

FA – Year 2 BICH 6XX Journal Club 1 cr. BICH 690 Theory of Biochemistry Research 2 cr. BICH 691 Research 5 cr. BICH 697 Teaching 1 cr.

SP – Year 2 ELECTIVE Elective 3 cr. BICH 6XX Journal Club 1 cr. BICH 690 Theory of Biochemistry Research 2 cr. BICH 691 Research 2 cr. BICH 697 Teaching 1 cr. OGAPS – Degree Plan Submission

SU – Year 2 BICH 691 Research 6 cr.

FA – Year 3 ELECTIVE Elective 3 cr. BICH 6XX Journal Club 1 cr. BICH 690 Theory of Biochemistry Research 2 cr. BICH 691 Research 3 cr.

SP – Year 3 BICH 6XX Journal Club 1 cr. BICH 690 Theory of Biochemistry Research 2 cr. BICH 691 Research 6 cr. Preliminary Examination

SU – Year 3 and Beyond BICH 6XX Journal Club X cr. BICH 690 Theory of Biochemistry Research X cr. BICH 691 Research X cr. Annual Committee Meetings Thesis Defense

TOTAL = 96 credit hours (minimum)

32 Return to Table of Contents. Appendix H – Graduate Recruiting Weekend and Life Sciences Symposium

All Zoom links can be found pinned in the corresponding Slack channel. A friendly reminder to keep your video on for the duration. You can find more information about our faculty and department at our website: bcbp.tamu.edu. Thursday, January 28

Slack channel: # session-1-welcome

1:45pm–2:00pm Event Overview Dr. Justine deGruyter, BCBP Graduate Program Coordinator, will provide an overview of the day’s events and offer platform navigation tips.

2:00pm–3:00pm Welcome Remarks Prof. Josh Wand, BCBP Department Head, will welcome you to the department and present our prestigious John Mack Prescott Award to a current graduate student.

Prof. Jean-Philippe Pellois, BCBP Associate Head, will walk you through a typical degree plan and help you understand what it means to be a TAMU graduate student.

3:00pm–3:30pm 360° Campus Tours Use your new VR viewers to explore the scenic TAMU campus and impressive research facilities.

Slack channel: # session-2-bcbp-research

3:30pm–4:15pm Research Talks Learn about ongoing research from current BCBP and GENE graduate students and faculty.

4:15pm–5:00pm Break and Q&A Take a short break or join us in a live Slack Q&A session with current graduate students. Eager to learn about housing options, first-year coursework, or a typical day-in-the-life? This is your chance to ask!

Slack channel: # session-3-poster-session

5:00pm–7:00pm Poster Session Enjoy your dinner (on us!) while you join the poster session. You are scheduled to visit the following breakout room “posters”: 5:00pm–5:20pm – Glasner Lab 5:25pm–5:45pm – Igumenova Lab 5:50pm–6:10pm – Raushel Lab 6:15pm–6:35pm – Meek Lab 6:40pm–7:00pm – Zeng Lab

EXAMPLE

Friday, January 29

Slack channel: # session-4-research-discussions

1:45pm–2:00pm Event Overview Once again, Dr. Justine deGruyter will walk you through the day’s events and offer platform navigation tips.

2:00pm–4:00pm Faculty Research Chat one-on-one with five of our esteemed faculty members. Be Discussions prepared to present a brief (5-minute, 3 slide) overview of your research experience and interests. You are scheduled to meet with the following professors: 2:00pm–2:20pm – A. Joshua Wand, PhD 2:25pm–2:45pm – Vytas Bankaitis, PhD 2:50pm–3:10pm – Jae-Hyun Cho, PhD 3:15pm–3:35pm – Hays Rye, PhD 3:40pm–4:00pm – Tim Devarenne, PhD

Slack channel: # session-5-panel-discussion

4:00pm–5:00pm Panel Discussion Hear from Associate Provost for Graduate and Professional Studies, Dr. Karen Butler-Purry; the Vice President for Research, Dr. Mark A. Barteau; BCBP Department Head, Dr. A. Joshua Wand; and a few other research-active faculty members in a panel discussion. Be prepared to contribute discussion questions.

5:00pm–5:30pm Featured Speaker Meet NASA-rocket-scientist-turned-comedian and TAMU Professor Shayla Rivera.

Slack channel: # session-6-pub-trivia

5:30pm–7:30pm Pub Trivia & Happy Hour Enjoy your dinner (and drinks!) as we join our current graduate students for a rousing game of pub-style trivia.

BCBP Graduate Recruitment Event | January 28–29, 2021 Thursday Friday

1:45pm CT | Event Overview 1:45pm CT | Event Overview 2pm CT | Welcome Remarks 2pm CT | Faculty Research Discussions

3pm CT | 360° Campus Tours

3:30pm CT | Student Talks

4pm CT | Narrative Videos + Q&A 4pm CT | Panel Discussion

4:30pm CT | Break

5pm CT | Poster Session & Dinner 5pm CT | Featured Speaker

5:30pm CT | Pub Trivia & Dinner

7pm CT | End of Day

7:30pm CT | End of Day Appendix I – Graduate Program | Degree Plan

Ph.D. Degree Plan FA – Year 1 BICH 603 Principles of Biochemistry and Biophysics 3 cr. BICH 608 Critical Analysis of the Biochemistry Literature 2 cr. BICH 631 Principles of Molecular Genetics 3 cr. BICH 689 Application of Scientific Values 1 cr.

SP – Year 1 BICH 6XX Advanced Modules* 6 cr. BICH 690 Theory of Biochemistry Research 2 cr. BICH 697 Teaching 1 cr. *Students must take six 1-credit modules. SU – Year 1 BICH 691 Research 6 cr.

FA – Year 2 ELECTIVE Elective (2) 6 cr. BICH 6XX Journal Club 1 cr. BICH 691 Research 1 cr. BICH 697 Teaching 1 cr.

SP – Year 2 BICH 681 Written Communication 2 cr. BICH 689 Oral Communication 1 cr. BICH 6XX Journal Club 1 cr. BICH 690 Theory of Biochemistry Research 2 cr. BICH 691 Research 3 cr.

SU – Year 2 and Beyond BICH 6XX Journal Club XX cr. BICH 690 Theory of Biochemistry Research XX cr. BICH 691 Research XX cr.

TOTAL = 96 credit hours (minimum)

Rotations, Advisory Committee Meetings, and Preliminary Examination Schedule:

Updated SU2020 Appendix J – Graduate Program | Summary of Courses Core Courses

Course Title Instructor Description BICH 603 Principles of Biochemistry Rye A modern, quantitative, analytical, and and Biophysics model-building-based approach to expand knowledge of the biochemical and biophysical properties of macromolecules found in living matter, including proteins, lips, carbohydrates, and nucleic acids BICH 608 Critical Analysis of the Young Reading and presentation of original articles in Biochemistry Literature Igumenova biochemistry and related fields to enhance understanding of experimental logic and scientific communication BICH 631 Biochemical Genetics Threadgill Genetic control of cellular metabolism; mechanism Shippen of gene action; gene–enzyme relationships; He regulation of gene expression; structure and organization of genomes; biochemical manipulation and characterization of genetic molecules BICH 689 Application of Scientific Herman Explores the common values of science, including Values curiosity, humility, honesty, objectivity, rigor, collegiality, and transparency; responsible conduct of research; and career planning BICH 689 Written Communication Tommos New course. Prepares students for the written Research Proposal component of the Preliminary Examination. BICH 689 Oral Communication Pellois New course. Prepares students for the oral component of the Preliminary Examination.

Modular Courses

Course Title Instructor Description BICH 657 Introduction to Structural Li Protein expression, purification, characterization, Biology crystallization and structural determination by X-ray crystallography; includes an 8-hour workshop on crystallography BICH 689 Introductory Curve Fitting Cho Analysis of thermodynamics and kinetics of various with Regression Analysis biochemical processes; introduction to basic concepts in curve fitting and interpretation of fit parameters BICH 689 Metabolism Gohil Explores eukaryotic metabolism with emphasis on catabolic and anabolic pathways of major macromolecules BICH 689 Biological Nuclear Magnetic Igumenova Explores the theoretical and practical aspects of Resonance Spectroscopy NMR spectroscopy, including sample preparation, data acquisition, processing and analysis BICH 689 Cryo-EM of Molecular J. Zhang Explores a range of topics in structural biology, with Machines emphasis on cryo-electron microscopy; includes introduction to electronic microscopic and computational techniques used to visualize three-dimensional structures of macromolecules BICH 689 Optical Spectroscopy Kurouski Introduces major optical spectroscopy techniques; understanding fundamental physical principles of molecular absorption, fluorescence, and vibrational spectroscopy; interpretation of spectroscopic request and predict molecular structures

Journal Clubs

Course Title Instructor Description BICH 671 Macromolecular Folding Bankaitis Oral presentations and discussions in the general and Design area of biomolecular structure, folding, function, and design BICH 674 Protein Folding and Stability Rye Selected topics from recent literature in the general areas of protein folding, structure, and stability BICH 675 Plant Biochemistry and Mullet Overview of current literature dealing with plant Genomics Devarenne biochemistry/genomics; biochemistry topics will include the function of protein–protein interactions related to plant specific processes such as plant–pathogen interactions; genomics topics will focus on current analysis of plant genomes and how the derived information is being utilized to elucidate biochemical pathways BICH 676 Bacteriophage Biology Young Oral presentation and discussion in the general area of the viruses of microbes and bacteria’ literature review with a broad scope, from basic molecular biology of phages to practical applications of microbial virus technology BICH 677 Chemical Genetics and Sacchettini Review, discuss, and present scientific literature Drug Discovery studies based on the usage of small molecules to alter protein function

Elective Courses

A non-comprehensive list of recommended elective courses is provided. Students may choose elective courses that are not listed, pending Advisory Committee approval. The courses shown here were/are offered in the 19–20 or 20–21 academic years, though not every course is offered every semester; the most recent instructor is listed. At least 3 of the 6 elective credits must be at the 600 level.

Course Title Instructor Description BICH 464 Bacteriophage Genomics Young Examines the latest technologies in genomic Gill analysis by sequencing and annotating the genomes of novel bacterial viruses (phage); generates real data which will be submitted to the NIH/NCBI public database; including phage biology and potential uses BICH 654 Structural Biochemistry Sacchettini Basic physics of X-ray diffraction, crystal structure methods, introduction to structural databases, molecular geometry, and molecular modeling BICH 655 Crystallographic Methods Sacchettini The practice of X-ray diffraction in the study of biomolecules; solving protein crystal structures BICH 656 RNA World X. Zhang Emphasis on newly discovered RNA-mediated Cruz-Reye processes and regulation; range of topics in modern s RNA biology include RNA silencing; RNA-guided epigenetic regulation, CRISPR/Cas immunity and genome editing, telomerase biogenesis, riboswitches, exosome and editosome; application of RNA biology in medicine and biotechnology BICH 665 Biochemical Kinetics Reinhart Theoretical principles and practical approaches to analysis of chemical kinetics with specific examples of applications to biochemistry and biochemical investigations

Course Title Instructor Description BIOL 606 Microbial Genetics Sorg Basic understanding of microbial genetic systems and how genetic analyses can be used to investigate fundamental biological processes in bacteria BIOL 608 Light Microscopy Aufderheide Provides biologists, material scientists, and Nan students from other disciplines with the theoretical Vitha background and practical techniques of sample preparation, operation of light microscopes, as well as image acquisition and processing; individual instruction which facilitates the completion of their research projects involving light microscopic techniques BIOL 611 Developmental Genetics Riley Major paradigms of eukaryotic gene regulation in terms of the role of gene expression during ontogeny and the effect of dysfunction in these processes on the neoplastic state BIOL 613 Cell Biology Ryan Consideration of the eukaryotic cell as a functional, Garcia integrated unit in living organisms including structure, composition, function, and biogenesis of subcellular components; dynamic processes and interactions of cells, including division, communication, and death; experimental approaches in modern cell biology and selected applications of experimental cell biology to problems in medicine BIOL 635 Plant Molecular Biology Pepper Molecular aspects of plant growth, development, Versaw reproduction, and evolution, emphasizing structure, function, regulation, interaction, and manipulation of plant genes; practical applications of plant molecular biology BIOL 644 Neural Development Dulin Classical and current research literature to explore the major events in the development of a nervous system, including topics ranging from neurogenesis to synapse information BIOL 651 Bioinformatics Lockless Introduction to applications related to information processing in biological research with practical training exercises; includes internet databases, sequence alignment, motif prediction, gene and prometer prediction, phylogenetic analysis, protein structure classification, analysis and prediction, genome annotation, assembly and comparative analysis, and proteomics analysis

Course Title Instructor Description CHEM Organic Chemistry III Michaudel Principles and applications of organic chemistry for 446 students majoring in chemistry, chemical engineering, materials science, biological, and physical science; emphasis on chemical reactivity, mechanistic chemistry, and synthesis CHEM Organic Reactions Thomas Introduction to mechanisms and scope of the basic 610 organic reaction types as applied to major functional groups CHEM Principles of Inorganic Nippe General principles of inorganic chemistry treated 633 Chemistry with a view to applications in other subfields of chemistry CHEM Introduction to X-ray Zhou Fundamentals of diffraction theory by crystals and 635 Diffraction Methods the solution of crystal structures using this methodology CHEM Structural Inorganic Hall Introduction to chemical bonding; ionic, covalent, 641 Chemistry coordinate, and hydrogen bonding; relationship of molecular orbital and ligand field theories to experimental studies of the electronic structure of inorganic molecules CHEM Physical Organic Chemistry Fang A detailed introduction to the theory and principles 646 of organic chemistry; bonding and structure in organic chemistry, stereochemistry, reactive intermediates in organic chemistry, and transition state theory; kinetics and thermodynamic approaches CHEM Molecular Modeling Perez An introduction to molecular modeling with an 658 emphasis on quantum level calculations; lectures cover the basic theory behind the calculations and lab work will focus on the practical application of modern computational chemistry codes CHEM Bioorganic Reaction Raushel Proposed mechanisms of action of various enzymes 672 Mechanisms and coenzymes from the “model systems” approach; new developments, theory, and established mechanisms

Course Title Instructor Description GENE Genetics Magill Development of fundamental concepts related to the 603 structure, function, organization, transmission, and distribution of genetic material GENE Analysis of Complex Zhang History and current status of genetic and molecular 654 Genomes analysis of higher eukaryotic genomes; coverage of techniques for dissection of genomes into manageable parts; investigations in genetics, breeding, and evolution; emphasis on quantitative inheritance, genetic mapping, physical mapping, map-based cloning, with examples drawn from a wide range of organisms

Course Title Instructor Description PHYS 408 Thermodynamics and State Agnolet Statistical methods, macroscopic thermodynamics, Mechanics kinetic theory, black body radiation; Maxwell-Boltzmann, Bose-Einstein, and Fermi-Dirac statistics PHYS 412 Quantum Mechanics I Weimer Postulates of wave mechanics; wave packets; harmonic oscillator; central field problem; hydrogen atom; approximation methods

Course Title Instructor Description STAT 645 Applied Biostatistics and Sinha Survey of crucial topics in biostatistics; application Data Analysis of regression in biostatistics; analysis of correlated data; logistic and Poisson regression for binary or count data; survival analysis for censored outcomes; design and analysis of clinical trials; sample size calculation by simulation; bootstrap techniques for assessing statistical significance; data analysis using R STAT 651 Statistics in Research I Chen For graduate students in other disciplines; Chakraborty non-calculus exposition of the concepts, methods, Akleman and usage of statistical data analysis; T-tests; analysis of variance and linear regression STAT 652 Statistics in Research II Akleman Continuation of STAT 651; concepts of experimental design, individual treatment comparisons, randomized blocks and factorial experiments, multiple regression; Chi-squared tests and a brief introduction to covariance, non-parametric methods, and sample surveys

Course Title Instructor Description VTPP 676 Genetic and Molecular Tian Mechanisms of toxicant-induced target organ Toxicology toxicity with emphasis on molecular control of mammalian and cell growth differentiation

Appendix K-Graduate Program | Committee Meeting Protocols and Evaluation Forms

Ph.D. Meeting Protocols Years 1 and 2 Advisory Committee Meeting Purpose: Guide pre-candidacy students through their first- and second-year coursework, rotation, and thesis committee selections.

Protocol: Students will meet with a standing Advisory Committee. The Advisory Committee will recommend elective coursework and offer suggestions for rotation selections based on student research interests. After meeting 4, the student should complete an Individual Development Plan; proof of submission should be sent to the Graduate Office.

Forms: Individual Development Plan (IDP) at http://myidp.sciencecareers.org.

SP – Year 2 Preliminary Examination Purpose: Assess student’s readiness to ascend to PhD candidacy.

Protocol: Students will meet with Preliminary Examination Committee. Students should submit a written proposal 14 days before the meeting and prepare a concise research presentation of 8 slides (approx. 15 min) to be given during the meeting. After the presentation, the Chair will open the meeting to questions (approx. 45–60 min). The Chair of the Preliminary Examination Committee should complete the Committee Meeting Report with input from the other Committee Members. Recommended duration: 1.5 hours.

Forms: Preliminary Examination Checklist [OGAPS] Report of the Preliminary Examination [OGAPS] Research Proposal Approval Form for Thesis, Dissertation, or Record of Study [OGAPS] Committee Meeting Report Laboratory Notebook(s)

SU – Year 2 OGAPS – Degree Plan Purpose: Formally establish a Degree Plan with the Office of Graduate and Professional Studies.

Protocol: Students must submit a Degree Plan through https://ogsdpss.tamu.edu.

Years 3 and 4 Annual Committee Meetings Purpose: Assess research and professional development progress.

Protocol: Students will meet with Thesis Committee. The Thesis Advisor should complete the Thesis Advisor Report before the meeting. Students should prepare a concise research presentation of 8 slides (approx. 15 minutes) to be given during the meeting. After the presentation, the Chair will open the meeting to questions (approx. 30 min). The Committee should meet with the student in the absence of the Thesis Advisor, and with the Thesis Advisor in the absence of the student (approx. 5–10 min each). The Chair of the Thesis Committee should complete the Committee Meeting Report with input from the Thesis Advisor and Committee Members. Recommended duration: 1 hour. At least one Committee Meeting should be held per academic year.

Forms: Committee Meeting Report [previous scores should be completed by Graduate Office prior to meeting] Updated SU2020

Thesis Advisor Report Laboratory Notebook(s) CV

Year 5 and Beyond Thesis Defense Purpose: Establish an exit strategy.

Protocol: Students will meet with Thesis Committee. The Thesis Advisor should complete the Thesis Advisor Report before the meeting. Students should submit a thesis outline 14 days before the meeting and prepare a concise research presentation of 8 slides (approx. 15 minutes) to be given during the meeting. After the presentation, the Chair will open the meeting to questions. The Committee should meet with the student in the absence of the Thesis Advisor, and with the Thesis Advisor in the absence of the student. Recommended duration: 1 hour.

Forms: Thesis Outline [template provided] Committee Meeting Report [previous scores should be completed by Graduate Office prior to meeting] Thesis Advisor Report Laboratory Notebook(s) CV

Thesis Defense Purpose: Defense of Ph.D. thesis.

Protocol: Students will meet with Thesis Committee. Students should prepare a research presentation (approx. 45 minutes) to be given at a public forum. After the presentation, the Chair will open the meeting to public questions. The Chair will then close the public session. The Chair will open the private session to Committee questions. The written thesis should be given to the Committee for review. Once approved, the student should submit the thesis to OGAPS. All OGAPS guidelines for thesis submissions should be carefully reviewed.

Updated SU2020

Committee Meeting Report Part 1 (completed by student) Student Name: Student Name Date: Click or tap to enter a date. UIN: Student UIN Date of Last Meeting: Click or tap to enter a date. Matriculation Year: Year (if applicable)

Did you participate in at least one Responsible Conduct in Research (RCR) training or lab meeting Choose an this year? item.

Did you participate in at least one Scientific Rigor and Responsibility (SRR) training or lab Choose an meeting this year? item.

Have you discussed your Individual Development Plan (IDP) with your Thesis Advisor this year? Choose an item.

Have you discussed post-graduation career plans with your Thesis Advisor this year? Choose an item.

Please tally the papers resulting from your thesis work. Published/In press: # Submitted/Under Review: # In preparation: #

Please tally the number of conference presentations you have given during your graduate studies. Poster: # Oral Presentation: #

Committee Members

Chair: Chair Last Name Present? ☐ Member: Member Last Name ☐ Member: Member Last Name ☐ Mentor or Thesis Advisor: Mentor / Thesis Advisor Last Name ☐ Substitute: Substitute Member Name

Part 2 (completed by Committee Chair) Tier 1 | Students should achieve general mastery of these skills (score = 7+) prior to ascension to Candidacy. If the student has not achieved a score of at lest 5 in any Tier 1 category at the Preliminary Examination, remedial action is recommended. Tier 2 | Pre-candidacy students may not have yet achieved mastery of these skills. Candidates should achieve general mastery (score = 7+) prior to the Thesis Defense. Tier 3 | Pre-candidacy / early candidacy students may not have yet achieved mastery of these skills. Candidates should achieve general mastery of these skills (score = 7+) prior to the Thesis Defense.

The mentor / thesis advisor was interviewed in the absence of the student. ☐ The student was interviewed in the absence of the mentor / thesis advisor. ☐

Evaluate the student’s mastery of the following skills (0 –10; 0 = poor, 10 = exceptional).

*Prior scores will be entered by the Graduate Office. Technical

Name the specific changes required to raise these scores.

Enter specific changes.

Professional / Personal Development Tier 1

Employ active listening techniques Choose an Choose an Is the student an active participant in the conversation? item. item. Demonstrate receptivity to new ideas Choose an Choose an Is the student receptive to alternative perspectives? item. item. Overcome and learn from failure Choose an Choose an When describing unsuccessful experiments or paths, is it clear that the student took item. item. lessons from the failure? Display self-motivation and enthusiasm Choose an Choose an Is it clear that the student seeks out learning opportunities? Are they excited about their item. item. work? Thoughtfully consider the broader impacts of their work Choose an Choose an Can the student contextualize their results within the larger field of research? Did they item. item. provide a scholarly background and articulate the significance of their work?

Name the specific changes required to raise these scores.

Enter specific changes.

Tier 2

Speak with well-informed confidence; build slides that are visually accessible and error Choose an Choose an free item. item. Was the talk well paced? Coherent? Reasonably eloquent? Were the slides easy to follow? Was there a clear flow? Draft clear and concise documents; integrate informative figures Choose an Choose an Preliminary Examination / Thesis Outline: Is the written proposal free of obvious item. item. grammatical / spelling errors? Is it coherent? Are the figures appropriate and well described? Do the figures convey data clearly? Ensure equitable division of labor and proper attribution of work Choose an Choose an If the student is working as part of a team, are their contributions clear? Are teammates item. item. appropriately credited? Is the student pulling their own weight? Justify choices Choose an Choose an Can the student provide rational justification for the choices they have made? Can the item. item. student independently recognize the strengths and weaknesses of the choices made?

Name the specific changes required to raise these scores.

Enter specific changes.

Tier 3

Develop cohesive narratives Choose an Choose an Has the student presented a convincing proposal? Has the student integrated item. item. appropriate literature background and presented logical ideas? Adapt presentations to a variety of formats / audiences Choose an Choose an Did all committee members understand the proposal, particularly those outside of the item. item. student’s field? Was it too esoteric? Too simplistic? Display versatility Choose an Choose an Does the student appear to be well rounded? Is the student able to change their point of item. item. view or approach where appropriate? Identify challenges early; critically evaluate and efficiently implement solutions Choose an Choose an Does the student appear to be proactive when faced with a challenge? Does the student item. item. appear to independently anticipate problems and provide creative solutions?

Name the specific changes required to raise these scores.

Enter specific changes.

Defense Date: Previously set date Projected date

Provide an actionable list of items required to stay on track.

Enter list.

Advisor Report Part 1 (completed by student)

Student Name: Student Name Date: Click or tap to enter a date. UIN: Student UIN Date of Last Meeting: Click or tap to enter a date. Matriculation Year: Year Advisor Name: Advisor Last Name

Part 2 (completed by mentor / thesis advisor) Tier 1 | Students should achieve general mastery of these skills (score = 7+) prior to ascension to Candidacy. If the student has not achieved a score of at lest 5 in any Tier 1 category at the Preliminary Examination, remedial action is recommended. Tier 2 | Pre-candidacy students may not have yet achieved mastery of these skills. Candidates should achieve general mastery (score = 7+) prior to the Thesis Defense. Tier 3 | Pre-candidacy / early candidacy students may not have yet achieved mastery of these skills. Candidates should achieve general mastery of these skills (score = 7+) prior to the Thesis Defense.

Evaluate the student’s mastery of the following skills (0 –10; 0 = poor, 10 = exceptional).

*Prior scores will be entered by the Graduate Office. Technical

Independently design and execute experiments Choose an Choose an Is the experimental design likely to lead to meaningful conclusions? Does the student item. item. anticipate different possible outcomes? Does the student include appropriate controls? Analyze and interpret scientific data Choose an Choose an Does the student understand the information contained in the data? Does the student item. item. understand the pros/cons of the technologies used to obtain the data? Does the student apply sound statistical analysis? Contextualize results and draw sound conclusions Choose an Choose an Does the student reach logical conclusions? Does the student tend to want to prove their item. item. model right? Does the student independently identify possible pitfalls and areas of uncertainty? Maintain a detailed laboratory notebook Choose an Choose an Is the laboratory notebook current? Would someone else be able to use the notebooks to item. item. reproduce experiments and results? Demonstrate general laboratory proficiency Choose an Choose an Is the student meticulous in experiments? item. item. Promote a culture of laboratory safety Choose an Choose an Does the student follow procedures safely? Does the student work to maintain the safety item. item. of others? Name the specific changes required to raise these scores.

Enter specific changes.

Professional / Personal Development Tier 1

Display integrity in acquisition / dissemination of scientific data Choose an Choose an Is the student honest in collecting data and reporting results? item. item. Demonstrate receptivity to new ideas and technologies Choose an Choose an Is the student eager and willing to take on new tasks, particularly those that they are item. item. unfamiliar with? Outcome and learn from failure Choose an Choose an Does the student accept failure with a generally good attitude? Is the student resilient? item. item. Constructively participate in collaborative work Choose an Choose an Is the student a team player? Do they appear to be a respectful labmate? Is the student a item. item. mentor to others? Display self-motivation Choose an Choose an Is the student self-motivated? item. item.

Name the specific changes required to raise these scores.

Enter specific changes.

Tier 2

Practice efficient time and resource management Choose an Choose an Is the student efficient? Can you count on them to produce work in a timely manner? item. item. Maintain a focused and productive workflow Choose an Choose an Is it clear that the student in focused when in the lab? item. item. Ensure equitable division of labor Choose an Choose an Is the student a leader in the group? Are they willing to contribute to the general lab item. item. operations, or do they leave it to other students? Demonstrate ownership of their project(s) Choose an Choose an Does the student display independence in their work? item. item. Name the specific changes required to raise these scores.

Enter specific changes.

Tier 3

Display versatility Choose an Choose an Are you confident that this student can go to another lab / institute / etc. and succeed? item. item. Identify challenges early; critically evaluate and efficiently implement solutions Choose an Choose an Does the student appear to be proactive when faced with a challenge? Does the student item. item. appear to independently anticipate problems and provide creative solutions?

Name the specific changes required to raise these scores.

Enter specific changes. Rotation Evaluation Form

1. How well did the student constructively contribute to group meetings and/or individual meetings? (Score 1–5; 1 = Did not attend or seek out meetings; 5 = Was an active participant) Comments?

2. How well did the student respond to constructive feedback? (Score 1–5; 1 = Completely unreceptive; 5 = Accepted feedback thoughtfully and implemented appropriate changes) Comments?

3. How well did the student’s technical skills develop over the course of the rotation period? (Score 1–5; 1 = Still cannot execute basic experiments/techniques; 5 = Demonstrated early mastery over the basic experiments/techniques learned) Comments?

4. How do you rate the student’s demonstrated regard for personal and laboratory safety? (Score 1–5; 1 = Refused to abide standard lab and/or COVID safety protocols; 5 = Demonstrated a clear commitment to best practices in safety) Comments?

5. How do you rate the student’s record keeping? (Score 1–5; 1 = Did not keep records; 5 = Kept meticulous, well-organized records that could be used for experimental reproduction) Comments?

6. How well did the student appear to understand the rotation project? (Score 1–5; 1 = Did not appear to understand, even at a fundamental level; 5 = Appeared to have a firm grasp on both the “big picture” and project intricacies) Comments?

7. How likely are you to accept this student as a permanent addition to your group? (Score 1–5; 1 = Would not take this student, even if they were free; 5 = Would enthusiastically recruit this student to my group) Comments? Appendix L - BCBP Seminar Series 2014 - 2021

2014 Feb 05 KC Huang, Department of Bioengineering and Microbiology & Immunology and Biochemistry, Stanford University “Mapping the structural dynamics of cytoskeletal filaments onto behavior”

Feb 12 Jan Skotheim, Department of Biology, Stanford University “Cell Size Control”

Feb 19 Kevin Lynch, Cancer Center Member, University of Virginia School of Medicine “Blood sphingosine 1-phosphate: Where, Why and How?”

Feb 26 Alice Cheung, Department of Biochemistry and Molecular Biology, University of Massachusetts “The birds and the bees.” How do plants produce seeds?

Mar 05 Wade Winkler, Department of Cell Biology and Molecular Genetics, The University of Maryland

Mar 19 Champak Chatterjee, Department of Chemistry, University of Washington “Chemical strategies to study post-translational modification of human histones”

Mar 26 Do-Hyung Kim, Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Twin City “The molecular machinery for induction of macroautophagy and mitophagy”

Apr 02 Zhiyong Wang, Department of Plant Biololgy, Carnegie Institution for Science “The Central Growth Regulation (CGR) Network in Arabidopsis”

Apr 16 Sergey N. Krylov, Department of Chemistry, York University “Kinetic Capillary Electrophhoresis-An Analytical Swiss Army Knife”

Apr 23 Michael Ibba, Department of Microbiology, Ohio State University “Oxidative stress and context dependent mistranslation of the genetic code”

Apr 30 Lorie Pile, Department of Biological Sciences, Wayne State University “Histone Modifying Complexes in Cell Proliferation and Development” Aug 25 Summa Datta, Department of Biochemistry & Biophysics, Texas A&M University “Perlecan modulation of Hedgehog singaling in Development and Diseases or from flies to men and back again”

Aug 27 Hays Rye, Department of Biochemistry and Biophysics, Texas A&M University “Beyond the Anfinsen Limit: Molecular Chaperones in Protein Folding and Disaggregation

Aug 28 Vlad Panin, Department of Biochemistry & Biophysics, Texas A&M University “Deciphering the function of protein glycosylation using Drosophila model”

Sep 01 Margy Glasner, Department of Biochemistry and Biophysics, Texas A&M University “Evolution of the OSVS Family: A Tale of Promiscuity, Bigamy and Diveorce”

Sep 02 Michael Polymenis, Department of Biochemistry & Biophysics, Texas A&M University “Linking cell growth with initation of cell division and aging”

Sep 03 Craig Kaplan, Department of Biochemistry and Biophysics, Texas A&M University “Mechanism and Regulation of RNA Polymerase II”

Sep 10 Michael Manson, Department of Biology, Texas A&M University “Bacterial chemotaxis to intradomain and interdomain biological signals”

Sep 17 Sergey N. Krylov, Department of Chemistry, York University “Kinetic Capillary Electrophoresis – An Analytical Swiss Army Knife”

Sep 24 Lingchong You, Department of Biomedical Engineering, Duke University “Stochastic E2F dynamics and fingerprints of cell physiology”

Oct 15 Lawrence Grossman, Center for Molecular Medicine and Genetics, Wayne University “CHCHD2, a new regulator of mitochondrial metabolism”

Oct 22 Karen Ottemann, UC Santa Cruz “Connection between bacterial chemotaxis and pathogeneiss in the ulcer- causing pathogen Helicobacter pylori”

Oct 29 Frank Raushel, Department of Biochemistry & Biophysics, Department of Chemistry, Texas A&M University “The Discovery of New Enzymes: The C-P Lyase Complex of Escherichia coli and Aerobic Methane Production”

Nov 05 Caroline Philpott, Liver Diseases Brand, NIDDK, NIH “Iron Chaperones, the System by which Iron is Distributed in Cells”

Nov 12 Mark Fisher, Department of Biochemistry and Molecular Biology, University of Kansas Medical Center “Catching Transients to Determine Toxin Structures and Validate Protein Stabilizers”

Nov 19 Francisco (Paco) Barona-Gomez, Cinvestav “Integrative biology of enzyme promiscuity”

Dec 03 Brian Kennedy, The Buck Institute for Research on Agining “Drugs That Forestall Aging – Extending Healthspan”

2015 Feb 04 Linda L. Randall, Department of Biochemistry, University of Missouri “The E. coli Sec secretory system: studies of protein interactions during export”

Feb 11 James C. Paulson, Department of Chemical Physiology, The Scripps Research Institute “Sialic acids as determinants of self”

Feb 18 Dave Pagliarini, Department of Biochemistry, University of Madison- Wisconsin “Mitochondrial proteins, pathways and pathogenesis”

Feb 25 David Stillman, Department of Pathology Division of Microbiology & Immunology, University of Utah Health Science Center “Changes in Chromatin Structure Can Regulate Gene Expression”

Mar 04 Bin Yu, School of Biological Sciences, University of Nebraska-Lincoln “

Mar 11 Yanhai Yin, Department of Genetics, Development and Cell Biology, Iowa State University “Mechanism and Network for Plant Steroid Hormone Regulated Growth and Stress Responses”

Mar 25 Qi Zhang, Department of Biochemistry & Biophysics, University of North Carolina “Observing Hierarchical Riboswitch Folding by NMR”

Apr 01 Charles Melancon III, Department of Chemistry & Chemical Biology, University of New Mexico “An Integrated Approach to Discover and Bioengineer Bacterial Natural Products”

Apr 08 Amy Caudy, Department of Molecular Genetics, University of Toronto “Metabolomics for Enzyme Discovery”

Apr 15 Blaine Mooers, Department of Biochemistry and Molecular Biology, University of Oklahoma Health Science Center “The role of RNA in the structural biology RNA editing in trypanosomes”

Apr 22 Vivian Bellofatto, Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey “The tail wagging the dog: a tale of how RNA polymerase II navigates the chromatin landscape in a lower eukaryote”

Apr 29 Jie Xiao, Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine “Transcription factor and stochastic gene expression –perspectives from single molecular studies in live cells”,

Aug 11 Girish Agarwal, FRS, Oklahoma State University “Quantum Biophotonics”

Aug 26 Jorge Cruz-Reyes, Department of Biochemistry & Biophysics, Texas A&M University “The ins and outs of RNA editing in kinetoplastid protozoa"

Sept 2 Jean-Philippe Pellois, Department of Biochemistry & Biophysics, Texas A&M University “Crossing cellular membranes or how to transport macromolecules into a cell”

Sept 16 Blaine Mooers, Department of Biochemistry and Molecular Biology University of Oklahoma Health Science Center “The role of RNA in the structural biology RNA editing in trypanosomes”

Sept 23 Marlan Scully, Department of Physics, Texas A&M University “The Dawn of Quantum Biophotonics”

Oct 07 John Mullet, Department of Biochemistry & Biophysics, Texas A&M University “Designing a Sustainable C4 Energy Crop Using Sorghum’s Genetic/Genomic Platform”

Oct 14 Christine Jacobs-Wagner, Department of Molecular, Cellular and Developmental Biology, Yale University “Spindle-less DNA segregation and cell size control”

Oct 21 Mark Winey, Department of Molecular, Cellular, and Developmental Biology, University of Colorado “Only one, please – Licensing Yeast Centrosome Duplication”

Oct 28 Peter Cornish, Department of Biochemistry, University of Missouri “Roadblocks in proteins synthesis: Unraveling the helicase activity of the ribosome with smFRET”

Nov 04 Markus Hafner, NIH “Characterization of Ribonucleoprotein Complexes by PAR-CLIP” Nov 11 Madesh Muniswamy, Department of Biochemistry, Temple University School of Medicine

Nov 18 Carol Gross, Department of Microbiology & Immunology, University of California at San Francisco “Manufacture of the Bacterial Proteome”

Dec 02 Jack Taunton, Cellular and Molecular Pharmacology, University of California, San Francisco, Howard Hughes Medical Institute “From serendipity to clinical trails: discovery of reversible covalent kinase inhibitors”

2016 Jan 20 Vytas A. Bankaitis, Department of Molecular and Cellular Medicine, Health Science Center, Texas A&M University “Strategies by Which Cells Convert Membrane Surfaces to High Definition Lipid Signaling Screens”

Feb 10 Jeffrey Long, Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles “It’s all in the family: Shoot patterning by closely related transcription factors”

Feb 17 Marie Elliot, Department of Biology, Biochemistry and Biomedical Sciences, McMaster University “The power of NAPs: nucleoid-associated proteins and their control of development and specialized metabolism in Streptomyces bacteria”

Feb 19 Veronique Dartois, Rutgers New Jersey Medical School “How do TB drugs partition into lung lesions, and does that matter?

Feb 24 Gábor Balázsi, Department of Biomedical Engineering, Stony Brook University “Synthetic gene circuits: Tools for biological discovery”

Mar 02 Dennis J. Thele, Department of Biochemistry, Duke University School of Medicine “The Cryptococcus neoformans copper homeostasis”

Mar 09 Gloria Brar, Department of Molecular and Cell Biology, University of California, Berekeleeyy “Unraveling the unusual properties of translation in meiosis”

Mar 23 Warner Greene, Gladstoen Institutes of Virology and Immunology, University of California, San Francisco “Death by Friendly Fire: How the Host Immune Response Drives CD4 T Cell Depletion During HIV Infection”

Mar 30 Xin Liu, Department of Obstetrics & Gynecology, Biophysics, UT Southwestern Medical Center “Structural Basis of Gene Regulation by Polycomb Repressive Complex”

Apr 06 John R. Kirby, Department of Microbiology, University of Iowa “Predator-Prey Dynamics Are Regulated by Small Molecules in Microbial Communities”

Apr 13 Roland Lill, Institute of Cytobiology, Marburg University-Germany “Biogenesis of Iron-Sulfure Proteins in Eukaryotes: The CIA syste”

Apr 27 Michael R. Sussman, Department of Biochemistry, University of Wisconsin-Madison “Application of mass spectrometric technology for quantifying changes in the phosphorylome and conformatiome during plasma membrane receptor-mediated signaling”

Aug 31 Jennifer Herman, Department of Biochemistry & Biophysics, Texas A&M University “Regulation of essential cell processes during Bacillus development”

Sep 02 Ping He, Department of Biochemistry & Biophysics, Texas A&M University “How do plants activate defense without running amok? The lessons from “aggie” to “bak to life” screens

Sep 07 Pingwei Li, Department of Biochemistry & Biophysics, Texas A&M University “Mechanism of Cytosolic DNA Sensing Through the cGAS-STING Pathway”

Sep 09 Jorge Cruz-Reyes, Department of Biochemistry & Biophysics, Texas A&M University “The Editosome Control Mechanisms in Trypanosomes”

Sep 21 Arum Han, Department of Electrical and Computer Engineering & Department of Biomedical Engineering, Texas A&M University “High Throughput Microfluidic Systems for Accelerating Next-Generation Algal Biofuel Development”

Sep 28 Kevin Young, Department of Microbiology and Immunology, University of Arkansas for Medical Sciences “Competing for undecaprenyl-phosphate: bacterial morphology, cell wall synthesis and other life lessons”

Oct 05 Kent Chapman, Department of Biological Sciences, University of North Texas “N-Acylethanolamine metabolism and the regulation of seedling development in Arabidopsis thaliana”

Oct 12 Ramendra Saha, School of Natural Sciences, University of California, Merced “A tale of two twins – H2A.Z hypervariants in neuronal gene transcription and development”

Oct 19 Tamara O’Connor, Department of Biochemistry, Cellular and Molecular Biology, John Hopkins Medical Institute “Genetic determinants of Legionella host range and transmission from environmental reservoirs to humans”

Oct 26 Petr Leiman, Biochemistry & Molecular Biology, UTMB -Galveston “Structure and Function of Bacteriophage T4 Baseplate in Atomic Detail”

Nov 02 Douglas Theobald, Department of Biochemistry, Brandeis University “Three stories of convergence: The independent re-evolution of LDH enzyme function, mechanism, structure, and dynamics”

Nov 09 Dennis J. Thiele, Department of Pharmacology & Cancer Biology, Department of Biochemistry, Duke University School of Medicine “The Cryptococcus neoformans copper homeostasis machinery as a therapeutic target in fungal pathogenesis”

Nov 16 Ben Burrowes, GeneWEAVE Biosciences, a Division of Roche Molecular Systems, Inc. “Startups: some pros and cons (but mostly pros) as a researcher in the biotech industry”

Nov 30 Susannah Rankin, Oklahoma Medical Research Foundation “Not separate but equal: Chromosome cohesion and the cell cycle”

2017 Jan 25 Dmitry Kurouski, Boehringer-Ingelheim Pharmaceuticals, Inc. “Tip-Enhanced Raman Spectroscopy: An Emergent Tool for Probing Biology and Electrochemistry at the Nanoscale”

Feb 02 Fake (Frank) Lu, Harvard Medical School “Transforming Coherent Raman Scattering Microscopy for Label-Free Biomolecular Imaging Toward Clinical Application”

Feb 08 Li Wei, Columbia University “Visualizing Molecular Vibrations: Chemical Imaging for Biomedicine”

Feb 15 Mart Long, Institute of Technology, University of Tartu “Disordered CDK substrates as signal processors to controlling the key decision points in the cell cycle”

Feb 22 Maitreya Dunham, Department of Genome Sciences, University of Washington “Comparative experimental evolution of yeasts and their hybrids”

Mar 01 Michael McMurray, Department of Cell and Developmental Biology, University of Colorado, Denver “Mechanisms of macromolecular complex assembly: insights from the study of septin hetero-oligomers”

Mar 08 Ilya Finkelstein, Department of Molecular Biosciences, University of Texas at Austin “Mechanisms of RNA-based adaptive immunity”

Mar 22 Andrzej Wierzbicki, Department of Molecular, Cellular, Developmental Biology, University of Michigan “Mechanisms of RNA-directed DNA methylation”

Mar 29 Aaron D. Gitler, Department of Genetics, Stanford University School of Medicine “Expanding mechanisms and therapeutic targets for neurodegenerative disease”

Apr 05 Roland Strong, Structural Biology, Fred Hutchinson Cancer Research Center “Sideroclains: ferric siderophore-binding proteins in anti-bacterial immunity, and cancer”

Apr 12 Julian Schroeder, Division of Biological Sciences, Cell and Developmental Biology, University of California, San Diego “Drought-Induced Signal transduction and CO2 Sensing in Plants”

Apr 19 Iqbal Hamza, Department of Cell Biology & Molecular Genetics, University of Maryland “Lessons from bloodless worms”

Apr 25 Richard Tennant, Department of Biosciences, University of Exeter “Unearthing Past Environments Using Paleogenomics”

Jun 06 Jolene Ramsey, Department of Microbiology, Indiana University, Bloomington “A tale of two (open reading) frames: The role of the alphavirus 6K and TF proteins in enveloped virus assembly and exit from host cell”

Aug 30 Vishal Gohil, Department of Biochemistry & Biophysics, Texas A&M University “Discovering novel proteins and pathways driving mitochondrial bioenergetics”

Sep 01 Lanying Zeng, Department of Biochemistry & Biophysics, Texas A&M University “Subcellular Decision-making of Bacteriophages”

Sep 06 Xiuren Zhang, Department of Biochemistry & Biophysics, Texas A&M University “Yin and Yang in RNA silencing”

Sept 13 Duane Winkler, Department of Biological Sciences, UT Dallas, “Sod1 is activated using a sulfenic acid intermediate at a copper ion entry site”

Sept 20 Xindan Wang, Biology Department, Indiana University “How Condensin Compacts and Resolves Chromosomes in Bacillus subtilis”

Sept 27 Nick Rhind, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School “Regulation of Cell Size”

Oct 04 Jay Keasling, Department of Chemical and Biomolecular and of Bioengineering, University of California, Berkeley “Engineered Polyketide Synthases for Production of Commodity and Speciality Chemicals”

Oct 11 Joydip Das, Department of Pharmacological and Pharmaceutical Sciences, University of Houston “Structure, dynamics and ligand selectivity of C1 domains”

Oct 18 Fumiaki Katagiri, Department of Plant and Microbial Biology, University of Minnesota “Dynamics, mechanisms, and evolution of a highly resilient plant immune signaling network”

Oct 25 Jade Wang, Department of Bacteriology, University of Wisconsin- Madison “The role of (p)ppGpp in stress response and homeostasis of Gram positive bacteria”

Nov 01 Philip West, TAMU Health Center “Mitochondrial Control of Innate Immunity”

Nov 08 Michael Petris, Department of Biochemistry, University of Missouri “Of Mice and Metals: Exploring the roles of copper in health and disease”

Nov 15 Blake Meyers, Danforth Center, University of Missouri “The diversity, function, and evolution of secondary siRNA pathways in plants”

Nov 28 John Panepinto, Department of Microbiology and Immunology, State University of New York at Buffalo “mRNA Decay in C. neoformans: Letting Go of the Past for a Pathogenic Future”

Nov 29 Jonathan Sczepanski, Department of Chemistry, TAMU “Heterochiral Nucleic Acid Technologies”

2018 Feb 07 Charalampos Kalodimos, St. Jude Children’s Research Hospital “Molecular chapernes in action”

Feb 21 Valerie de Crecy-Lagard, Department of Microbiology and Cell Science, University of Florida “Discovery of 7-deazapurine synthesis pathways: where RNA and DNA modifications intersect with secondary metabolites”

Feb 28 Peter Tessier, Department of Chemical Engineering and Pharmaceutical Sciences, University of Michigan “Improved methods for designing, evolving and characterizing monoclonal antibodies”

Mar 07 Miriam Greenberg, Department of Biological Sciences, Wayne State University “Cardiolipin - mitochondrial phospholipid at the epicenter of energy metabolism”

Mar 21 Wolfgang Peti, Department of Chemistry and Biochemistry, University of Arizona “Using NMR spectroscopy to unravel enzyme function”

Mar 28 Chris Welch, Welch Innovation “High Throughput Analysis and High Throughput Experimentation in Pharmaceutical Development ”

Apr 04 Andreas Doncic, Department of Cell Biology, UT Southwestern Medical Center “Integration of multiple metabolic signals determines cell fates prior to commitment”

Apr 11 Hamed Jafar-Nejad, Molecular & Human Genetics, Baylor College of Medicine “O-glucose glycans in animal development and human disease”

Apr 25 Walter Chazin, Department of Biochemistry and Chemistry, Vanderbilt University “Functional Dynamics of Modular Multi-Domain Proteins”

Aug 27 Jae-Hyun Cho, Biochemistry and Biophysics Department, Texas A&M University “Eppur si muove: Tales of a tail”

Aug 29 Frank Raushel, Department of Biochemistry & Biophysics, Chemistry, Texaws A&M University “Biosynthesis of the O-Methyl Phosphoramidate Modification to the Capsular Polysaccharide of Campylobacter jejuni”

Sep 05 David Threadgill, Department of Veterinary Pathobiology, Department of Molecular and Cellular Medicine, Texas A&M University “A Winding Journey from an EGFR Knockout to Metabolic Syndrome Polygenes”

Sep 12 Yunsun Nam, Department of Biophysics, UT Southwestern “Chemical regulation of functional RNAs”

Sep 19 Volker Blank, Department of Medicine, McGill University, Lady Davis Institute for Medical Research “CNC and MAF transcription factors: stress, cancer, knock outs and other serious matters.”

Sep 26 Sivaraj Sivaramakrishnan, Department of Genetics, Cell Biology & Development, University of Minnesota Twin Cities “Bridging the information transfer gap: How weak protein interactions shape signal transduction”

Oct 03 Randall Morse, Biomedical Sciences, Laboratory of Molecular Genetics, Wadsworth Center “Recruitment and Dynamics of the Mediator Complex”

Oct 10 Yinghao Wu, Department of Systems and Computational Biology, Albert Einstein College of Medicine “Understand Binding Kinetics of Membrane Receptors and Their Functional Roles in Cell adhesion and Signaling by Multi-scale Modeling”

Oct 12 Stefan Dübel, Department of Biotechnology, Technische Universitȁt Braunschweig “Programming antibodies: from specificity engineering to intracellular applications and affinity switches”

Oct. 17 Jung-Hyun Min, Department of Chemistry and Biochemistry, Baylor University “Structure and dynamics of DNA damage recognition by Rad4 nucleotide excision repair protein complex”

Oct 24 Michael Baym, Department of Biomedical Informatics & Laboratory of Systems Pharmacology, Harvard Medical School “Evolutionary Approaches to Antibiotic Resistance”

Oct 31 Charalampos Kalodimos, Structural Biology, St. Jude Children’s Research Hospital “Atomic view of regulation and drug resistance in Abl kinase”

Nov 07 Joshua Modell, Department of Molecular Biology and Genetics, Johns Hopkins Medical School “Bacterial and phage determinants of CRISPR-Cas acquired immunity”

Nov 14 Fanxiu Zhu, Department of Biological Sciences, Florida State University “Subversion of cGAS-STING DNA sensing by Kaposi sarcoma-associated herpesvirus”

Nov 16 Michael W Deem, Department of Bioengineering, Department of Physics & Astronomy, Rice University “Virus-Bacterial Co-Evolution Mediated by CRISPR and Efficiency of CRISPR-Cas9 Mediated by Modular Regulation”

Nov 26 Michael Tiemeyer, Department of Biochemistry and Molecular Biology, University of Georgia “Glycans, Glycomes, and the Glycobiology of Neural Development and Dysfunction”

Nov 28 Oleh Khalimonchuk, Department of Biochemistry, University of Nebraska “Proteolytic control of mitochondrial shape and function”

Dec 03 James Ames, Department of Chemistry, University of California “Calmodulin Capping of PSD-95 Triggers its Postsynaptic Release and Decreases Neuronal Excitability”

Dec 12 A. Joshua Wand, Department of Biochemistry and Biophysics, University of Pennsylvania “The dark energy of proteins comes to light: Entropy in molecular recognition by proteins”

2019

Jan 23 Bryan Davies, Department of Molecular Biosciences, University of Texas at Austin “Investigating the spread and treatment of hospital pathogens”

Jan 30 Wenshe Liu, Department of Chemistry, Texas A&M University “Using an expanded genetic code to study epigenetic modifications”

Feb 06 Alexey Makarov, Principal Scientist, Analytical Chemistry Enabling Technologies, from Merck “Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Screening Approaches for Studying Global Conformational Structures of Peptides/ Proteins in Solution.”

Feb 13 Jing-Ke Weng, Department of Biology, Massachusetts Institute of Technology “Metabolic Evolution in Plants”

Feb 20 Lance Wells, Department of Biochemistry and Molecular Biology, University of Georgia, Athens “Congenital Diseases of Unusual O-Glycosylation”

Feb 27 Laurie K. Read, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo “Trypanosome RNA editing: the complexity of getting U in and taking U out”

Mar 06 Jason Brickner, Department of Molecular Biosciences, Northwestern University “Transcription factors and nuclear pores regulate the spatial organization of the yeast genome to facilitate epigenetic transcriptional regulation.”

Mar 20 Yungki Park, Department of Biochemistry, SUNY Buffalo “Myrf (myelin regulatory factor): A story of a bioinformatician-turned neurobiologist”

Apr 03 Peter Freddolino, Biological Chemistry, University of Michigan Medical School “New surprises from the E. coli K12 genome”

Apr 10 Sean O’Leary, Department of Biochemistry, University of California, Riverside “Dynamics of mRNA recognition for translation initiation.”

Apr 17 Alex Evilevitch, Department of Pathobiology and Physics, University of Illinois “Herpesvirus infectivity facilitated by internal DNA pressure and capsid stability”

Apr 24 Scot Leary, Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan “Functional genetic investigation of cell non-autonomous regulation of adaptive immunity by the liver in response to bioenergetic stress

May 8 William Prinz, Cell and Molecular Biology, NIDDK, NIH “Lipid droplet biogenesis”

Aug 28 Junjie Zhang, Department of Biochemistry & Biophysics, Texas A&M University “Towards an efficient RNA delivery system - structural insights into the infection cycle of ssRNA phages”

Sept 04 Dr. Kathryn Fixen, Department of Plant and Microbial Biology, University of Minnesota “”Fix”ing to make fuel: controlling electron transfer to nitrogenase to make energy-rich compounds”

Sep 11 Chuanbin Mao, Department of Chemistry & Biochemistry, Stephenson LIfe Sciences Research Center, Institute for Biomedical Engineering, Science, and Technology, University of Oklahoma “Phage-based nanomedicine and regenerative medicine: from probes to therapeutics”

Sep 18 Dr. Phanourios Tamamis, Department of Chemical Engineering, Texas A&M University “Biophysical Simulations and Calculations Bridging Gaps and “Provoking” Experiments”

Sep 25 Dr. Heedeok Hong, Department of Chemistry, Michigan State University “Folding and degradation of membrane proteins”

Oct 02 Dr. Gregg Howe, Department of Biochemistry & Molecular Biology, Michigan State University “Molecular mechanism of jasmonate signaling: new insgihts into the dilemma of plants to grow or defend”

Oct 08 John D. Helmann, Department of Microbiology, Cornell University “Nutrition, stress, and antibiotic susceptibility: Bacillus subtilis as a model”

Oct 09 Dr. Carlos Bustamante, UC Berkeley/Howard Hughes Med. Inst. “Co-translational Protein Folding One Molecular at a Time”

Oct 16 Dr. Bryan Shaw, Department of Chemistry and Biochemistry, Baylor University “Measuring and manipulating the net charge of proteins – what have we been missing?”

Oct 18 Dave Ousterout, Chief Scientific Officer, Locus Biosciences, Inc. “crPhage: A recombinant phage platform on CRISPR-Cas3 to address AMR and diseases of the microbiome.”

Oct 23 Dr. Petr Leiman, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston “Function, structure, and evolution of phage spike tip proteins”

Oct 30 Amanda Haes, Department of Chemistry, University of Iowa “Nanoparticles and SERS – To Stability and Beyond!”

Nov 06 Dr. Alexander Mankin, Center for Biomolecular Sciences, University of Illinois at Chicago “Stopping the ribosome at the finish line: how PrAMPs inhibit termination of translation”

Nov 13 Igor Jouline, Department of Microbiology, The Ohio State University “How novel sensors arise in bacteria”

Nov 20 Dr. Suzanne McDermott, Center for Global Infectious Disease Research, Seattle Children’s Research Institute “High-resolution mapping of protein motifs and interactions essential for RNA editing”

2020 Feb 24 Xiaowei Hou, Memorial Sloan-Kettering Cancer Center “Structural studies reveal insights into CRAC channel activation”

Feb 26 Wen Jiang, Department of Biological Science, Purdue University “High-Resolution Cryo-EM: Past, Present, and Future”

Mar 02 Shaotong Zhu, Department of Neuroscience and Biophysics, UT Southwestern Medical Center “Structural Mechanisms of Fast Inhibitory Neurotransmission”

Mar 04 Sheng Luan, Department of Plant and Microbial Biology, University of California, Berekeley “Regulation of nutrient homeostasis by a calcium signaling network”

Jul 23 Libo Shan, Institute for Plant Genomics and Biotechnbology, The Norman E. Borlaug Research Center, AgriLife Research, Texas A&M University “Non-self recognition and signaling mechanisms in plants”

Aug 26 Jae Cho, Department of Biochemistry and Biophysics, Texas A&M University “The devil is in the details: Towards a mechanistic understanding of strain- specific virus-host interaction”

Sep 02 Thomas Meek, Department of Biochemistry and Biophysics, Texas A&M University “The Roles of Cysteine Proteases in Infectious Diseases: From Chagas Disease to COVID-19”

Sep 09 Jun Liu, Microbial Pathogenesis, Yale University School of Medicine “Dissecting a molecular machine by cryo-electron tomography”

Sep 16 Richard Gomer, Department of Biology, Texas A&M University “Extracellular signals that may contribute to lung diseases”

Sep 23 Susan Bellis, Department of Cell, Developmental and Integrative Biology, University of Alabama “ST6Gal1 sialyltransferase is a novel molecular driver of pancreatic ductal adenocarcinoma”

Sep 30 Vera Moiseenkova-Bell, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania “Structural pharmacology of TRPV channels”

Oct. 07 Enrico Gratton, Department of Biomedical Engineering and Physics, University of California, Irvine “Single cell physiological characterization in living tissue”

Oct 14 David Cowburn, Department of Biochemistry, Physiology and Biophysics, Albert Einstein College of Medicine “Dynamic mechanisms in the nuclear pore complex”

SPRING 2020 | BCBP (On-Campus) Seminar Series-CANCELLED DUE TO Covid-19 FALL 2020 | BCBP VIRTUAL Seminar Series

Date Name University School / Department Host

26-Aug Jae-Hyun Cho TAMU BCBP Sacchettini / PATC

2-Sep Thomas Meek TAMU BCBP

9-Sep Jun Liu Yale University School of Medicine J. Zhang

16-Sep Richard Gomer TAMU BIOL Polymenis

23-Sep Susan Bellis University of Alabama Cell, Developmental, and Panin Integrative Biology 30-Sep Vera Moiseenkova-Bell University of Pennsylvania Wand

7-Oct Enrico Gratton UC Irvine Biomedical Engineering Wand / Reinhart Lecture 14-Oct David Cowburn Albert Einstein College of Biochemistry Cho Medicine 21-Oct Carol Fierke TAMU Provost Wand

28-Oct Alexander Serganov New York University Biochemistry and Krieger Molecular Biology 4-Nov Kimberly Seed UC Berkeley Plant and Microbial BGA Biology 11-Nov Walter Fast University of Texas Chemical Biology Meek

18-Nov Michael Laub MIT Biology Herman

SPRING 2021 | BCBP VIRTUAL Seminar Series

Date Name University School / Department Host

20-Jan Jason Yang Rutger New Jersey Medical Microbiology, Herman School Biochemistry and Molecular Genetics 27-Jan

3-Feb Christopher Hayes UC Santa Barbara Molecular, Cellular and Zeng Developmental Biology 10-Feb

17-Feb

24-Feb

3-Mar Val Culotta Johns Hopkins University Biochemistry and Gohil Molecular Biology 10-Mar Sun Hur Harvard Medical School Cellular and Molecular Li Medicine 17-Mar Silvi Rouskin Whitehead Institute for X. Zhang Biomedical Research

24-Mar Elizabeth Tran Purdue University Biochemistry Cruz-Reyes

31 Mar Aimin Liu The University of Texas at Chemistry BGA San Antonio 7-Apr Chuan He University of Chicago Chemistry X. Zhang

14-Apr Wei Min Columbia University in the Chemistry Kurouski City of New York 21-Apr Jennifer Kohler Southwestern Medical Biochemistry Panin Center 28-Apr Phyllis Hanson University of Michigan Biological Chemistry Pellois Medicine

Appendix M – 2014 External Review | Report and Departmental Response

Appendix N – BICH/GENE 491W Rubric for Assessment of Undergraduate Classes WRITTEN COMMUNICATION VALUE RUBRIC for more information, please contact [email protected]

The VALUE rubrics were developed by teams of faculty experts representing colleges and universities across the United States through a process that examined many existing campus rubrics and related documents for each learning outcome and incorporated additional feedback from faculty. The rubrics articulate fundamental criteria for each learning outcome, with performance descriptors demonstrating progressively more sophisticated levels of attainment. The rubrics are intended for institutional-level use in evaluating and discussing student learning, not for grading. The core expectations articulated in all 15 of the VALUE rubrics can and should be translated into the language of individual campuses, disciplines, and even courses. The utility of the VALUE rubrics is to position learning at all undergraduate levels within a basic framework of expectations such that evidence of learning can by shared nationally through a common dialog and understanding of student success.

Definition Written communication is the development and expression of ideas in writing. Written communication involves learning to work in many genres and styles. It can involve working with many different writing technologies, and mixing texts, data, and images. Written communication abilities develop through iterative experiences across the curriculum.

Framing Language This writing rubric is designed for use in a wide variety of educational institutions. The most clear finding to emerge from decades of research on writing assessment is that the best writing assessments are locally determined and sensitive to local context and mission. Users of this rubric should, in the end, consider making adaptations and additions that clearly link the language of the rubric to individual campus contexts. This rubric focuses assessment on how specific written work samples or collectios of work respond to specific contexts. The central question guiding the rubric is "How well does writing respond to the needs of audience(s) for the work?" In focusing on this question the rubric does not attend to other aspects of writing that are equally important: issues of writing process, writing strategies, writers' fluency with different modes of textual production or publication, or writer's growing engagement with writing and disciplinarity through the process of writing. Evaluators using this rubric must have information about the assignments or purposes for writing guiding writers' work. Also recommended is including reflective work samples of collections of work that address such questions as: What decisions did the writer make about audience, purpose, and genre as s/he compiled the work in the portfolio? How are those choices evident in the writing -- in the content, organization and structure, reasoning, evidence, mechanical and surface conventions, and citational systems used in the writing? This will enable evaluators to have a clear sense of how writers understand the assignments and take it into consideration as they evaluate The first section of this rubric addresses the context and purpose for writing. A work sample or collections of work can convey the context and purpose for the writing tasks it showcases by including the writing assignments associated with work samples. But writers may also convey the context and purpose for their writing within the texts. It is important for faculty and institutions to include directions for students about how they should represent their writing contexts and purposes. Faculty interested in the research on writing assessment that has guided our work here can consult the National Council of Teachers of English/Council of Writing Program Administrators' White Paper on Writing Assessment (2008; http://www.wpacouncil.org/whitepaper) and the Conference on College Composition and Communication's Writing Assessment: A Position Statement (2008; http://www.ncte.org/cccc/resources/positions/123784.htm)

Glossary The definitions that follow were developed to clarify terms and concepts used in this rubric only. • Content Development: The ways in which the text explores and represents its topic in relation to its audience and purpose. • Context of and purpose for writing: The context of writing is the situation surrounding a text: who is reading it? who is writing it? Under what circumstances will the text be shared or circulated? What social or political factors might affect how the text is composed or interpreted? The purpose for writing is the writer's intended effect on an audience. Writers might want to persuade or inform; they might want to report or summarize information; they might want to work through complexity or confusion; they might want to argue with other writers, or connect with other writers; they might want to convey urgency or amuse; they might write for themselves or for an assignment or to remember. • Disciplinary conventions: Formal and informal rules that constitute what is seen generally as appropriate within different academic fields, e.g. introductory strategies, use of passive voice or first person point of view, expectations for thesis or hypothesis, expectations for kinds of evidence and support that are appropriate to the task at hand, use of primary and secondary sources to provide evidence and support arguments and to document critical perspectives on the topic. Writers will incorporate sources according to disciplinary and genre conventions, according to the writer's purpose for the text. Through increasingly sophisticated use of sources, writers develop an ability to differentiate between their own ideas and the ideas of others, credit and build upon work already accomplished in the field or issue they are addressing, and provide meaningful examples to readers. • Evidence: Source material that is used to extend, in purposeful ways, writers' ideas in a text. • Genre conventions: Formal and informal rules for particular kinds of texts and/or media that guide formatting, organization, and stylistic choices, e.g. lab reports, academic papers, poetry, webpages, or personal essays. • Sources: Texts (written, oral, behavioral, visual, or other) that writers draw on as they work for a variety of purposes -- to extend, argue with, develop, define, or shape their ideas, for example. WRITTEN COMMUNICATION VALUE RUBRIC for more information, please contact [email protected]

Evaluators are encouraged to assign a zero to any work sample or collection of work that does not meet benchmark (cell one) level performance.

Capstone Milestones Benchmark 4 3 2 1 Context of and purpose for writing Demonstrates a thorough understanding Demonstrates adequate consideration of Demonstrates awareness of context, Demonstrates minimal attention to Includes considerations of audience, of context, audience, and purpose that is context, audience, and purpose and a audience, purpose, and to the assigned context, audience, purpose, and to the purpose, and the circumstances responsive to the assigned task(s) and clear focus on the assigned task(s) (e.g., tasks(s) (e.g., begins to show awareness assigned tasks(s) (e.g., expectation of surrounding the writing task(s). focuses all elements of the work. the task aligns with audience, purpose, of audience's perceptions and instructor or self as audience). and context). assumptions). Content Development Uses appropriate, relevant, and Uses appropriate, relevant, and Uses appropriate and relevant content to Uses appropriate and relevant content to compelling content to illustrate mastery compelling content to explore ideas develop and explore ideas through most develop simple ideas in some parts of the of the subject, conveying the writer's within the context of the discipline and of the work. work. understanding, and shaping the whole shape the whole work work. Genre and disciplinary conventions Demonstrates detailed attention to and Demonstrates consistent use of Follows expectations appropriate to a Attempts to use a consistent system for Formal and informal rules inherent in successful execution of a wide range of important conventions particular to a specific discipline and/or writing task(s) basic organization and presentation the expectations for writing in particular conventions particular to a specific specific discipline and/or writing task(s), for basic organization, content, and forms and/or academic fields (please see discipline and/or writing task (s) including organization, content, presentation glossary). including organization, content, presentation, and stylistic choices presentation, formatting, and stylistic choices Sources and evidence Demonstrates skillful use of high quality, Demonstrates consistent use of credible, Demonstrates an attempt to use credible Demonstrates an attempt to use sources credible, relevant sources to develop relevant sources to support ideas that are and/or relevant sources to support ideas to support ideas in the writing. ideas that are appropriate for the situated within the discipline and genre that are appropriate for the discipline and discipline and genre of the writing of the writing. genre of the writing. Control of syntax and mechanics Uses graceful language that skillfully Uses straightforward language that Uses language that generally conveys Uses language that sometimes impedes communicates meaning to readers with generally conveys meaning to readers. meaning to readers with clarity, although meaning because of errors in usage clarity and fluency, and is virtually error- The language in the portfolio has few writing may include some errors. free. errors. OFFICE OF THE PROVOST

Appendix O – Institutional Profile

November 18, 2019

TO: External Program Reviewers and Program Accreditors

FROM: Michael T. Stephenson Vice Provost for Academic Affairs & Strategic Initiatives

RE: Information required for USDOE Accrediting Bodies

Texas A&M University is accredited by the Southern Association of Colleges and Schools Commission on Colleges to award baccalaureate, master's, and doctoral degrees. Consistent with standard 14.4, the following provides the institution’s official position on its purpose, governance, programs, degrees, diplomas, certificates, personnel, finances, and constituencies and is published in official university documents as noted.

Purpose

Classified by the Carnegie Foundation as a Research Doctoral University (Highest Research Activity), Texas A&M embraces its mission of the advancement of knowledge and human achievement in all its dimensions. The research mission is a key to advancing economic development in both public and private sectors. Integration of research with teaching prepares students to compete in a knowledge-based society and to continue developing their own creativity, learning, and skills beyond graduation.

The institution’s official mission statement, published both on the institution’s web page as well as in its annual university catalog, is:

Texas A&M University (Texas A&M) is dedicated to the discovery, development, communication and application of knowledge in a wide range of academic and professional fields. Its mission of providing the highest quality undergraduate and graduate programs is inseparable from its mission of developing new understandings through research and creativity. It prepares students to assume roles in leadership, responsibility and service to society. Texas A&M assumes as its historic trust the maintenance of freedom of inquiry and an intellectual environment nurturing the human mind and spirit. It welcomes and seeks to serve persons of all racial, ethnic and geographic groups, women and men alike, as it addresses the needs of an increasingly diverse population and a global economy. In the twenty-first century, Texas A&M University seeks to assume a place of preeminence among public universities while respecting its history and traditions.

Governance

The governance of the institution was described in the 2012 certification of compliance submitted to SACSCOC.

Jack K. Williams Administration Building, Suite 100 1248 TAMU College Station, TX 77843-1248 USA

Tel. +1 979.845.4016 Fax. +1 979.845.6994 http://provost.tamu.edu/ Texas A&M University at College Station, the flagship institution of the Texas A&M University System, has branch campuses located in Galveston, Texas and Doha, Qatar. A ten-member Board of Regents, appointed by the Governor, directs the Texas A&M University System. The appointment of each Regent follows Texas Education Code (TEC, Chapter 85, Section 21).

TEC outlines the duties and responsibilities of the Board of Regents. These responsibilities are also defined in System Policy 02.01 Board of Regents and TEC 51.352. The Board elects two officers: Chair and Vice Chair. There are four standing committees: Audit, Academic & Student Affairs, Finance, and Buildings & Physical Plant. Special committees may be appointed by the Chair with Board approval.

At Texas A&M University the President is the chief executive officer; the President is not the presiding officer of the Board of Regents. The President reports to the state-appointed Board of Regents through the Chancellor of the Texas A&M University System. System Policy 2.05 Presidents of System Member Universities defines the duties of the President. The appointment of the President follows conditions set forth in System Policy 01.03 Appointing Power and Terms and Conditions of Employment, section 2.2.

Personnel

The institution is led by the President and members of his cabinet:

Michael K. Young, President Carol A. Fierke, Provost and Executive Vice President, Chief Academic Officer Jerry R. Strawser, Executive Vice President and Chief Financial Officer Michael Benedik, Vice Provost and Chief International Officer Michael T. Stephenson, Vice Provost for Academic Affairs & Strategic Initiatives M. Dee Childs, Vice President for Information Technology and CIO Michael G. O’Quinn, Vice President for Government Relations & Strategic Initiatives Col. Michael E. Fossum, Chief Operating Officer, TAMU-Galveston Jeff Risinger, Vice President for HR & Organizational Effectiveness Robin Means Coleman, Vice President and Associate Provost for Diversity Mark Barteau, Vice President for Research Greg Hartman, Vice Chancellor for Strategic Initiatives, TAMU & Interim Senior Vice President, TAMU-HSC Daniel J. Pugh, Sr., Vice President for Student Affairs Joseph P. Pettibon, II, Vice President for Enrollment and Academic Services Gen Joe E. Ramirez, Jr. Commandant, Corps of Cadets Amy B. Smith, Senior Vice President and Chief Marketing and Communications Officer Ross Bjork, Athletics Director Jonathan Bowling, Sr. Associate Athletics Director, Athletics Compliance Shane Hinckley, Vice President for Brand Development Andrew P. Morris, VP of Entrepreneurship & Economic Development, Dean of the I-School C.J. Woods, Associate Vice President and Chief of Staff Kevin McGinnis, Chief Compliance Officer

Programs, Degrees, Diplomas, and Certificates

See the appended Degrees and Programs Offered tables.

Finances

See the 2019 SACSCOC Financial Profile and Indicators

Southern Association of Colleges and Schools Commission on Colleges

INSTITUTIONAL SUMMARY FORM PREPARED FOR COMMISSION REVIEWS

GENERAL INFORMATION

Name of Institution Texas A&M University

Name, Title, Phone number, and email address of Accreditation Liaison Michael T. Stephenson Vice Provost for Academic Affairs and Strategic Initiatives, and SACSCOC Accreditation Liaison 979.845.4016 [email protected]

Name, Title, Phone number, and email address of Technical Support person for the Compliance Certification Alicia M. Dorsey Assistant Provost for Institutional Effectiveness 979.862.2918 [email protected]

IMPORTANT:

Accreditation Activity (check one): x Submitted at the time of Reaffirmation Orientation ☐ Submitted with Compliance Certification for Reaffirmation ☐ Submitted with Materials for an On-Site Reaffirmation Review ☐ Submitted with Compliance Certification for Fifth-Year Interim Report ☐ Submitted with Compliance Certification for Initial Candidacy/Accreditation Review ☐ Submitted with Merger/Consolidations/Acquisitions ☐ Submitted with Application for Level Change

Submission date of this completed document: November 13, 2019

EDUCATIONAL PROGRAMS

1. Level of offerings (Check all that apply)

X Diploma or certificate program(s) requiring less than one year beyond Grade 12 X Diploma or certificate program(s) of at least two but fewer than four years of work beyond Grade 12 ☐ Associate degree program(s) requiring a minimum of 60 semester hours or the equivalent designed for transfer to a baccalaureate institution ☐ Associate degree program(s) requiring a minimum of 60 semester hours or the equivalent not designed for transfer X Four or five-year baccalaureate degree program(s) requiring a minimum of 120 semester hours or the equivalent X Professional degree program(s) X Master's degree program(s) ☐ Work beyond the master's level but not at the doctoral level (such as Specialist in Education) X Doctoral degree program(s) ☐ Other (Specify)

2. Types of Undergraduate Programs (Check all that apply)

☐ Occupational certificate or diploma program(s) ☐ Occupational degree program(s) ☐ Two-year programs designed for transfer to a baccalaureate institution X Liberal Arts and General X Teacher Preparatory X Professional ☐ Other (Specify)

GOVERNANCE CONTROL

Check the appropriate governance control for the institution: ☐ Private (check one) ☐ Independent, not-for-profit Name of corporation OR Name of religious affiliation and control: ☐ Independent, for-profit * If publicly traded, name of parent company:

X Public state * (check one) ☐ Not part of a state system, institution has own independent board X Part of a state system, system board serves as governing board ☐ Part of a state system, system board is super governing board, local governing board has delegated authority ☐ Part of a state system, institution has own independent board

* If an institution is part of a state system or a corporate structure, a description of the system operation must be submitted as part of the Compliance Certification for the decennial review. See Commission policy “Reaffirmation of Accreditation and Subsequent Reports” for additional direction. 2

INSTITUTIONAL INFORMATION FOR REVIEWERS

Directions: Please address the following and attach the information to this form.

1. History and Characteristics Provide a brief history of the institution, a description of its current mission, an indication of its geographic service area, and a description of the composition of the student population. Include a description of any unusual or distinctive features of the institution and a description of the admissions policies (open, selective, etc.). If appropriate, indicate those institutions that are considered peers. Please limit this section to one-half page.

History. Texas A&M University (TAMU) opened in 1876 as the state’s first public institution of higher education. TAMU is one of a select few institutions in the nation to hold land grant, sea grant (1971) and space grant (1989) designations. A mandatory military component was a part of the land grant designation until 1965; currently, it is one of only three institutions with a full-time Corps of Cadets, leading to commissions in all branches of service. TAMU has two branch campuses, one in Galveston, Texas, (established in 1962, officially merged with TAMU in 1991) and one in Doha, Qatar (established in 2003) and 16 approved off-campus instructional locations. In 2013, the Texas A&M University System Health Science Center merged with TAMU. This same year, TAMU acquired the School of Law from Texas Wesleyan University. Finally, TAMU is classified by the Carnegie Foundation as a Research University (very high research activity).

Mission. Texas A&M University is dedicated to the discovery, development, communication, and application of knowledge in a wide range of academic and professional fields. Its mission of providing the highest quality undergraduate and graduate programs is inseparable from its mission of developing new understandings through research and creativity. It prepares students to assume roles in leadership, responsibility and service to society. Texas A&M assumes as its historic trust the maintenance of freedom of inquiry and an intellectual environment nurturing the human mind and spirit. It welcomes and seeks to serve persons of all racial, ethnic and geographic groups as it addresses the needs of an increasingly diverse population and a global economy. In the 21st century, Texas A&M University seeks to assume a place of preeminence among public universities while respecting its history and traditions.

Enrollment Profile. Fall 2018 total enrollment was 69,367 students (across all campuses and locations), with 64,126 (92.4%) located on the main campus in College Station. Undergraduate enrollment made up 78.3% of the total student body, with Hispanic, Black, and American Indian students making up 24.9% of the total student body. TAMU Galveston enrolled 1,815 students as of Fall, 2018, with TAMU Qatar enrolling 549 students.

Admissions Process. Automatic admission is available in two ways: (1) for Texas resident applicants in the top 10% of their high school graduating class; and, (2) for applicants who rank in the top 25% of their high school graduating class and achieve a combined SAT math and SAT critical reading score of at least 1300, with a test score of at least 600 in each component or 30 composite on the ACT with a 27 in the math and English components. The review of all other applicants is based on academic potential, distinguishing characteristics, exceptional circumstances, and personal achievements.

Peer Institutions. Georgia Institution of Technology; The Ohio State University; Pennsylvania State University; Purdue University; University of California at Berkeley, Davis, Los Angeles, and San Diego; University of Florida; University of Illinois at Urbana-Champaign; University of Michigan; University of Minnesota; University of North Carolina at Chapel Hill; University of Texas at Austin; and University of Wisconsin – Madison.

2. List of Degrees List all degrees currently offered (A. S., B.A., B.S., M.A., Ph.D., for examples) and the majors or concentrations within those degrees, as well as all certificates and diplomas. For each credential offered, indicate the number of graduates in the academic year previous to submitting this report. Indicate term dates.

Does the institution offer any credit, non-credit, or pathways English as a Second Language (ESL) programs? If yes, list the programs. 3

College Academic Program Program Level AY 18-19

AGRICULTURE AND ADVANCED PEDAGOGY IN AGRICULTURE CERT - G 1 LIFE SCIENCES AGRICULTURE AND AGRIBUSINESS BS 91 LIFE SCIENCES

AGRICULTURE AND AGRICULTURAL COMMUNICATION & JOURNALISM BS 103 LIFE SCIENCES

AGRICULTURE AND AGRICULTURAL DEVELOPMENT MAGR 5 LIFE SCIENCES AGRICULTURE AND AGRICULTURAL ECONOMICS BS 222 LIFE SCIENCES AGRICULTURE AND AGRICULTURAL ECONOMICS MS 16 LIFE SCIENCES AGRICULTURE AND AGRICULTURAL ECONOMICS PHD 11 LIFE SCIENCES AGRICULTURE AND AGRICULTURAL ECONOMICS MAGR 0 LIFE SCIENCES AGRICULTURE AND AGRICULTURAL EDUCATION EDD 5 LIFE SCIENCES AGRICULTURE AND AGRICULTURAL LEADERSHIP & DEVELOPMENT BS 130 LIFE SCIENCES AGRICULTURE AND AGRICULTURAL LEADERSHIP EDUCATION & MED 10 LIFE SCIENCES COMMUNICATION AGRICULTURE AND AGRICULTURAL LEADERSHIP EDUCATION & MS 11 LIFE SCIENCES COMMUNICATION AGRICULTURE AND AGRICULTURAL LEADERSHIP EDUCATION & PHD 5 LIFE SCIENCES COMMUNICATION AGRICULTURE AND AGRICULTURAL SCIENCE BS 35 LIFE SCIENCES AGRICULTURE AND AGRICULTURAL SYSTEMS MANAGEMENT BS 41 LIFE SCIENCES AGRICULTURE AND AGRICULTURAL SYSTEMS MANAGEMENT MS 3 LIFE SCIENCES AGRICULTURE AND AGRICULTURAL SYSTEMS MANAGEMENT MAGR 0 LIFE SCIENCES AGRICULTURE AND AGRICULTURE ELEARNING DEVELOPMENT CERT - G 3 LIFE SCIENCES AGRICULTURE AND AGRONOMY MS 6 LIFE SCIENCES AGRICULTURE AND AGRONOMY PHD 4 LIFE SCIENCES AGRICULTURE AND ANIMAL BREEDING MS 1 LIFE SCIENCES 4

AGRICULTURE AND ANIMAL BREEDING PHD 2 LIFE SCIENCES AGRICULTURE AND ANIMAL SCIENCE BS 152 LIFE SCIENCES AGRICULTURE AND ANIMAL SCIENCE MAGR 10 LIFE SCIENCES AGRICULTURE AND ANIMAL SCIENCE MS 18 LIFE SCIENCES AGRICULTURE AND ANIMAL SCIENCE PHD 12 LIFE SCIENCES AGRICULTURE AND ANIMAL SCIENCE-PRODUCTION/ INDUSTRY BS 130 LIFE SCIENCES AGRICULTURE AND ANIMAL SCIENCE-SCIENCE BS 0 LIFE SCIENCES AGRICULTURE AND BIOCHEMISTRY BS 47 LIFE SCIENCES AGRICULTURE AND BIOCHEMISTRY MS 4 LIFE SCIENCES AGRICULTURE AND BIOCHEMISTRY PHD 13 LIFE SCIENCES AGRICULTURE AND BIOENVIRONMENTAL SCIENCES BS 62 LIFE SCIENCES AGRICULTURE AND BIOLOGICAL AND AGRI ENGINEERING BS 46 LIFE SCIENCES AGRICULTURE AND BIOLOGICAL AND AGRI ENGINEERING MENGR 2 LIFE SCIENCES AGRICULTURE AND BIOLOGICAL AND AGRI ENGINEERING MS 2 LIFE SCIENCES AGRICULTURE AND BIOLOGICAL AND AGRI ENGINEERING PHD 10 LIFE SCIENCES AGRICULTURE AND COMMUNITY DEVELOPMENT BS 1 LIFE SCIENCES AGRICULTURE AND COMMUNITY DEVELOPMENT CERT - G 2 LIFE SCIENCES AGRICULTURE AND COMMUNITY RECREATION AND PARK ADMINISTRATION* CERT - UG 32 LIFE SCIENCES AGRICULTURE AND DIETETIC INTERNSHIP CERT - G 0 LIFE SCIENCES AGRICULTURE AND ECOLOGICAL RESTORATION BS 11 LIFE SCIENCES AGRICULTURE AND ECOSYSTEM SCIENCE & MGMT MS 7 LIFE SCIENCES AGRICULTURE AND ECOSYSTEM SCIENCE & MGMT PHD 4 LIFE SCIENCES AGRICULTURE AND ECOSYSTEM SCIENCE & MGMT MAGR 0 LIFE SCIENCES AGRICULTURE AND ENOLOGY CERT - UG 9 LIFE SCIENCES AGRICULTURE AND ENTOMOLOGY BS 22 LIFE SCIENCES 5

AGRICULTURE AND ENTOMOLOGY MS 3 LIFE SCIENCES AGRICULTURE AND ENTOMOLOGY PHD 11 LIFE SCIENCES AGRICULTURE AND EQUINE INDUSTRY MANAGEMENT MEIM 3 LIFE SCIENCES AGRICULTURE AND EQUINE SCIENCE CERT -UG 33 LIFE SCIENCES AGRICULTURE AND EXTENSION EDUCATION 6 LIFE SCIENCES CERT - G AGRICULTURE AND FOOD SAFETY 0 LIFE SCIENCES CERT - G AGRICULTURE AND FOOD SCI & TCHN-FOOD SCI BS 8 LIFE SCIENCES AGRICULTURE AND FOOD SCI & TCHN-INDUSTRY BS 31 LIFE SCIENCES AGRICULTURE AND FOOD SCIENCE & TECHNOLOGY BS 1 LIFE SCIENCES AGRICULTURE AND FOOD SCIENCE & TECHNOLOGY MS 5 LIFE SCIENCES AGRICULTURE AND FOOD SCIENCE & TECHNOLOGY PHD 3 LIFE SCIENCES AGRICULTURE AND FOOD SCIENCE & TECHNOLOGY MAGR 0 LIFE SCIENCES AGRICULTURE AND FOOD SYSTEMS INDUSTRY MANAGEMENT BS 0 LIFE SCIENCES AGRICULTURE AND FORENSIC & INVESTIGATIVE SCIENCES BS 24 LIFE SCIENCES AGRICULTURE AND FORESTRY BS 16 LIFE SCIENCES AGRICULTURE AND GENETICS BS 51 LIFE SCIENCES AGRICULTURE AND HORTICULTURE BA 11 LIFE SCIENCES AGRICULTURE AND HORTICULTURE BS 33 LIFE SCIENCES AGRICULTURE AND HORTICULTURE MAGR 1 LIFE SCIENCES AGRICULTURE AND HORTICULTURE MS 3 LIFE SCIENCES AGRICULTURE AND HORTICULTURE PHD 5 LIFE SCIENCES AGRICULTURE AND HOSPITALITY MANAGEMENT CERT - UG 32 LIFE SCIENCES AGRICULTURE AND INTERNATIONAL AGRICULTURE AND RESOURCE CERT - G 2 LIFE SCIENCES MANAGEMENT AGRICULTURE AND INTERNATIONAL TRADE & AGRICULTURE - CERT CERT - UG 33 LIFE SCIENCES AGRICULTURE AND LEADERSHIP EDUCATION, THEORY, AND PRACTICE CERT - G 15 LIFE SCIENCES

AGRICULTURE AND MEAT SCIENCE CERT - UG 19 LIFE SCIENCES AGRICULTURE AND MILITARY LAND SUSTAINABILITY CERT - G 3 LIFE SCIENCES AGRICULTURE AND NATURAL RESOURCES DEVELOPMENT MNRD 9 LIFE SCIENCES AGRICULTURE AND NUTRITION BS 128 LIFE SCIENCES AGRICULTURE AND NUTRITION MS 2 LIFE SCIENCES AGRICULTURE AND NUTRITION PHD 3 LIFE SCIENCES AGRICULTURE AND NUTRITIONAL SCIENCE BS 27 LIFE SCIENCES AGRICULTURE AND PARKS AND CONSERVATION* CERT - UG 25 LIFE SCIENCES AGRICULTURE AND PHYSIOLOGY OF REPRODUCTION MS 3 LIFE SCIENCES AGRICULTURE AND PHYSIOLOGY OF REPRODUCTION PHD 1 LIFE SCIENCES AGRICULTURE AND PLANT & ENVRNMNTL SOIL SCIENCE BS 26 LIFE SCIENCES AGRICULTURE AND PLANT BREEDING MS 5 LIFE SCIENCES AGRICULTURE AND PLANT BREEDING PHD 11 LIFE SCIENCES AGRICULTURE AND PLANT PATHOLOGY MS 2 LIFE SCIENCES AGRICULTURE AND PLANT PATHOLOGY PHD 5 LIFE SCIENCES AGRICULTURE AND POULTRY SCIENCE BS 6 LIFE SCIENCES AGRICULTURE AND POULTRY SCIENCE MAGR 1 LIFE SCIENCES AGRICULTURE AND POULTRY SCIENCE MS 2 LIFE SCIENCES AGRICULTURE AND POULTRY SCIENCE PHD 8 LIFE SCIENCES AGRICULTURE AND POULTRY SCIENCE-INDUSTRY BS 38 LIFE SCIENCES AGRICULTURE AND PROF EVENT MANAGER CERT - UG 94 LIFE SCIENCES AGRICULTURE AND PUBLIC HEALTH ENTOMOLOGY CERT - UG 30 LIFE SCIENCES AGRICULTURE AND RANGELAND ECOLOGY & MANAGEMENT BS 1 LIFE SCIENCES AGRICULTURE AND RANGLND ECL & MGT-RANCH MANAGEMENT BS 14 LIFE SCIENCES AGRICULTURE AND RANGLND ECL & MGT-RANGELAND RESOURCES BS 12 LIFE SCIENCES

AGRICULTURE AND REC, PARK & TOURISM SCI-COM REC & PRKS ADMIN BS 0 LIFE SCIENCES AGRICULTURE AND REC, PARK & TOURISM SCIENCES BS 145 LIFE SCIENCES AGRICULTURE AND REC, PARK & TOURISM SCI-PARKS & CONSERVATION BS 0 LIFE SCIENCES AGRICULTURE AND REC, PARK & TOURISM SCI-TOURISM MANAGEMENT BS 1 LIFE SCIENCES AGRICULTURE AND REC, PARK & TOURISM SCI-YOUTH DEVELOPMENT BS 1 LIFE SCIENCES AGRICULTURE AND RECREATION & RESOURCES DEVELOPMENT MRRD 1 LIFE SCIENCES AGRICULTURE AND RECREATION, PARK & TOURISM SCI MS 13 LIFE SCIENCES AGRICULTURE AND RECREATION, PARK & TOURISM SCI PHD 8 LIFE SCIENCES AGRICULTURE AND RENEWABLE NATURAL RESOURCES BS 26 LIFE SCIENCES AGRICULTURE AND SOIL SCIENCE MS 5 LIFE SCIENCES AGRICULTURE AND SOIL SCIENCE PHD 1 LIFE SCIENCES AGRICULTURE AND SPACE LIFE SCIENCES CERT - G 0 LIFE SCIENCES AGRICULTURE AND SPATIAL SCIENCES BS 5 LIFE SCIENCES AGRICULTURE AND TOURISM MANAGEMENT CERT - UG 74 LIFE SCIENCES AGRICULTURE AND TURFGRASS SCIENCE BS 8 LIFE SCIENCES VECTOR BIOL-BORN DISEAS RESPVECTOR BIOLOGY AND AGRICULTURE AND VECTOR-BORNE DISEASE RESPONSE IN HUMAN AND CERT - G 0 LIFE SCIENCES ANIMAL SYSTEMS AGRICULTURE AND WATERSHED CERT - UG 5 LIFE SCIENCES AGRICULTURE AND WILDLIFE & FISHERIES SCIENCES BS 73 LIFE SCIENCES AGRICULTURE AND WILDLIFE & FISHERIES SCIENCES MS 6 LIFE SCIENCES AGRICULTURE AND WILDLIFE & FISHERIES SCIENCES PHD 13 LIFE SCIENCES AGRICULTURE AND WILDLIFE SCIENCE MWSC 4 LIFE SCIENCES AGRICULTURE AND WL & FS SCI-VERTEBRATE ZOOLOGY BS 9 LIFE SCIENCES AGRICULTURE AND WL & FS SCI-WILDLIFE ECOLOGY & CONSERVATION BS 41 LIFE SCIENCES AGRICULTURE AND YOUTH DEVELOPMENT* CERT - UG 43 LIFE SCIENCES

ARCHITECTURE ARCHITECTURE MARCH 39 ARCHITECTURE ARCHITECTURE MS 3 ARCHITECTURE ARCHITECTURE PHD 6 ARCHITECTURE CONSTRUCTION SCIENCE BS 295 ARCHITECTURE CONSTRUCTION MANAGEMENT MS 15 ARCHITECTURE DIVERSITY (AR) CERT - UG 7 ARCHITECTURE ENVIRONMENTAL DESIGN ARCHITECHURAL STUDIES BED 79 ARCHITECTURE ENVIRONMENTAL HAZARD MANAGEMENT CERT - G 3 ARCHITECTURE FACILITY MANAGEMENT CERT - G 3 ARCHITECTURE HEALTH SYSTEMS AND DESIGN CERT - G 14 ARCHITECTURE HISTORIC PRESERVATION CERT - G 9 ARCHITECTURE LAND & PROPERTY DEVELOPMENT MLPD 33 ARCHITECTURE LANDSCAPE ARCHITECTURE BLA 31 ARCHITECTURE LANDSCAPE ARCHITECTURE MLA 17 ARCHITECTURE SUSTAINABLE URBANISM CERT - G 5 ARCHITECTURE TRANSPORTATION PLANNING CERT - G 3 ARCHITECTURE URBAN & REGIONAL PLANNING BS 46 ARCHITECTURE URBAN & REGIONAL PLANNING MUP 18 ARCHITECTURE URBAN & REGIONAL SCIENCE PHD 5 ARCHITECTURE VISUALIZATION BS 92 ARCHITECTURE VISUALIZATION MFA 10 ARCHITECTURE VISUALIZATION MS 11 BUSH SCHOOL OF GOVERNMENT & HOMELAND SECURITY CERT - G 24 PUBLIC SERVICE BUSH SCHOOL OF GOVERNMENT & INTERNATIONAL AFFAIRS MIA 73 PUBLIC SERVICE BUSH SCHOOL OF GOVERNMENT & ADVANCED INTERNATIONAL AFFAIRS CERT - G 35 PUBLIC SERVICE BUSH SCHOOL OF GOVERNMENT & INTERNATIONAL POLICY MIP 1 PUBLIC SERVICE BUSH SCHOOL OF GOVERNMENT & NATIONAL SECURITY AFFAIRS CERT - G 0 PUBLIC SERVICE BUSH SCHOOL OF GOVERNMENT & NON-PROFIT MANAGEMENT CERT - G 31 PUBLIC SERVICE

BUSH SCHOOL OF GOVERNMENT & PUBLIC MANAGMENT CERT - G 26 PUBLIC SERVICE BUSH SCHOOL OF GOVERNMENT & PUBLIC SERVICE AND ADMINISTRATION MPSA 103 PUBLIC SERVICE 9

BUSINESS ACCOUNTING BBA 349 BUSINESS ACCOUNTING MS 128 BUSINESS ADVERTISING STRATEGY CERT - UG 0 BUSINESS ANALYTICS & CONSULTING CERT - UG 0 BUSINESS BUSINESS MS 32 BUSINESS BUSINESS ADMINISTRATION MBA 58 BUSINESS BUSINESS ADMINISTRATION PHD 14 BUSINESS BUSINESS DATA ANALYSIS* CERT - G 8 BUSINESS BUSINESS HONORS BBA 60 BUSINESS BUSINESS INTELLIGENCE & ANALYTICS CERT - G 0 BUSINESS BUSINESS MANAGEMENT* CERT - G 0 BUSINESS CAPITAL MARKETS & INVESTMENTS* CERT - UG 0 BUSINESS COMMERCIAL BANKING* CERT - UG 0 BUSINESS CORPORATE FINANCE* CERT - UG 0 BUSINESS ENERGY ACCOUNTING CERT - UG 15 BUSINESS ENTREPRENEURIAL LEADERSHIP CERT - UG 1 BUSINESS ENTREPRENEURIAL LEADERSHIP MS 13 BUSINESS ENTREPRENEURSHIP CERT - G 13 BUSINESS EUROPEAN UNION BUSINESS CERT - UG 1 BUSINESS EXECUTIVE MBA MBA 36 BUSINESS FINANCE BBA 212 BUSINESS FINANCE* CERT - G 11 BUSINESS FINANCE MS 41 BUSINESS FINANCIAL MANAGEMENT MFM 123 BUSINESS HUMAN RESOURCE MANAGEMENT MS 39 BUSINESS INTERNAL AUDIT* CERT - UG 12 BUSINESS INTERNATIONAL BUSINESS* CERT - G 0 BUSINESS INTERNATIONAL BUSINESS STUDIES CERT - UG 47 BUSINESS INVESTMENT BANKING & PRIVATE EQUITY* CERT - UG 0 BUSINESS INVESTMENT BANKING* CERT - UG 1 BUSINESS LAND ECONOMICS & REAL ESTATE MRE 42 BUSINESS LATIN AMERICAN BUSINESS CERT - UG 0 BUSINESS MANAGEMENT BBA 216 BUSINESS MANAGEMENT PHD 2 BUSINESS MANAGEMENT INFORMATION SYSTEMS BBA 92 BUSINESS MANAGEMENT INFORMATION SYSTEMS MS 148 BUSINESS MARKETING BBA 214 BUSINESS MARKETING* CERT - G 13 BUSINESS MARKETING MS 35 BUSINESS NONPROFIT & SOCIAL INNOV CERT - UG 14 BUSINESS NONPROFIT & SOCIAL INNOVATION CERT - UG 0 BUSINESS PROFESSIONAL MBA MBA 46 BUSINESS SUPPLY CHAIN AND OPERATIONS* CERT - G 6 10

BUSINESS SUPPLY CHAIN MANAGEMENT BBA 124 BUSINESS TRADING, RISK & INVESTMENTS* CERT - UG 0 DENTISTRY ADVANCED EDUCATON IN GENERAL DENTISTRY CERT - G 9 DENTISTRY DENTAL HYGIENE BS 28 DENTISTRY DENTAL HYGIENE MS 0 DENTISTRY DENTAL PUBLIC HEALTH CERT - G 0 DENTISTRY DENTISTRY DDS 104 DENTISTRY ENDODONTICS CERT - G 4 DENTISTRY ORAL AND MAXILLOFACIAL PATHOLOGY CERT - G 1 DENTISTRY ORAL AND MAXILLOFACIAL RADIOLOGY CERT - G 1 DENTISTRY ORAL AND MAXILLOFACIAL SURGERY CERT - G 3 DENTISTRY ORAL BIOLOGY MS 15 DENTISTRY ORAL BIOLOGY PHD 3 DENTISTRY ORTHODONTICS* CERT - G 6 DENTISTRY PEDIATRIC DENTISTRY CERT - G 10 DENTISTRY PERIODONTICS* CERT - G 3 DENTISTRY PROSTHODONTICS* CERT - G 4 EDUCATION & HUMAN APPLIED BEHAVIOR ANALYSIS CERT - G 30 DEVELOPMENT EDUCATION & HUMAN ATHLETIC TRAINING MS 16 DEVELOPMENT EDUCATION & HUMAN BILINGUAL EDUCATION MED 1 DEVELOPMENT EDUCATION & HUMAN BILINGUAL EDUCATION MS 0 DEVELOPMENT EDUCATION & HUMAN COMMUNITY HEALTH BS 85 DEVELOPMENT EDUCATION & HUMAN COUNSELING PSYCHOLOGY PHD 6 DEVELOPMENT EDUCATION & HUMAN CREATIVE STUDIES CERT - UG 0 DEVELOPMENT EDUCATION & HUMAN CURRICULUM & INSTRUCTION EDD 14 DEVELOPMENT EDUCATION & HUMAN CURRICULUM & INSTRUCTION MED 180 DEVELOPMENT EDUCATION & HUMAN CURRICULUM & INSTRUCTION MS 3 DEVELOPMENT

EDUCATION & HUMAN CURRICULUM & INSTRUCTION PHD 16 DEVELOPMENT EDUCATION & HUMAN EDUC & SOC SCI ADV RES METH CERT - G 22 DEVELOPMENT EDUCATION & HUMAN EDUC HUMAN RESOURCE DEVELOPMENT MS 37 DEVELOPMENT EDUCATION & HUMAN EDUC HUMAN RESOURCE DEVELOPMENT PHD 7 DEVELOPMENT EDUCATION & HUMAN EDUCATIONAL ADMINISTRATION EDD 3 DEVELOPMENT EDUCATION & HUMAN EDUCATIONAL ADMINISTRATION MED 56 DEVELOPMENT EDUCATION & HUMAN EDUCATIONAL ADMINISTRATION MS 27 DEVELOPMENT EDUCATION & HUMAN EDUCATIONAL ADMINISTRATION PHD 7 DEVELOPMENT EDUCATION & HUMAN EDUCATIONAL PSYCHOLOGY MED 47 DEVELOPMENT EDUCATION & HUMAN EDUCATIONAL PSYCHOLOGY MS 2 DEVELOPMENT EDUCATION & HUMAN EDUCATIONAL PSYCHOLOGY PHD 5 DEVELOPMENT EDUCATION & HUMAN EDUCATIONAL TECHNOLOGY MED 28 DEVELOPMENT EDUCATION & HUMAN HEALTH BS 285 DEVELOPMENT EDUCATION & HUMAN HEALTH EDUCATION MS 24 DEVELOPMENT EDUCATION & HUMAN HEALTH EDUCATION PHD 7 DEVELOPMENT EDUCATION & HUMAN HUMAN RESOURCES DEVELOPMENT BS 104 DEVELOPMENT EDUCATION & HUMAN INTERDISCIPLINARY STUDIES BS 435 DEVELOPMENT EDUCATION & HUMAN KINESIOLOGY BS 278 DEVELOPMENT 12

EDUCATION & HUMAN KINESIOLOGY MS 23 DEVELOPMENT EDUCATION & HUMAN KINESIOLOGY PHD 8 DEVELOPMENT EDUCATION & HUMAN LATINO MENTAL HEALTH* CERT - G 0 DEVELOPMENT EDUCATION & HUMAN PREVENTION SCIENCE CERT - G 2 DEVELOPMENT EDUCATION & HUMAN SCHOOL PSYCHOLOGY PHD 10 DEVELOPMENT EDUCATION & HUMAN SCI TECH ENGR MATH (STEM) CERT - G 8 DEVELOPMENT EDUCATION & HUMAN SPECIAL EDUCATION MED 29 DEVELOPMENT EDUCATION & HUMAN SPECIAL EDUCATION MS 0 DEVELOPMENT EDUCATION & HUMAN SPORTS MANAGEMENT BS 204 DEVELOPMENT EDUCATION & HUMAN SPORTS MANAGEMENT MS 61 DEVELOPMENT EDUCATION & HUMAN TECHNOLOGY MANAGMENT BS 74 DEVELOPMENT EDUCATION & HUMAN UNIVERSITY STUDIES - EDUCATION BS 97 DEVELOPMENT ENGINEERING AEROSPACE ENGINEERING BS 147 ENGINEERING AEROSPACE ENGINEERING MENGR 17 ENGINEERING AEROSPACE ENGINEERING MS 15 ENGINEERING AEROSPACE ENGINEERING PHD 14 ENGINEERING BIOMEDICAL ENGINEERING BS 130 ENGINEERING BIOMEDICAL ENGINEERING MENGR 23 ENGINEERING BIOMEDICAL ENGINEERING MS 4 ENGINEERING BIOMEDICAL ENGINEERING PHD 9 ENGINEERING CHEMICAL ENGINEERING BS 242 ENGINEERING CHEMICAL ENGINEERING MENGR 9 ENGINEERING CHEMICAL ENGINEERING MS 22 ENGINEERING CHEMICAL ENGINEERING PHD 26 ENGINEERING CIVIL ENGINEERING BS 248 ENGINEERING CIVIL ENGINEERING MENGR 108 13

ENGINEERING CIVIL ENGINEERING MS 32 ENGINEERING CIVIL ENGINEERING PHD 24 ENGINEERING COMPUTATIONAL SCIENCES CERT - G 0 ENGINEERING COMPUTER ENGINEERING BS 141 ENGINEERING COMPUTER ENGINEERING MENGR 91 ENGINEERING COMPUTER ENGINEERING MS 34 ENGINEERING COMPUTER ENGINEERING PHD 15 ENGINEERING COMPUTER SCIENCE BS 227 ENGINEERING COMPUTER SCIENCE MCS 82 ENGINEERING COMPUTER SCIENCE MS 19 ENGINEERING COMPUTER SCIENCE PHD 9 ENGINEERING COMPUTING BA 0 ENGINEERING DATA CENTER OPERATIONS ENGINEERING CERT - UG 9 ENGINEERING ELECTRICAL ENGINEERING BS 276 ENGINEERING ELECTRICAL ENGINEERING MENGR 71 ENGINEERING ELECTRICAL ENGINEERING MS 37 ENGINEERING ELECTRICAL ENGINEERING PHD 43 ENGINEERING ELECTRONIC SYSTEMS ENGINEERING TECHNOLOGY BS 73 ENGINEERING ENERGY ENGINEERING CERT - UG 4 ENGINEERING ENERGY-CERTIFICATE CERT - G 3 ENGINEERING ENGINEERING MENGR 15 ENGINEERING ENGINEERING DENGR 0 ENGINEERING ENGINEERING LEADERSHIP CERT - UG 24 ENGINEERING ENGINEERING SYSTEMS MANAGEMENT CERT - UG 1 ENGINEERING ENGINEERING SYSTEMS MANAGEMENT MS 17 ENGINEERING ENGR TCHN-MANUFACTURING & MCHNCL ENGR BS 1 ENGINEERING ENGR THERAPEUTICS MANUF CERT - UG 6 ENGINEERING ENGR THERAPEUTICS MANUF CERT - G 0 ENGINEERING ENGR THERAPEUTICS MANUF CERT - UG 0 ENGINEERING HOLISTIC LEADERSHIP IN ENGR CERT - UG 5 ENGINEERING INDUSTRIAL DATA ANALYTICS CERT - UG 11 ENGINEERING INDUSTRIAL DISTRIBUTION BS 383 ENGINEERING INDUSTRIAL DISTRIBUTION MID 45 ENGINEERING INDUSTRIAL ENGINEERING BS 194 ENGINEERING INDUSTRIAL ENGINEERING MENGR 59 ENGINEERING INDUSTRIAL ENGINEERING MS 35 ENGINEERING INDUSTRIAL ENGINEERING PHD 5 ENGINEERING INTERDISCIPLINARY ENGINEERING BS 2 ENGINEERING INTERDISCIPLINARY ENGINEERING MS 2 ENGINEERING INTERDISCIPLINARY ENGINEERING PHD 1 ENGINEERING INTERNATIONAL ENGINEERING* CERT - UG 16 ENGINEERING INTERNATIONAL PETROLEUM MANAGEMENT CERT - G 0 ENGINEERING MANUFACTURING & MECHANICAL ENGR TECHNOLOGY BS 93 14

ENGINEERING MATERIALS SCIENCE & ENGINEERING MS 15 ENGINEERING MATERIALS SCIENCE & ENGINEERING PHD 15 ENGINEERING MATERIALS SCIENCE & ENGINEERING BS 0 ENGINEERING MATERIALS SCIENCE & ENGINEERING MENGR 0 ENGINEERING MATERIALS, INFORMATICS &DESIGN CERT - G 3 ENGINEERING MECHANICAL ENGINEERING BS 412 ENGINEERING MECHANICAL ENGINEERING MENGR 37 ENGINEERING MECHANICAL ENGINEERING MS 51 ENGINEERING MECHANICAL ENGINEERING PHD 47 ENGINEERING MULTIDISCIPLINARY ENGINEERING TECHNOLOGY BS 5 ENGINEERING NUCLEAR ENGINEERING BS 80 ENGINEERING NUCLEAR ENGINEERING MENGR 1 ENGINEERING NUCLEAR ENGINEERING MS 15 ENGINEERING NUCLEAR ENGINEERING PHD 17 ENGINEERING NUCLEAR SECURITY CERT - G 2 ENGINEERING OCEAN ENGINEERING BS 35 ENGINEERING OCEAN ENGINEERING MENGR 16 ENGINEERING OCEAN ENGINEERING MS 6 ENGINEERING OCEAN ENGINEERING PHD 4 ENGINEERING PETROLEUM ENGINEERING BS 179 ENGINEERING PETROLEUM ENGINEERING MENGR 23 ENGINEERING PETROLEUM ENGINEERING MS 29 ENGINEERING PETROLEUM ENGINEERING PHD 43 ENGINEERING PETROLEUM VETURES CERT - UG 27 ENGINEERING POLYMER SPECIALTY CERT - UG 1 QUALITY ENGINEERING FOR REGULATED MED ENGINEERING CERT - G 5 TECHNOLOGIES QUALITY ENGINEERING FOR REGULATED MED ENGINEERING CERT - UG 1 TECHNOLOGIES ENGINEERING RADIOLOGICAL HEALTH ENGINEERING BS 5 ENGINEERING SAFETY ENGINEERING CERT - UG 42 ENGINEERING SAFETY ENGINEERING MS 6 ENGINEERING SAFTEY ENGINEERING CERT - G 2 ENGINEERING SYSTEMS ENGINEERING MENGR 0 ENGINEERING TECHNICAL MANAGEMENT METM 0 GEOSCIENCES ATMOSPHERIC SCIENCE MS 6 GEOSCIENCES ATMOSPHERIC SCIENCE PHD 4 GEOSCIENCES ENVIRONMENTAL GEOSCIENCE BS 53 GEOSCIENCES GEOGRAPHIC INFORMATION SCIENCE AND TECHNOLOGY BS 46 GEOSCIENCES GEOGRAPHY BS 20 GEOSCIENCES GEOGRAPHY MS 7 GEOSCIENCES GEOGRAPHY PHD 2 GEOSCIENCES GEOL-ENGINEERING GEOLOGY BS 0

GEOSCIENCES GEOLOGY BA 5 GEOSCIENCES GEOLOGY BS 66 GEOSCIENCES GEOLOGY MS 10 GEOSCIENCES GEOLOGY PHD 7 GEOSCIENCES GEOPHYSICS BS 40 GEOSCIENCES GEOPHYSICS MS 5 GEOSCIENCES GEOPHYSICS PHD 7 GEOSCIENCES GEOSCIENCE MGSC 12 GEOSCIENCES METEOROLOGY BS 25 GEOSCIENCES OCEAN OBSERVING SYSTEMS CERT - G 2 GEOSCIENCES OCEAN SCIENCE AND TECHNOLOGY MOST 6 GEOSCIENCES OCEANOGRAPHY BS 2 GEOSCIENCES OCEANOGRAPHY MS 3 GEOSCIENCES OCEANOGRAPHY PHD 6 GEOSCIENCES PETROLEUM GEOSCIENCE* CERT - G 0 GEOSCIENCES SPATIAL SCIENCES BS 0 LIBERAL ARTS AFRICANA STUDIES CERT - G 2 LIBERAL ARTS ANTHROPOLOGY BA 38 LIBERAL ARTS ANTHROPOLOGY BS 7 LIBERAL ARTS ANTHROPOLOGY MA 6 LIBERAL ARTS ANTHROPOLOGY PHD 9 LIBERAL ARTS APPLIED BEHAVIORIAL HEALTH* CERT - UG 35 LIBERAL ARTS BUSINESS ECONOMICS* CERT - UG 0 LIBERAL ARTS CLASSICS BA 3 LIBERAL ARTS CLINICAL PSYCHOLOGY PHD 4 LIBERAL ARTS COMMUNITY & GLOBAL MEDIA CERT - UG 0 LIBERAL ARTS COMMUNICATION BA 342 LIBERAL ARTS COMMUNICATION MA 1 LIBERAL ARTS COMMUNICATION PHD 7 LIBERAL ARTS COMMUNICATION AND GLOBAL MEDIA CERT - UG 6 COMMUNICATION LEADERSHIP AND CONFLICT LIBERAL ARTS CERT - UG 9 MANAGEMENT LIBERAL ARTS CONSERVATION TRAINING CERT - G 3 LIBERAL ARTS DIGITAL HUMANITIES CERT - G 2 LIBERAL ARTS DIVERSITY (LA) CERT - UG 4 LIBERAL ARTS ECONOMICS BA 13 LIBERAL ARTS ECONOMICS BS 239 LIBERAL ARTS ECONOMICS MS 111 LIBERAL ARTS ECONOMICS PHD 12 LIBERAL ARTS ENGLISH BA 157 LIBERAL ARTS ENGLISH MA 10 LIBERAL ARTS ENGLISH PHD 13 LIBERAL ARTS EUROPEAN UNION POLITICS - CERTIFICATE CERT - UG 0 16

LIBERAL ARTS FILM & MEDIA STUDIES CERT - G 0 LIBERAL ARTS HEALTH COMMUNICATION CERT - UG 2 LIBERAL ARTS HEALTHY DEVELOPMENT* CERT - UG 6 LIBERAL ARTS HISPANIC STUDIES PHD 5 LIBERAL ARTS HISPANIC STUDIES MA 0 LIBERAL ARTS HISTORY BA 142 LIBERAL ARTS HISTORY MA 1 LIBERAL ARTS HISTORY PHD 6 LIBERAL ARTS INDUSTRIAL/ORGANIZATIONAL PSYCHOLOGY PHD 1 LIBERAL ARTS INTERNATIONAL RELATIONS CERT - UG 0 LIBERAL ARTS INTERNATIONAL STUDIES BA 178 LIBERAL ARTS INTERNATIONAL COMMUNICATION & PUBLIC DIPLOMACY CERT - G 0 LIBERAL ARTS LATINO AND MEXICAN AMERICAN STUDIES CERT - G 1 LIBERAL ARTS MARITIME ARCHAEOLOGY AND CONSERVATION MS 3 LIBERAL ARTS MODERN LANGUAGES BA 9 LIBERAL ARTS MUSIC BA 2 LIBERAL ARTS PERFORMANCE STUDIES BA 19 LIBERAL ARTS PERFORMANCE STUDIES MA 6 LIBERAL ARTS PHILOSOPHY BA 42 LIBERAL ARTS PHILOSOPHY MA 2 LIBERAL ARTS PHILOSOPHY PHD 2 LIBERAL ARTS PHILOSOPHY PRE-LAW CERT - UG 4 LIBERAL ARTS POLITICAL SCIENCE BA 139 LIBERAL ARTS POLITICAL SCIENCE BS 133 LIBERAL ARTS POLITICAL SCIENCE MA 5 LIBERAL ARTS POLITICAL SCIENCE PHD 6 LIBERAL ARTS PSYCHOLOGY BA 97 LIBERAL ARTS PSYCHOLOGY BS 397 LIBERAL ARTS PSYCHOLOGY MS 4 LIBERAL ARTS PSYCHOLOGY PHD 3 LIBERAL ARTS PSYCHOLOGY OF DIVERSITY* CERT - UG 11 LIBERAL ARTS QUANTITATIVE ECON METHODS* CERT - UG 0 LIBERAL ARTS RACE,ETHN & GEN POLITICS CERT - UG 1 LIBERAL ARTS SOCIAL MEDIA* CERT - UG 0 LIBERAL ARTS SOCIOLOGY BA 61 LIBERAL ARTS SOCIOLOGY BS 185 LIBERAL ARTS SOCIOLOGY MS 1 LIBERAL ARTS SOCIOLOGY PHD 10 LIBERAL ARTS SPANISH BA 20 LIBERAL ARTS STRATEGIC COMMUNICATION* CERT - UG 27 LIBERAL ARTS TELECOMMUNICATION MEDIA STUDIES BA 45 LIBERAL ARTS TELECOMMUNICATION MEDIA STUDIES BS 23

LIBERAL ARTS THEATER ARTS BA 1 LIBERAL ARTS WOMEN'S & GENDER STUDIES - CERTIFICATE CERT - G 4 LIBERAL ARTS WOMEN'S AND GENDER STUDIES BA 7 LIBERAL ARTS WORK & ORGANIZATIONS* CERT - UG 8 MEDICINE EDUCATION FOR HEALTHCARE PROFESSIONALS CERT - G 2 MEDICINE EDUCATION FOR HEALTHCARE PROFESSIONALS MS 6 MEDICINE MEDICAL SCIENCES MS 5 MEDICINE MEDICAL SCIENCES PHD 21 MEDICINE MEDICINE MD 193 MILITARY SCIENCE LDRSHP STUDY & DEVELOPMNT CERT - UG 61 NURSING FAMILY NURSE PRACTITIONER MSN 17 NURSING FORENSIC HEALTHCARE - CERTIFICATE CERT - G 1 NURSING FORENSIC NURSING MSN 0 NURSING NURSING BSN 197 NURSING NURSING EDUCATION MSN 8 PHARMACY PHARMACY PHARMD 110 PUBLIC HEALTH BIOSTATISTICS MPH 5 PUBLIC HEALTH BIOSTATISTICS MSPH 0 PUBLIC HEALTH ENVIRONMENTAL HEALTH MPH 11 PUBLIC HEALTH ENVIRONMENTAL HEALTH MSPH 0 PUBLIC HEALTH EPIDEMIOLOGY MPH 45 PUBLIC HEALTH EPIDEMIOLOGY MSPH 0 PUBLIC HEALTH EPIDEMIOLOGY AND ENVIRONMENTAL HEALTH DRPH 5 PUBLIC HEALTH EXECUTIVE HEALTH ADMINISTRATION MHA 11 PUBLIC HEALTH HEALTH ADMINISTRATION MHA 18 PUBLIC HEALTH HEALTH POLICY AND MANAGMENT MPH 10 PUBLIC HEALTH HEALTH POLICY AND MANAGMENT MSPH 0 PUBLIC HEALTH HEALTH PROMOTION AND COMMUNITY HEALTH SCIENCES DRPH 6 PUBLIC HEALTH HEALTH PROMOTION AND COMMUNITY HEALTH SCIENCES MPH 19 PUBLIC HEALTH HEALTH PROMOTION AND COMMUNITY HEALTH SCIENCES MSPH 0 PUBLIC HEALTH HEALTH SERVICES RESEARCH PHD 2 PUBLIC HEALTH HEALTH SYSTEMS MGMT CERT - G 0 PUBLIC HEALTH HLTH COACH CHRON DIS PREV MGMT CERT - G 11 PUBLIC HEALTH MATERNAL & CHILD HEALTH CERT - G 1 PUBLIC HEALTH OCCUPATIONAL SAFETY AND HEALTH MPH 11 PUBLIC HEALTH PUBLIC HEALTH BS 121 PUBLIC HEALTH PUBLIC HEALTH CERT - G 1 SCIENCE ANALYTICS MS 54 SCIENCE APPLIED MATHEMATICAL SCIENCES BS 89 SCIENCE APPLIED PHYSICS PHD 1 SCIENCE APPLIED STATISTICS CERT - G 20 SCIENCE ASTRONOMY MS 5

SCIENCE ASTRONOMY PHD 1 SCIENCE BIOLOGY BA 12 SCIENCE BIOLOGY BS 151 SCIENCE BIOLOGY MS 2 SCIENCE BIOLOGY PHD 7 SCIENCE CHEMISTRY BA 17 SCIENCE CHEMISTRY BS 48 SCIENCE CHEMISTRY MS 3 SCIENCE CHEMISTRY PHD 34 SCIENCE MATHEMATICS BA 26 SCIENCE MATHEMATICS BS 9 SCIENCE MATHEMATICS MS 26 SCIENCE MATHEMATICS PHD 15 SCIENCE MICROBIOLOGY BS 23 SCIENCE MICROBIOLOGY MS 1 SCIENCE MICROBIOLOGY PHD 1 SCIENCE MOLECULAR & CELL BIOLOGY BS 9 SCIENCE NEUROSCIENCE CERT - UG 2 SCIENCE PHYSICS BA 8 SCIENCE PHYSICS BS 26 SCIENCE PHYSICS MS 8 SCIENCE PHYSICS PHD 14 SCIENCE QUANTITATIVE FINANCE MS 0 SCIENCE STATISTICS BS 11 SCIENCE STATISTICS MS 70 SCIENCE STATISTICS PHD 8 SCIENCE ZOOLOGY BS 12 TAMU AT GALVESTON MARINE BIOLOGY BS 92 TAMU AT GALVESTON MARINE BIOLOGY MS 6 TAMU AT GALVESTON MARINE BIOLOGY PHD 0 TAMU AT GALVESTON MARINE ENGINEERING TECHNOLOGY BS 41 TAMU AT GALVESTON MARINE FISHERIES BS 21 TAMU AT GALVESTON MARINE RESOURCES MANAGMENT MMRM 12 TAMU AT GALVESTON MARINE SCIENCES BS 10 TAMU AT GALVESTON MARINE TRANSPORTATION BS 70 TAMU AT GALVESTON MARITIME ADMINISTRATION BS 106 TAMU AT GALVESTON MARITIME ADMINISTRATION & LOGISTICS MMAL 27 TAMU AT GALVESTON MARITIME STUDIES BA 21 TAMU AT GALVESTON OCEAN AND COASTAL RESOURCES BS 21 TAMU AT GALVESTON OFFSHORE & COASTAL SYSTEMS ENGINEERING BS 22 TEXAS A&M SCHOOL HEALTH CARE LAW JM 0 OF LAW

TEXAS A&M SCHOOL INTELLECTUAL PROPERTY LLM 0 OF LAW TEXAS A&M SCHOOL INTELLECTUAL PROPERTY MJUR 0 OF LAW TEXAS A&M SCHOOL JURISPRUDENCE MJUR 40 OF LAW TEXAS A&M SCHOOL LAW JD 130 OF LAW TEXAS A&M SCHOOL LAWS LLM 18 OF LAW UNIVERSITY AGRIBUSINESS MAB 20 INTERDISCIPLINARY UNIVERSITY AGRIBUSINESS & MANAGERIAL ECONOMICS PHD 2 INTERDISCIPLINARY UNIVERSITY BIOTECHNOLOGY MBIOT 11 INTERDISCIPLINARY UNIVERSITY ECOLOGY AND EVOLUTIONARY BIOLOGY PHD 0 INTERDISCIPLINARY UNIVERSITY ENERGY MS 9 INTERDISCIPLINARY UNIVERSITY ENVIRONMENTAL STUDIES BS 52 INTERDISCIPLINARY UNIVERSITY GENETICS MS 3 INTERDISCIPLINARY UNIVERSITY GENETICS PHD 11 INTERDISCIPLINARY UNIVERSITY GEOGRAPHIC INFORMATION SCIENCE CERT - G 25 INTERDISCIPLINARY UNIVERSITY MARINE BIOLOGY MS 1 INTERDISCIPLINARY UNIVERSITY MARINE BIOLOGY PHD 2 INTERDISCIPLINARY UNIVERSITY MOLECULAR & ENVIRONMENTAL PLANT SCIENCE MS 3 INTERDISCIPLINARY UNIVERSITY MOLECULAR & ENVIRONMENTAL PLANT SCIENCE PHD 1 INTERDISCIPLINARY UNIVERSITY NEUROSCIENCE PHD 2 INTERDISCIPLINARY UNIVERSITY NEUROSCIENCE MS 0 INTERDISCIPLINARY UNIVERSITY REMOTE SENSING - CERTIFICATE CERT - G 2 INTERDISCIPLINARY UNIVERSITY SPATIAL SCIENCES BS 0 INTERDISCIPLINARY UNIVERSITY TOXICOLOGY MS 1 INTERDISCIPLINARY UNIVERSITY TOXICOLOGY PHD 2 INTERDISCIPLINARY UNIVERSITY UNIVERSITY STUDIES - AGRICULTURE BS 96 INTERDISCIPLINARY

UNIVERSITY UNIVERSITY STUDIES - ARCHITECTURE BS 196 INTERDISCIPLINARY UNIVERSITY UNIVERSITY STUDIES - BUSINESS ADMIN BS 165 INTERDISCIPLINARY UNIVERSITY UNIVERSITY STUDIES - ENGINEERING BS 0 INTERDISCIPLINARY UNIVERSITY UNIVERSITY STUDIES - GALVESTON BS 9 INTERDISCIPLINARY UNIVERSITY UNIVERSITY STUDIES - GALVESTON BA 0 INTERDISCIPLINARY UNIVERSITY UNIVERSITY STUDIES - GENERAL AGRICULTURE BS 0 INTERDISCIPLINARY UNIVERSITY UNIVERSITY STUDIES - GEOSCIENCES BS 6 INTERDISCIPLINARY UNIVERSITY UNIVERSITY STUDIES - LEADERSHIP STUDIES BS 0 INTERDISCIPLINARY UNIVERSITY UNIVERSITY STUDIES - LIBERAL ARTS BA 24 INTERDISCIPLINARY UNIVERSITY UNIVERSITY STUDIES - LIBERAL ARTS BS 26 INTERDISCIPLINARY UNIVERSITY UNIVERSITY STUDIES - SCIENCE BS 10 INTERDISCIPLINARY UNIVERSITY UNIVERSITY STUDIES - VETERINARY MED BS 52 INTERDISCIPLINARY UNIVERSITY WATER MANAGEMENT AND HYDRO SCI MS 6 INTERDISCIPLINARY UNIVERSITY WATER MANAGEMENT AND HYDRO SCI MWM 9 INTERDISCIPLINARY UNIVERSITY WATER MANAGEMENT AND HYDRO SCI PHD 3 INTERDISCIPLINARY VETERINARY MEDICINE & BIOMEDICAL RESEARCH AND DEVELOPMENT CERT - UG 34 BIOMEDICAL SCIENCES VETERINARY MEDICINE & BIOMEDICAL BIOMEDICAL SCIENCES BS 466 SCIENCES VETERINARY MEDICINE & BIOMEDICAL BIOMEDICAL SCIENCES MS 51 SCIENCES

VETERINARY MEDICINE & BIOMEDICAL BIOMEDICAL SCIENCES PHD 14 SCIENCES

VETERINARY MEDICINE & CULTURAL COMPETENCY & COMMUNICATION IN CERT - UG 34 BIOMEDICAL SPANISH* SCIENCES VETERINARY MEDICINE & SCIENCE & TECHNOLOGY JOURNALISM MS 3 BIOMEDICAL SCIENCES VETERINARY MEDICINE & VETERINARY MEDICINE DVM 131 BIOMEDICAL SCIENCES VETERINARY MEDICINE & VETERINARY PATHOBIOLOGY PHD 6 BIOMEDICAL SCIENCES VETERINARY MEDICINE & VETERINARY PUBLIC HEALTH - EPIDEMIOLOGY MS 4 BIOMEDICAL SCIENCES

*Major dependent certificates

3. Off-Campus Instructional Locations and Branch Campuses List all approved off-campus instructional locations where 25% or more credit hours toward a degree, diploma, or certificate can be obtained primarily through traditional classroom instruction. Report those locations in accord with the Commission’s definitions and the directions as specified below.

Table 1: Off-campus instructional sites—a site located geographically apart from the main campus at which the institution offers 50 % or more of its credit hours for a diploma, certificate, or degree. This includes high schools where courses are offered as part of dual enrollment. For each site, provide the information below. The list should include only those sites reported to and approved by SACSCOC. Listing unapproved sites below does not constitute reporting them to SACSCOC. In such cases when an institution has initiated an off-campus instructional site as described above without prior approval by SACSCOC, a prospectus for approval should be submitted immediately to SACSCOC.

Is the site currently active? (At any time Date during the past 5 Date Physical Address (street, Approved Educational programs offered (specific years, have students Implemente Name of Site city, state, country) Do by degrees, certificates, diplomas) with 50% been enrolled and d by the not include PO Boxes. SACSCOC or more credits hours offered at each site courses offered? If institution not, indicate the date of most recent activity.) MEDICAL SCIENCES MS

8441 State Highway 47 Texas A&M Clinical Building 1, Suite MEDICAL SCIENCES PHD Health Science 2000 2000 Yes 3100 Center MEDICINE MD Bryan, TX 77807

NURSING BSN Baylor 3500 Gaston Avenue University Dallas, TX 75246 2012 2011 MEDICINE MD Yes Medical Center ADVANCED EDUCATION CERT-G IN GENERAL DENTISTRY DENTAL HYGIENE BS DENTAL PUBLIC HEALTH CERT-G DENTISTRY DDS ENDODONTICS CERT-G

ORAL AND MAXILLOFACIAL CERT-G SURGERY ORAL AND MAXILLOFACIAL CERT-G College of 3302 Gaston Ave. 2001 2000 PATHOLOGY Yes Dentistry Dallas, TX 75246 ORAL AND MAXILLOFACIAL CERT-G RADIOLOGY ORAL BIOLOGY MS ORAL BIOLOGY PHD CERT-G ORTHODONTICS

CERT-G PEDIATRIC DENTISTRY

CERT-G PERIODONTICS

CERT-G PROSTHODONTICS

HEALTH CARE LAW JM INTELLECTUAL ML PROPERTY Texas A&M 1515 Commerce St INTELLECTUAL University 2013 2013 MJ Yes Fort Worth, TX 76102 PROPERTY School of Law JURISPRUDENCE MJ LAW JD LAWS ML ANALYTICS MS 800 West Sam Houston BUSINESS Parkway North, Suite ADMINISTRATION - MBA City Centre 200 2012 2012 EXECUTIVE Yes Houston, TX 77024- BUSINESS 3920 ADMINISTRATION - MBA PROFESSIONAL MEDICINE MD 6670 Bertner Avenue, Houston R2-216 MEDICAL SCIENCES MS Methodist 2015 2015 Yes Houston, TX 77030 Hospital MEDICAL SCIENCES PHD

ENGINEERING MEN HEALTH MHA ADMINISTRATION Institute of 2121 W. Holcombe Biosciences and Blvd. 2000 2000 MEDICINE MD Yes Technology Houston, TX 77030 MEDICAL SCIENCES MS MEDICAL SCIENCES PHD Rangel College 1010 W. Avenue B. 2011 2006 PHARMACY PHMD Yes of Pharmacy Kingsville, TX 78363 Lawrence Livermore 7000 East Avenue NATIONAL SECURITY 2018 2008 CERT-G National Livermore, CA 94550 AFFAIRS Laboratory Sandia National 7011 East Avenue NATIONAL SECURITY Laboratories, 2018 2008 CERT-G Livermore, CA 94550 AFFAIRS California Sandia National 1515 Eubank S.E. NATIONAL SECURITY Laboratories, Albuquerque, NM 2018 2008 CERT-G AFFAIRS New Mexico 87123

School of Public HEALTH PROMOTION 2101 South McColl Health - AND COMMUNITY MPH Road 2011 2010 Yes McAllen HEALTH SCIENCES McAllen, TX 78503 Teaching Site PUBLIC HEALTH BS BIOMEDICAL SCIENCES BS FOOD SYSTEMS Texas A&M BS INDUSTRY MANGEMENT Higher 6200 Tres Lagos Blvd Education 2017 2018 INTERDISCIPLINARY McAllen, TX 78504 BS Center at ENGINEERING McAllen MULTIDISCIPLINARY ENGINEERING BS TECHNOLOGY Health Professions Building MEDICINE MD Clinical Learning 3950 North A. W. 2011 2010 Yes Resource Center Grimes Blvd. NURSING BSN Round Rock, TX 78665

711 Navarro Street, Travis Park Suite 250 2017 2017 JURISPRUDENCE MJ Yes Plaza San Antonio, TX 78205

College of MEDICINE MD

Medicine - 2401 S. 31st Street 2000 2000 MEDICAL SCIENCES MS Yes Temple Temple, TX 76508

MEDICAL SCIENCES PHD

Table 2: Off-campus instructional sites at which the institution offers 25-49% of its credit hours for a diploma, certificate, or degree—including high schools where courses are offered as dual enrollment. Note: institutions are required to notify SACSCOC in advance of initiating coursework at the site. For each site, provide the information below.

Name of Site Physical Address Date of Date Educational Is the site currently active? (At any (Indicate if site is (street, city, state, SACSCOC Implemented by programs time during the past 5 years, have currently active country) Do not letter accepting the institution offered (specific students been enrolled and courses or inactive. If include PO Boxes. notification degrees, certificates, offered? If not, indicate the date of inactive, date of diplomas) with 25- most recent activity.) last course 49% credit hours offerings and date offered at each site of projected reopening

Table 3: Branch campus—an instructional site located geographically apart and independent of the main campus of the institution. A location is independent of the main campus if the location is (1) permanent in nature, (2) offers courses in educational programs leading to a degree, certificate, or other recognized educational credential, (3) has its own faculty and administrative or supervisory organization, and (4) has its own budgetary and hiring authority. The list should include only those branch campuses reported to and approved by SACSCOC. Listing unapproved branch campuses below does not constitute reporting them to SACSCOC. A prospectus for an unapproved branch campuses should be submitted immediately to SACSCOC.

Is the campus currently active? (At any time during the Physical Address Date Date Educational programs (specific degrees, past 5 years, have Name of Branch (street, city, state, Implement Approved by certificates, diplomas) with 50% or more students been Campus country) Do not ed by the SACSCOC credits hours offered at the branch campus enrolled and courses include PO Boxes. institution offered? If not, indicate the date of most recent activity.) INTERDISCIPLINARY BS ENGINEERING MARINE BIOLOGY BS MARINE BIOLOGY MS MARINE BIOLOGY PHD MARINE ENGINEERING BS TECHNOLOGY MARINE FISHERIES BS Texas A&M 200 Seawolf Pkwy MARINE RESOURCES University at Galveston, TX 1992 1991 MMR Yes Galveston 77553 MANAGEMENT MARINE SCIENCES BS MARINE BS TRANSPORTATION MARITIME BS ADMINISTRATION MARITIME ADMINISTRATION & MML LOGISTICS 25

MARITIME STUDIES BA OCEAN AND COASTAL BS RESOURCES OCEAN ENGINEERING BS UNIVERSITY STUDIES BA, BS CHEMICAL ENGINEERING BS CHEMICAL ENGINEERING MS 253 Texas A&M CHEMICAL ENGINEERING MEN Qatar Engineering CHEMICAL ENGINEERING PhD Texas A&M Building ELECTRICAL University at 2005 2003 BS Yes Education City ENGINEERING Qatar Al Luqta St MECHANICAL BS Doha, Qatar ENGINEERING PETROLEUM BS ENGINEERING

4. Distance and Correspondence Education Provide an initial date of approval for your institution to offer distance education. Provide a list of credit-bearing educational programs (degrees, certificates, and diplomas) where 50% or more of the credit hours are delivered through distance education modes. For each educational program, indicate whether the program is delivered using synchronous or asynchronous technology, or both. For each educational program that uses distance education technology to deliver the program at a specific site (e.g., a synchronous program using interactive videoconferencing), indicate the program offered at each location where students receive the transmitted program. Please limit this description to one page, if possible.

Synchronous, Credit Bearing Degree Programs Asynchronous, or Site Both Advance International Affairs CERT-G Asynchronous Aerospace Engineering MENGR Asynchronous Agricultural Development MAGR Asynchronous Agricultural Education EDD Asynchronous Agricultural Systems Management MS Asynchronous Agriculture eLearning Development CERT-G Asynchronous Analytics MS Synchronous North America Applied Behavior Analysis CERT-G Both World-wide Applied Statistics CERT-G Asynchronous Bilingual Education MED Asynchronous Bilingual Education MS Asynchronous Biological & Agricultural Engineering MENGR Asynchronous Computer Engineering MENGR Asynchronous Curriculum & Instruction EDD Asynchronous Curriculum & Instruction MED Asynchronous Education for Health Care Professionals CERT-G Asynchronous Education for Health Care Professionals MS Asynchronous Educational Administration MED Asynchronous Educational Human Resource Development MS Asynchronous Educational Psychology MED Asynchronous Educational Psychology MS Asynchronous 26

Educational Technology MED Asynchronous Electrical Engineering MENGR Asynchronous Energy CERT-G Asynchronous Energy MS Asynchronous Engineering MENGR Asynchronous Engineering Systems Management MS Asynchronous Epidemiology MPH Asynchronous Extension Education CERT-G Asynchronous Family Nurse Practitioner MSN Asynchronous Forensic Healthcare CERT Asynchronous Forensic Nursing MSN Asynchronous Geoscience MGS Asynchronous Health Coaching for Chronic Disease Prevention and CERT-G Synchronous World-wide Management Health Education MS Asynchronous Hispanic Bilingual Education CERT-G Asynchronous Homeland Security Certificate CERT-G Asynchronous Hospitality Management CERT-UG Asynchronous Industrial Data Analytics CERT-G Asynchronous Industrial Distribution MID Asynchronous Industrial Engineering MENGR Asynchronous International Agriculture & Resource Management CERT-G Asynchronous Jurisprudence MJ Asynchronous Laws ML Asynchronous Leadership Education, Theory, and Practice CERT-G Asynchronous Maritime Administration & Logistics MMAL Asynchronous Mathematics MS Asynchronous Mechanical Engineering MENGR Asynchronous Bryan, TX; Medical Science MS Synchronous Houston, TX; Temple, TX Bryan, TX; Medical Science PHD Synchronous Houston, TX; Temple, TX Military Land Sustainability CERT-G Asynchronous Livermore, CA; National Security Affairs CERT-G Synchronous Albuquerque, NM Natural Resources Development MNRD Asynchronous Non-Profit Management CERT-G Asynchronous Nuclear Security CERT-G Asynchronous Bryan, TX; Round Nursing BSN Both Rock, TX Nursing Education MSN Asynchronous Petroleum Engineering MENGR Asynchronous Plant Breeding MS Asynchronous 27

Plant Breeding PHD Asynchronous Poultry Science MAGR Asynchronous Public Health CERT-G Asynchronous Public Management CERT-G Asynchronous Public Service & Administration MPSA Asynchronous Recreation & Resources Development MRRD Asynchronous Regulatory Science in Food Systems CERT-G Asynchronous Safety Engineering CERT-G Asynchronous Safety Engineering MS Asynchronous Science, Technology, Engineering and Mathematics CERT-G Asynchronous Education Special Education MED Asynchronous Special Education MS Asynchronous Sport Management MS Asynchronous Statistics MS Asynchronous Technical Management METM Asynchronous Tourism Management* CERT-UG Asynchronous Wildlife Science MWSC Asynchronous *Major dependent certificates

5. Accreditation

(1) List all agencies that currently accredit the institution and any of its programs and indicate the date of the last review by each.

Accrediting Agency Program Last Reviewed

Accreditation Council for Irma Lerma Rangel College of Pharmacy April 2014 Pharmacy Education American Bar Association Texas A&M University School of Law October 2016 American Chemical Society Chemistry May 2013 American Council for Construction Management October 2017 Construction Education Construction Science October 2017 American Psychological Clinical Psychology May 2015 Association Counseling Psychology May 2015 School Psychology October 2017 American Society of Agricultural Systems Management September 2015 Agricultural and Biological Engineers American Veterinary Medical Veterinary Medicine December 2015 Association Council on Education Association to Advance The business baccalaureate, master’s, and January 2017 Collegiate Schools of doctoral programs in Mays Business School Business Commission on Accreditation for Dietetics Didactic Program in Dietetics January 2015 Education Commission on Accreditation of Athletic Athletic Training April 2018 Training Education

Commission on Accreditation of Healthcare The Master of Health Administration November 2019 Management Education Commission on Collegiate Nursing – Baccalaureate March 2014 Nursing Education Nursing – Master’s February 2015 Commission on Dental Dental Public Health October 2016 Accreditation Oral & Maxillofacial Surgery September 2019

Oral & Maxillofacial Radiology March 2017

Dental Hygiene October 2018 Predoctoral Dental Education Advanced Clinical Certificates: • Advanced Education in General Dentistry • Endodontics • Oral Maxillofacial Pathology • Orthodontics & Dentofacial Orthopedics • Pediatric Dentistry • Periodontics • Prosthodontics Computing Accreditation Computer Science August 2017 Commission of ABET Council on Education for School of Public Health October 2018 Public Health Engineering Accreditation College Station Undergraduate Programs in: September 2016 Commission of ABET • Aerospace Engineering • Agricultural Engineering • Bioengineering • Biological & Agricultural Engineering • Biological Systems Engineering • Biomedical Engineering • Chemical Engineering • Civil Engineering

• Computer Engineering

• Electrical Engineering

• Industrial Engineering

• Mechanical Engineering

• Nuclear Engineering

• Ocean Engineering • Petroleum Engineering • Radiological Health Engineering

TAMU at Qatar Undergraduate Programs in: October 2014 • Chemical Engineering • Electrical Engineering • Mechanical Engineering • Petroleum Engineering

TAMU at Galveston Undergraduate Programs in: October 2016 • Marine Engineering • Maritime Systems Engineering • Offshore and Coastal Systems Engineering

Engineering Technology College Station Undergraduate Programs in: October 2013 Accreditation Commission • Electronic Systems Engineering of ABET • Electronic(s) Engineering Technology • Manufacturing & Mechanical Engineering Technology • Manufacturing Engineering Technology • Mechanical Engineering Technology • Telecommunications Engineering Technology

Galveston Undergraduate Programs in: October 2013 • Marine Engineering Technology Forensic Science Education Forensics & Investigative Sciences Program September 2016 Programs Accreditation Commission (FEPAC) Institute of Food Food Science & Technology December 2016 Technologists Landscape Architectural Bachelor – Landscape Architecture February 2015 Accreditation Board Master – Landscape Architecture September 2017 Liaison Committee on Medical Education Degree Program August 2012 Medical Education National Architectural Architecture March 2017 Accrediting Board Network of Schools of Public The Master of Public Service and Administration April 2014 Policy, Affairs, and degree in the Bush School of Government and Administration Public Service National Recreation and Recreation, Park and Tourism Sciences January 2016 Park Association Planning Accreditation Urban and Regional Planning March 2013 Board Society for Range Rangeland Ecology and Management April 2017 Management Society of American Forestry March 2013 Foresters Texas Education Agency Programs in professional education March 2011

(2) If SACS Commission on Colleges is not your primary accreditor for access to USDOE Title IV funding, identify which accrediting agency serves that purpose.

Not applicable.

(3) List any USDOE-recognized agency (national and programmatic) that has terminated the institution’s accreditation (include the date, reason, and copy of the letter of termination) or list any agency from which the institution has voluntarily withdrawn (include copy of letter to agency from institution).

1. COMMISSION ON ENGLISH LANGUAGE PROGRAM ACCREDITATION (CEA) – The English Language Institute at Texas A&M University voluntarily withdrew from CEA. The English Language Institute was accredited in good standing through August, 2018, at the time of the voluntary withdrawal (with no history of adverse action). The university made the decision to close the English Language Institute as an administrative unit on May 31, 2017. Please see attached correspondence.

(4) Describe any sanctions applied or negative actions taken by any USDOE-recognized accrediting agency (national, programmatic, SACSCOC) during the two years previous to the submission of this report. Include a copy of the letter from the USDOE-recognized agency to the institution.

None.

6. Relationship to the U.S. Department of Education Indicate any limitations, suspensions, or termination by the U.S. Department of Education in regard to student financial aid or other financial aid programs during the previous three years. Report if on reimbursement or any other exceptional status in regard to federal or state financial aid.

None.

Document History Adopted: September 2004 Revised: March 2011 Revised: January 2014 Revised: January 2018

2019 SACSCOC Financial Profile and Indicators

Institution Name Address: Texas A&M University, College Station, TX

Thank you for completing the 2019 Financial Profile and Indicators:

The Profile was submitted by Michael T. Stephenson on 7/8/2019 and approved by Michael K. Young on 7/12/2019.

FINAL SUBMISSION

!Fields: !Hint !collection Year: 2019 Total All Revenues And Other (IPEDs Part B, line 1$3 ,555,016,110 Additions: 25) (IPEDs Part C-1 , line IInstructi on: 1$926,898,557 01 , column 1) (IPEDs Part C-1 , line 1$762,679,906 !Research: 02, column 1) (IPEDs Part C-1 , line !Public Service: 1$266,994,355 03 , column 1) (IPEDs Part C-1 , line !Academic Support: 1$305,925,803 05, column 1) (IPEDs Part C-1 , line lstudent Services: 1$103,196,685 06, column 1) (IPEDs Part C-1 , line !Institutional Support: 1$136,728,213 07, column 1) (IPEDs Part C-1 , line !Auxiliary Enterprises: 1$267,808,281 11 , column 1) (IPEDs Part C-1 , line !Hospital Services: 12, column 1) 1$0 (IPEDs Part C-1 , line !Independent Operations: 13 , column 1) 1$0 (IPEDs Part C-1 , line Others Expenses And Deductions: 1$320,645,045 14, column 1) (IPEDs Part C-1 , line !scholarships And Fellowships: 1$111 ,646,861 10, column 1)

FROM AUDITED FY 2018 Financial Statements !Total Assets (add Deferred Outflows): 1$6,628,763,587 Total Liabilities (add Deferred 1$786,296,833 Inflows): Total Unrestricted Net Assets (and (add UNA & CA for 1$4,697,292,384 Capital Assets, Net): this field) Expendable/Temporary Restricted Net Assets: 1$240,443 ,828 Expendable/Temporary Restricted Net Assets: 1$904,730 ,542 Total Revenue (operating plus Non- 1$2,352,488,830 operating): !Tuition and Fees, Net: 1$641 ,703 ,109

!current Debt: (maturities due within 1$133,772,475 12 months) (maturities beyond !Long-term Debt: 12 1$1,643 ,534,514 months) Appendix P – Annual Extramural Research Grant Expenditures

NAME ERGEC-2015 ERGEC-2016 ERGEC-2017 ERGEC-2018 ERGEC-2019 ERGEC-2020 Bryk, Mary (25%)* ($ - )($ - )($ - )($ - )($ - )($ - ) Cho, Jae-Hyun ($ - )($ - )($ - )($ - )($ 199,485) ($ 461,802) Cruz-Reyes, Jorge ($ 91,200) ($ 62,259) ($ 262,404) ($ 164,299) ($ 10,508) ($ 44,169) Devarenne, Tim ($ 351,473) ($ 298,791) ($ 188,654) ($ 5,883) Glasner, Margaret ($ 169,938) ($ 165,129) ($ 197,676) ($ 93,248) ($ 246,201) ($ 195,473) Gohil, Vishal ($ 472,685) ($ 346,566) ($ 404,851) ($ 386,169) ($ 254,544) ($ 418,861) He, Ping ($ 528,079) ($ 226,252) ($ 88,590) ($ 307,791) ($ 422,712) ($ 443,846) Herman, Jennifer ($ 15,016) ($ 206,144) ($ 152,784) ($ 160,632) ($ 115,569) ($ 223,001) Igumenova, Tatyana ($ 306,367) ($ 424,441) ($ 375,925) ($ 443,117) ($ 381,183) ($ 266,491) Kurouski, Dmitry na na ($ - )($ - )($ - )($ 60,522) Li, Pingwei ($ 255,712) ($ 204,824) ($ 309,133) ($ 348,674) ($ 375,617) ($ 436,102) Meek, Thomas ($ - )($ - )($ 174,827) ($ 1,028,015) ($ 713,752) ($ 872,989) Mullet, John ($ 849,849) ($ 877,036) ($ 813,906) ($ 1,329,371) ($ 451,203) ($ 387,572) Panin, Vladislav ($ 368,014) ($ 228,188) ($ 153,015) ($ 316,999) ($ 303,817) ($ 236,097) Park, William ($ 222,603) ($ 142,792) ($ - )($ - )($ 14,456) ($ 18,737) Pellois, Jean-Philippe ($ 243,879) ($ 301,027) ($ 374,799) ($ 295,796) ($ 438,446) ($ 328,530) Polymenis, Michael ($ - )($ - )($ 94,843) ($ 393,206) ($ 262,418) ($ 314,739) Rye, Hays ($ 42,956) ($ 330,397) ($ 190,318) ($ 292,099) ($ 363,885) ($ 251,474) Sacchettini, James ($ 4,794,898) ($ 4,659,884) ($ 3,054,749) ($ 2,305,281) ($ 3,189,767) ($ 4,430,183) Shan, Libo ($ 387,501) ($ 340,133) ($ 267,208) ($ 272,585) ($ 672,418) ($ 673,085) Shippen, Dorothy ($ 506,709) ($ 622,293) ($ 562,245) ($ 457,355) ($ 377,032) ($ 431,984) Straight, Paul ($ 224,021) ($ 172,631) ($ 133,124) ($ 100,451) ($ 41,622) ($ 5,323) Sze, Sing-Hoi (40%)* ($ - )($ - )($ - )($ - )($ - )($ - ) Threadgill, David (50%) ($ 248,702) ($ 318,813) ($ 1,485,210) ($ 2,629,470) ($ 1,927,979) ($ 2,022,946) Tommos, Cecilia na na na na na ($ 5,344) Wand, Josh na na na na na ($ 309,391) Young, Ry ($ 202,466) ($ 342,815) ($ 1,041,841) ($ 798,258) ($ 613,132) ($ 659,288) Zeng, Lanying ($ 95,614) ($ 326,507) ($ 424,638) ($ 385,759) ($ 443,724) ($ 165,272) Zhang, Junjie ($ 170,647) ($ 162,543) ($ 77,907) ($ 83,899) ($ 206,036) ($ 353,721) Zhang, Xiuren ($ 298,515) ($ 231,091) ($ 288,981) ($ 336,111) ($ 632,692) ($ 560,342) Hu, James ($ 178,064) ($ 292,177) ($ 255,788) ($ 204,555) ($ 13,090) na Kaplan, Craig ($ 334,225) ($ 212,504) ($ 409,679) ($ 729,102) na na Reinhart, Greg ($ 186,528) ($ 195,837) ($ 252,290) ($ 218,134) na ($ 870) Peterson, David na ($ - ) ($ - ) na na na Kunkel, Gary ($ 151,020) ($ 128,667) ($ 42,442) ($ 142,626) ($ 50,634) ($ 216)

*Did not have any extramural research grant's in BCBP Appendix Q – Faculty Curriculum Vitae's

Nicola M. Ayres Senior Lecturer | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Texas A&M University 1989–2008 Postdoctoral Cornell University and Institute of Molecular Biology (Taipei, Taiwan) 1988–1989 Postdoctoral USDA, ARS, and Texas A&M University 1987–1988 Ph.D. University of Nebraska, Lincoln 1987 B.S. SUNY/Binghamton 1982

PROFESSIONAL APPOINTMENTS Senior Lecturer Biochemistry and Biophysics Texas A&M University 2015–present Lecturer Biochemistry and Biophysics Texas A&M University 2007–2014 Visiting Scientist Cornell University Texas A&M University 1994

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Faculty Senate TAMU 2020–present Member Pandemic Safety Committee BCBP 2020–present Member Safety Committee BCBP 2000–present Member Department Head Search Committee BCBP 2019

COURSES TAUGHT (2015–present) BICH 412 Biochemistry Laboratory I 1 cr. 2015–present BICH 414 Biochemical Techniques I 2 cr. 2015–present Vytas A. Bankaitis University Distinguished Professor E. L. Wehner-Welch Foundation Chair, Chemistry Professor | Departments of Molecular and Cellular Medicine, Biochemistry and Biophysics, Chemistry

EDUCATION Postdoctoral The California Institute of Technology with S. D. Emr 1986 Ph.D. University of North Carolina with P. J. Bassford, Jr. 1984

PROFESSIONAL APPOINTMENTS University Distinguished Professor Molecular and Cellular Medicine Texas A&M University 2018–present Biochemistry and Biophysics Texas A&M Health Science Chemistry Center E. L. Wehner-Welch Foundation Chemistry Texas A&M University 2012–present Chair Professor Molecular and Cellular Medicine Texas A&M University 2012–present Biochemistry and Biophysics Texas A&M Health Science Chemistry Center Professor Cell and Developmental Biology University of North Carolina 2011–2012 School of Medicine Member Lineberger Comprehensive Cancer University of North Carolina 2001–2012 Center School of Medicine Professor and Chairman Cell and Developmental Biology University of North Carolina 2001–2011 School of Medicine Professor Cell Biology University of Alabama at 1996–2000 Birmingham Medical Center Associate Professor Cell Biology University of Alabama at 1992–1996 Birmingham Medical Center Assistant Professor Microbiology University of Illinois 1986–1992 Urbana-Champaign

PEER-REVIEWED PUBLICATIONS (2015–present) 170. Lete, M. G.; Tripathi, A.; Chandra, V.; Bankaitis, V. A.; McDermott, M. I. Lipid transfer proteins and instructive regulation of lipid kinase activities: Implications for inositol lipid signaling and disease. Adv. In Biol. Reg. (2021). 169. Khan, D.; Lee, D.; Gulten, G.; Aggarwal, A.; Krieger, I.; Wofford, J.; Tripathi, A.; Patrick, J. W.; Eckert, D.; Laganowsky, A.; Sacchettini, J.; Lindahl, P.; Bankaitis, V. A. An unconventional Sec14-like phosphatidylinositol transfer protein paralog binds heme via a unique coordination mechanism. eLife 9, e57081 (2021). 168. Sugiura, T.; Nakao, H.; Ikeda, K.; Khan, D.; Nile, A. H.; Bankaitis, V. A.; Nakano, M. Regulation of Sec14 lipid transfer by lipid packing in membranes. BBA Biomembranes 1863, 183450–183457 (2020). 167. Wang, Y.; Yuan, P.; Grabon, A.; Tripathi, A.; Lee, D.; Rodriguez, M.; Lonnfors, M.; Eisenberg-Bord, Wang, Z.; Lam, S. M.; Schuldiner, M.; Bankaitis, V. A. Non-canonical regulation of phosphatidylserine metabolism by a Sec14-like protein and lipid kinase. J. Cell Biol. 219, e201907128 (2020). 166. Bankaitis, V. A.; Wang, Y. Lipoprotein lipase sorting: Sphingomyelin and a proteoglycan show the way. Trends in Cell Biology 30, 170–172 (2020). 165. McDermott, M. I.; Wang, Y.; Wakelam, M. J. O.; Bankaitis, V. A. Mammalian phospholipase D: Function and therapeutics. Prog. Lipid Res. 78, 101018 (2020). 164. Bankaitis, V. A.; Xie, Z. The neutral stem cell/carnitine malnutrition hypothesis: New prospects for effective reduction of autism risk? J. Biol. Chem. 294, 19424–19435 (2019). 163. Tripathi, A.; Martinez, E.; Ahmad J. Obaidullah, A. J.; Lete, M. G.; Lonnfors, M.; Khan, D.; Soni, K. G.; Mousley, C. J.; Kellogg, G. E.; Bankaitis, V. A. Functional diversification of the chemical landscapes of yeast Sec14-like phosphatidylinositol transfer protein lipid-binding cavities. J. Biol. Chem. 294, 19081–19098 (2019). 162. Wang, Y.; Mousley, C. J.; Lete, M. G.; Bankaitis, V. A. An equal opportunity collaboration between lipid metabolism and proteins in the control of membrane trafficking in the trans-Golgi and endosomal systems. Curr. Op. in Cell Biol. 59, 58–72 (2019). 161. Aziz, M.; Wang, X.; Tripathi, A.; Bankaitis, V. A.; Chapman, K. D. Structural insights into the evolutionary divergence of acylenthanolamide signaling. J. Biol. Chem. 294, 7419–7432 (2019). 160. Taichi, S.; Takahashi, C.; Chuma, Y.; Fukuda, M.; Yamada, M.; Yoshida, U.; Nakao, H.; Ikeda, K.; Khan, D.; Nile, A. H.; Bankaitis, V. A.; Nakano, M. Biophysical parameters of the Sec14 phospholipid exchange cycle. Biophys. J. 116, 92–103 (2019). 159. Grabon, A.; Bankaitis, V. A.; McDermott, M. I. The interface between phosphatidylinositol transfer protein function and phosphoinositide signaling in higher eukaryotes. J. Lipid. Res. 60, 242–268 (2018). 158. McDermott, M. I.; Thelin, W. R.; Chen, Y.; Lyons, P. T.; Haddock, G.; Gentzsch, M.; Lei, C.; Hong, W.; Stutts, M. J.; Playford, M. P.; Milgram, S. L.; Bankaitis, V. A. Sorting nexin 27: A novel regulator of CFTR trafficking. BioRxiv (2018). 157. Roy, K. R.; Smith, J. D.; Vonesch, S. C.; Gen, L.; Chu, A.; Suresh, S.; Nguyen, M.; Horecka, J.; Tripathi, A.; Tu, C. S.; Burnett, W. T.; Morgan, M. A.; Schulz, J.; Orsley, K. M.; Lederer, A.; Wei, W.; Aiyar, R. S.; Davis, R. W.; Bankaitis, V. A.; Haber, J. E.; Salit, M. L.; St. Onge, R. P.; Steinmetz, L. M. Multiplexed precision genome editing with trackable genomic barcodes. Nat. Biotech. 36, 512–520 (2018). 156. Xie, Z.; Hur, S. K.; Zhao, L.; Abrams, C.; Bankaitis, V. A. A Golgi lipid signaling pathway controls apical Golgi distribution and cell polarity during neurogenesis. Develop. Cell 44, 725–744.e4 (2018). 155. Pries, V.; Nocker, C.; Khan, D.; Johnen, P.; Hong, Z.; Tripathi, A.; Keller, A.-L.; Fitz, M.; Perruccio, F.; Filipuzzi, I.; Thavam, S.; Aust, T.; Riedl, R.; Ziegler, S.; Bono, F.; Schaaf, G.; Bankaitis, V.; Waldmann, H.; Hoepfner, D. Target identification and mechanisms of action of picolinamide and benzamide chemotypes with antifungal properties. Cell Chem. Biol. 25, 279–290.e7 (2018). 154. Koe, C. T.; Tan, Y. S.; Lonnfors, M.; Hur, S. K.; Low, C. S. L.; Zhang, Y.; Yu, F.; Kanchanawong, P. Bankaitis, V. A.; Wang, H. Vibrator and PI4KIIIα govern neuroblast polarity by anchoring non-muscle myosin II. eLife 7, e33555 (2018). 153. Huang, J.; Mousley, C. J.; Dacquay, L.; Maitra, N.; Drin, G.; He, C.; Kennedy, M.; Ridgway, N.; Kennedy, B.; Baetz, K.; Polymenis, M.; Bankaitis, V. A. The Kes1-Sec14 lipid signaling axis controls cell cycle and membrane trafficking systems. Develop. Cell 44, 378–391 (2018). 152. Eisenberg-Bord, M.; Castro, I. G.; Mari, M.; Weill, U.; Rosenfeld-Gur, E.; Modavski, O.; Persiani, E.; Soni, K. G.; Rochford, J. J.; Levine, T. P.; Futerman, A. H.; Reggiori, F.; Bankaitis, V. A.; Schuldiner, M.; Bohnert, M. Identification of seipin-linked factors that act as determinants of a lipid droplet subpopulation. J. Cell Biol. 217, 269–282 (2018). 151. Grabon, A.; Orlowski, A.; Tripathi, A.; Vuorio, J.; Javanainen, M.; Rog, T.; Lonnfors, M.; Siebert, G.; McDermott, M. I.; Somerharju, P.; Vattulainen, I.; Bankaitis, V. A. Atomistic insights into the dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle. J. Biol. Chem. 292, 14438–14455 (2017). 150. Tripathi, A.; Bankaitis, V. A. Molecular docking: From lock and key to combination lock. J. Mol. Med. Clin. Appl. 2 (2017). 149. Blank, H. M.; Perez, R.; He, C.; Maitra, N.; Metz, R.; Hill, J.; Lin, Y.; Johnson, C. D.; Bankaitis, V. A.; Kennedy, B. K.; Aramayo, R.; Polymenis, M. Translational control of lipogenic enzymes in the cell cycle of synchronous, growing yeast cells. EMBO J. 36, 487–502 (2017). 148. Tribble, E.; Ivanova, P. T.; Grabon, A.; Alb, J. G., Jr.; Faenza, I.; Cocco, L.; Brown, H. A.; Bankaitis, V. A. Quantitative profiling of the endonuclear phospholipidome of murine embryonic fibroblasts. J. Lipid Res. 57, 1492–1506 (2016). 147. Huang, J.; Ghosh, R.; Tripathi, A.; Lonnfors, M.; Somerharju, P.; Bankaitis, V. A. Two-ligand priming mechanisms for potentiated phosphoinositide synthesis is an evolutionarily conserved. feature of Sec14-like phosphatidylinositol and phosphatidylcholine exchange proteins. Mol. Biol. Cell 27, 2317–2330 (2016). 146. Huang, J.; Ghosh, R.; Bankaitis, V. A. Sec14-like phosphatidylinositol transfer proteins and the biological landscape of phosphoinositide signaling in plants. Biochim. Biophys. Acta 1861, 1352–1364 (2016). 145. Bankaitis, V. A.; Xie, Z. New autism research: A nutrient called carnitine might counteract gene mutations linked with ASD risk. The Conversation (2016). 144. Khan, D.; McGrath, K. R.; Dorosheva, O.; Bankaitis, V. A.; Tripathi, A. Structural elements that govern Sec14-like phosphatidylinositol transfer protein sensitivities to potent small molecular inhibitors. J. Lipid Res. 57, 650–652 (2016). 143. Xie, Z.; Jones, A.; Deeney, J. T.; Huh, S. K.; Bankaitis, V. A. Inborn errors of long-chain fatty acid β-oxidation link neural stem cell homeostasis to autism. Cell Rep. 14, 991–999 (2016). 142. Bankaitis, V. A. Unsaturated fatty acid-induced noncanonical autophagy: unusual? Or unappreciated? EMBO J. 34, 978–980 (2015). 141. Ghosh, R.; de Kampos, M. K. F.; Huang, J.; Hur, S.; Orlowski, A.; Yang, Y.; Tripathi, A.; Nile, A. H.; Lee, H.-C.; Schafer, H.; Dynowski, M.; Rog, T.; Lete, M. G.; Ahyayauch, H.; Alonso, A.; Vattylainen, I.; Igumenova, T. I.; Schaaf, G.; Bankaitis, V. A. Sec14-nodulin proteins and the patterning of phosphoinositide landmarks for developmental control of membrane morphogenesis. Mol. Biol. Cell. 26, 1764–1781 (2015). 140. Grabon, A.; Khan, D.; Bankaitis, V. A. Phosphatidylinositol transfer proteins and instructive regulation of lipid kinase biology. Biochim. Biophys. A. 1851, 724–735 (2015).

CURRENT SUPPORT NIH R35 GM131804 Bankaitis, V. A. 2019–2024 “The biology and biochemistry of lipid transfer protein-regulated phosphoinositide signaling.” BE0017 Bankaitis, V. A. 2012–present Wehner-Welch Foundation Chair Endowed Chair.

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Member, Site-Visit Team - Review National Cancer Institute Regulation of Cell Growth Laboratory (delayed) 2020 Avanti Award in Lipids American Society of Biochemistry and Molecular Biology 2019 Member NRSA Cell Biology and Development Fellowship Program 2016–2019 Director, Lipid Division American Society of Biochemistry and Molecular Biology 2013–2017 Member NIH, BBM 2015 Member Faculty of 1000, Cell Biology Section – Membranes & Sorting 2009–present Associate Editor Japanese Journal of Biochemistry 2006–present Editorial Academy Journal of Molecular Medicine 1997–present Editorial Board Methods, EMBO Reports, Chemistry and Physics of Lipids, Various Bioscience Reports, Traffic Peer Reviewer Various scientific journals Various

Mary Bryk Associate Professor | Department of Biochemistry and Biophysics Associate Dean for Academic Affairs | College of Agriculture and Life Sciences

EDUCATION Postdoctoral Harvard Medical School with F. Winston 1997–2002 Postdoctoral New York State Department of Health with M. J. Curcio 1995–1997 Ph.D. Albany Medical College with M. Belfort 1994 M.S. Albany Medical College 1991 B.S. Cornell University 1985

PROFESSIONAL APPOINTMENTS Associate Dean, Academic Affairs College of Agriculture and Life Sciences Texas A&M University 2019–present Associate Professor Biochemistry and Biophysics Texas A&M University 2008–present Faculty Genetics IDP Texas A&M University 2003–present Assistant Professor Biochemistry and Biophysics Texas A&M University 2002–2008

CURRENT SUPPORT NSF #DBI-1949893 Kunkel, G.; Bryk, M. (co-PI) 2020–2023 “REU Site: Summer Undergraduate Research Program in Biochemistry” COMPLETED SUPPORT (2015–present) NSF #DBI-1358941 Kunkel, G.; Bryk, M. (co-PI) 2014–2019 “REU Site: Summer Undergraduate Research Program in Biochemistry”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) NSF Panel Member Postdoctoral Fellowship: Rules of Life and Broadening Participation 2020 Faculty Advisor Recognition Texas Academic Advising Network 2019 Margaret Annette Peters Advising TAMU Advisors and Counselors 2018 Award Faculty Recognition Award TAMU Biochemistry Graduate Association 2016, 2017 NIH Panel Member Genes, Genomes, and Genetics Fellowships; Molecular Genetics A; Various Molecular Genetics B; Nuclear Dynamics and Transport

DEPARTMENT AND SYSTEM SERVICE (2015–present) University Facilitator/Trainer Faculty Mentoring Academy TAMU 2019–present Reviewer Distinguished Graduate Student Awards Committee TAMU 2019 Associate Head, Chair, Co-Chair Graduate Program Committee BCBP 2014–2019 Associate Head, Chair, Co-Chair Executive Committee BCBP 2014–2019 Representative, Chair TAMU Council of Principal Investigators COALS 2009–2016 Member Undergraduate Program Committee BCBP 2008–2015 CPI Representative Council for Strategic Budgeting, Sub-Council for TAMU Various Strategic Reallocation, TOP Proposal Review Committee, Budget Reallocation Committee, Laboratory Safety Committee Member Developmental Strategy Committee, Facilities Utilization TAMU Various Sub-Committee of the Council for the Built Environment, President’s Excellence Fund Steering Committee, IDP Genetics, GENE Graduate Admission Committee, Research Development Services Workshop Member Faculty Search Committee, Graduate Recruitment and BCBP Various Admissions Committee

COURSES TAUGHT (2015–present) BICH 491/691 Research Variable 2007–present BICH 631 Biochemical Genetics 3 cr. 2019 BICH 681 Seminar 1 cr. 2018–2019 BICH 673 Gene Expression (Journal Club) 1 cr. 2007–2019 GENE 302 Principles of Genetics 4 cr. 2004–2019 BICH/GENE 431 Molecular Genetics 3 cr. 2017–2018 BICH/GENE 101 Perspectives in Biochemistry and Genetics 1 cr. 2016

Chavela M. Carr Senior Lecturer | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Yale University Medical School with P. J. Novack 1995–2000 Ph.D. Massachusetts Institute of Technology with P. S. Kim 1995 B.S. Vanderbilt University 1988

PROFESSIONAL APPOINTMENTS Senior Lecturer Biochemistry and Biophysics Texas A&M University 2018–present Lecturer Biochemistry and Biophysics Texas A&M University 2014–2018 Research Scientist Biochemistry and Biophysics Texas A&M University 2009–2014 Assistant Professor Pathology Robert Wood Johnson Medical School 2000–2009

COMPLETED SUPPORT (2015–present) AgriLife EdRFP Carr, C. M. 2019 Online Course Development

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Distinguished Achievement in Teaching TAMU Association of Former Students 2020 Certification TAMU Instructional Technology Certification Program 2019 Vice Chancellor’s Award for Excellence in Texas A&M University 2017 Teaching Dean’s Outstanding Achievement Award in Early Texas A&M University 2017 Career Teaching

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Department Head Search Committee BCBP 2018

COURSES TAUGHT (2015–present) BICH 409 Principles of Biochemistry 3 cr. 2020–present BICH 410 Comprehensive Biochemistry I 3 cr. 2015–present BICH 411 Comprehensive Biochemistry II 3 cr 2014–2017 BICH 603 Principles of Biochemistry & Biophysics 3 cr. 2010–present José Alfredo Caro Research Assistant Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral University of Pennsylvania NIH F32 NRSA Fellow with A. Joshua Wand 2015–2019 Ph.D. Johns Hopkins University with B. Garcia-Moreno E. 2015 B.S. U.C. Santa Barbara 2007

PROFESSIONAL APPOINTMENTS Research Assistant Professor Biochemistry and Biophysics Texas A&M University 2019–present

PEER-REVIEWED PUBLICATIONS (2015–present) 11. Stetz, M. A.; Caro, J. A.; Kotaru, S.; Yao, X.; Marques, B. S.; Valentine, K. G.; Wand, A. J. Characterization of internal protein dynamics and conformational entropy by NMR relaxation. Methods Enzymol. 615, 237–284 (2019). 10. Caro, J. A.; Wand, A. J. Practical aspects of high-pressure NMR spectroscopy and its applications in protein biophysics and structural biology. Methods 148, 67–80 (2018). 9. Kougentakis, C. M.; Grasso, E. M.; Robinson, A. C.; Caro, J. A.; Schlessman, J. L.; Majumdar, A.; Garcia-Moreno E., 15 B. Anomalous properties of Lys residues buried in the hydrophobic interior of a protein revealed with N-detect NMR spectroscopy. J. Phys. Chem. Lett. 9, 383–387 (2017). 8. Caro, J. A.; Harpole, K. W.; Kasinath, V.; Lim, J.; Granja, J.; Valentine, K. G.; Sharp, K. A.; Wand, A. J. Entropy in molecular recognition by proteins. Proc. Natl. Acad. Sci. 114, 6563–6568 (2017). 7. Dellarole, M.; Caro, J. A.; Roche, J.; Fossat, M.; Barthe, P.; Garcia-Moreno E., B.; Royer, C. A.; Roumestand, C. Evolutionarily conserved pattern of interactions in a protein revealed by local thermal expansion properties. J. Am. Chem. Soc. 137, 9354–9362 (2015).

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Poster Award Gordon Research Conference, Protein Dynamics 2020 Poster Award University of Pennsylvania, Department Retreat 2018 NIH Fellowship NIGMS, F32 Postdoctoral NRSA 2016

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Outreach and Recruitment Committee BCBP 2020–present

Robert S. Chapkin University Distinguished Professor | Departments of Nutrition, Biochemistry and Biophysics

EDUCATION Postdoctoral University of California – Davis 1986–1988 Ph.D. University of California – Davis 1986 M.Sc. University of Guelph 1983 B.Sc. University of Guelph 1981

PROFESSIONAL APPOINTMENTS University Distinguished Professor Nutrition Texas A&M University 2014–present Biochemistry and Biophysics Professor Nutrition Texas A&M University 1999–present Biochemistry and Biophysics Associate Professor Veterinary Integrated Biosciences Texas A&M University 1994–1999 and Nutrition Assistant Professor Human Nutrition Texas A&M University 1988–1993

PEER-REVIEWED PUBLICATIONS (2015–present) 288. Fuentes, N. R.; Mlih, M.; Wang, X.; Webster, G.; Cortes-Acosta, S.; Salinas, M. L.; Corbin, I. R.; Karpac, J.; Chapkin, R. S. Membrane therapy using DHA suppresses epidermal growth factor receptor signaling by disrupting nanocluster formation. J. Lipid Res. (2021). 287. Han, H.; Davidson, L. A.; Hensel, M.; Yoon, G.; Landrock, K.; Allred, C.; Jayaraman, A.; Ivanov, I.; Safe, S. H.; Chapkin, R. S. Loss of aryl hydrocarbon receptor promotes colon tumorigenesis in ApcS580/+; KrasG12D/+ mice. Mol. Cancer Res. (2021). 286. Kuklinski, E. J.; Hom, M. M.; Yin, G. S.; Lin, M. C.; Chapkin, R. S.; Jones, R.; Moser, A.; Kim, K. Y.; Maguire, M. G.; Asbell, P. A. Associations between systemic omega-3 fatty acid levels with moderate-to-severe dry eye disease signs and symptoms at baseline in the dry eye assessment and management study. Eye Contact Lens 47, 2–7 (2021). 285. He, K.; Donovan, S. M.; Ivanov, I. V.; Goldsby, J. S.; Davidson, L. A.; Chapkin, R. S. Assessing the multivariate relationship between the human infant intestinal exfoliated cell transcriptome (exfoliome) and microbiome in response to diet. Mircoorg. 8 (2020). 284. Yang, F.; DeLuca, J. A. A.; Menon, R.; Garcia-Vilarato, E.; Callaway, E.; Landrock, K. K.; Lee, K.; Safe, S. H.; Chapkin, R. S.; Allred, C. D.; Jayaraman, A. Effect of diet and intestinal AhR expression on fecal microbiome and metabolomic profiles. Microb. Cell Fact. 19, 219 (2020). 283. Park, H.; Jin, U. H.; Karki, K.; Jayaraman, A.; Allred, C.; Michelhaugh, S. K.; Mittal, S.; Chapkin, R. S.; Safe, S. Dopamine is an aryl hydrocarbon receptor agonist. Biochem. J. 477, 3899–3910 (2020). 282. Han, H.; Davidson, L. A.; Fan, Y. Y.; Goldsby, J. S.; Yoon, G.; Jin, U. H.; Wright, G. A.; Landrock, K. K.; Weeks, B. R.; Wright, R. C.; Allred, C. D.; Jayaraman, A.; Ivanov, I.; Roper, J.; Safe, S. H.; Chapkin, R. S. Loss of aryl hydrocarbon receptor potentiates FoxM1 signaling to enhance self-renewal of colonic stem and progenitor cells. EMBO J. 39, e104319 (2020). 281. Safe, S.; Jin, U. H.; Park, H.; Chapkin, R. S.; Jayaraman, A. Aryl hydrocarbon receptor (AHR) ligands as selective AHR modulators (SAhRMs). Int. J. Mol. Sci. 21 (2020). 280. Safe, S.; Jayaraman, A.; Chapkin, R. S. Ah receptor ligands and their impacts on gut resilience: structure-activity effects. Crit. Rev. Toxicol. 50, 463–473 (2020). 279. Navarro, S. L.; Levy, L.; Curtis, K. R.; Elkon, I.; Kahsai, O. J.; Ammar, H. S.; Randolph, T. W.; Hong, N. N.; Carnevale Neto, F.; Raftery, D.; Chapkin, R. S.; Lampe, J. W.; Hullar, M. A. J. Effect of a flaxseed lignan intervention on circulating bile acids in a placebo-controlled randomized, crossover trial. Nutrients 19 (2020). 278. Levental, K. R.; Malmberg, E.; Symons, J. L.; Fan, Y. Y.; Chapkin, R. S.; Ernst, R.; Levental, I. Lipidomic and biophysical homeostasis of mammalian membranes counteracts dietary lipid perturbations to maintain cellular fitness. Nat. Commun. 11, 1339 (2020). 277. Chapkin, R. S.; Navarro, S. L.; Hullar, M. A. J.; Lampe, J. W. Diet and gut microbes act coordinately to enhance programmed cell death and reduce colorectal cancer risk. Dig. Dis. Sci. 65, 840–851 (2020). 276. Garcia-Villatoro, E. L.; DeLuca, J. A. A.; Callaway, E. S.; Allred, K. F.; Davidson, L. A.; Hensel, M. E.; Menon, R.; Ivanov, I.; Safe, S. H.; Jayaraman, A.; Chapkin, R. S.; Allred, C. D. Effects of high-fat diet and intestinal aryl hydrocarbon receptor deletion on colon carcinogenesis. Am. J. Physiol. Gastrointest. Liver Physiol. 318, G451–G463 (2020). 275. Salinas, M. L.; Fuentes, N. R.; Choate, R.; Wright, R. C.; McMurray, D. N.; Chapkin, R. S. AdipoRon attenuates Wnt signaling by reducing cholesterol-dependent plasma membrane rigidity. Biophys. J. 118, 885–897 (2019). 274. Park, H.; Jin, U. H.; Orr, A. A.; Echegaray, S. P.; Davidson, L. A.; Allred, C. D.; Chapkin, R. S.; Jayaraman, A.; Lee, K.; Tamamis, P.; Safe, S. Isoflavones as Ah receptor agonists in colon-derived cell lines: Structure-activity relationships. Chem. Res. Toxicol. 32, 2353–2364 (2019). 273. Kim, E.; Wright, G. A.; Zoh, R. S.; Patil, B. S.; Jayaprakasha, G. K.; Callaway, E. S.; Ivanov, I.; Turner, N. D.; Chapkin, R. S. Establishment of a multicomponent dietary bioactive human equivalent dose to delete damaged Lgr5+ stem cells using a mouse colon tumor initiation model. Eur. J. Cancer Prev. 28, 383–389 (2019). 272. Lampe, J. W.; Kim, E.; Levy, L.; Davidson, L. A.; Goldsby, J. S.; Miles, F. L.; Navarro, S. L.; Randolph, T. W.; Zhao, N.; Ivanov, I.; Kaz, A. M.; Damman, C.; Hockenbery, D. M.; Hullar, M. A. J.; Chapkin, R. S. Colonic mucosal and exfoliome transcriptomic profiling and fecal microbiome response to flaxseed lignan extract intervention in humans. Am. J. Clin. Nut. 110, 377–390 (2019). 271. Torres-Adorno, A. M.; Vitrac, H.; Qi, Y.; Tan, L.; Levental, K. R.; Fan, Y. Y.; Yang, P.; Chapkin, R. S.; Eckhardt, B. L.; Ueno, N. T. Eicosapentaenoic acid in combination with EPHA2 inhibition shows efficacy in preclinical models of triple-negative breast cancer by disrupting cellular cholesterol efflux. Oncogene 38, 2135–2150 (2019). 270. Fan, Y. Y.; Davidson, L. A.; Chapkin, R. S. Murine colonic organoid culture system and downstream assay applications. Methods Mol. Biol. 1576, 171–181 (2019). 269. Fuentes, N. R.; Kim, E.; Fan, Y. Y.; Chapkin, R. S. Omega-3-fatty acids, membrane remodeling and cancer prevention. Mol. Aspects Med. 64, 79–91 (2018). 268. Safe, S.; Han, H.; Goldsby, J.; Mohankumar, K.; Chapkin, R. S. Aryl hydrocarbon receptor (AhR) ligands as selective AhR modulators: Genomics studies. Curr. Opin. Toxicol. (2018). 267. Triff, K.; McLean, M. W.; Callaway, E.; Goldsby, J.; Ivanov, I.; Chapkin, R. S. Dietary fat and fiber interact to uniquely modify global histone post-translational epigenetic programming in a rat colon cancer progression model. Int. J. Cancer 143, 1402–1415 (2018). 266. Erazo-Oliveras, A.; Fuentes, N. R.; Wright, R. C.; Chapkin, R. S. Functional link between plasma membrane spatiotemporal dynamics, cancer biology, and dietary membrane-altering agents. Cancer Metastasis Rev. 37, 519–544 (2018). 265. Fuentes, N. R.; Mlih, M.; Barhoumi, R.; Fan, Y. Y.; Hardin, P.; Steele, T. J.; Behmer, S.; Prior, I. A.; Karpac, J.; Chapkin, R. S. Long-chain n-3 fatty acids attenuate oncogenic KRas-driven proliferation by altering plasma membrane nanoscale proteolipid composition. Cancer Res. 78, 3899–3912 (2018). 264. Jin, U. H.; Park, H.; Davidson, L. A.; Allred, C.; Patil, B.; Jayaprakasha, G.; Orr, A.; Mao, L.; Chapkin, R. S.; Jayaraman, A.; Tamamis, P.; Safe, S. H. Structure-dependent modulation of aryl hydrocarbon receptor-mediated activities by flavones. Toxicol. Sci. 164 (2018). 263. Kim, S. M.; Neuendorff, N.; Alaniz, R. C.; Sun, Y.; Chapkin, R. S.; Earnest, D. J. Shift work cycle-induced alterations of circadian rhythms potentiate the effects of high-fat diet on inflammation and metabolism. FASEB J. 32, 3085–3095 (2018). 262. Chapkin, R. S. Robert Chapkin on relationships between the gut microbiome, diet, and colorectal cancer. Oncology (Williston Park) 32, 248–249 (2018). 261. Knight, J. M.; Ivanov, J.; Triff, K.; Chapkin, R. S.; Dougherty, E. R. Detecting multivariate gene interactions in RNA- Seq data using optimal Bayesian classification. IEEE/ACM Trans. Comput. Biol. Bioinform. 15, 484–493 (2018). 260. Fan, Y. Y.; Fuentes, N. R.; Hou, T. Y.; Barhoumi, R.; Li, X. C.; Deutz, N. E.; Engelen, M. P.; McMurray, D. N.; Chapkin, R. S. Remodeling of primary human CD4+ T cell plasma membrane order by n-3 polyunsaturated fatty acids. Br. J. Nutr. 119, 163–175 (2018). 259. Whitfield-Cargile, C. M.; Cohen, N. D.; He, K.; Ivanov, I.; Goldsby, J. S.; Chamoun-Emanuelli, A.; Weeks, B. R.; Davidson, L. A.; Chapkin, R. S. The non-invasive exfoliated transcriptome (exfoliome) reflects the tissue-level transcriptome in a mouse model of NSAID enteropathy. Sci. Rep. 7, 14687 (2017). 258. Wei, Q.; Lee, J. H.; Wang, H.; Bongmba, O. Y. N.; Wu, C. S.; Pradhan, G.; Sun, Z.; Chew, L.; Bajaj, M.; Chan, L.; Chapkin, R. S.; Chen, M. H.; Sun, Y. Adiponectin is required for maintaining normal body temperature in a cold environment. BMC Physiol. 17, 8 (2017). 257. Seidel, D. V.; Azcarate-Peril, M. A.; Chapkin, R. S.; Turner, N. D. Shaping functional gut microbiota using dietary bioactives to reduce colon cancer risk. Semin. Cancer Biol. 46, 191–204 (2017). 256. Fuentes, N. R.; Salinas, M. L.; Kim, E.; Chapkin, R. S. Emerging role of chemoprotective agents in the dynamic shaping of plasma membrane organization. Biochim. Biophys. Acta Biomembr. 1859, 1668–1678 (2017). 255. Jin, U. H.; Cheng, Y.; Park, H.; Davidson, L. A.; Callaway, E. S.; Chapkin, R. S.; Jayaraman, A.; Asante, A.; Allred, C.; Weaver, E. A.; Safe, S. Short chain fatty acids enhance aryl hydrocarbon (Ah) responsiveness in mouse colonocytes and Caco-2 human colon cancer cells. Sci. Rep. 7, 10163 (2017). 254. Armstrong, C. M.; Allred, K. F.; Weeks, B. R.; Chapkin, R. S.; Allred, C. D. Estradiol has differential effects on acute colonic inflammation in the presence and absence of estrogen receptor β expression. Dig. Dis. Sci. 62, 1977–1984 (2017). 253. Kumar, R.; Herold, J. L.; Schady, D.; Davis, J.; Kopetz, S.; Martinez-Mocygemba, M.; Murray, B. E.; Han, F.; Li, Y.; Callaway, E.; Chapkin, R. S.; Dashwood, W. M.; Dashwood, R. H.; Berry, T.; Mackenzie, C.; Xu, Y. Streptococcus gallolyticus subsp. gallolyticus promotes colorectal tumor development. PLoS Pathog. 13, e1006440 (2017). 252. Fan, Y. Y.; Vaz, F. M.; Chapkin, R. S. Dietary fat and fiber interactively modulate apoptosis and mitochondrial bioenergetic profiles in mouse colon in a site-specific manner. Eur. J. Cancer Prev. 26, 301–308 (2017). 251. Kim, E.; Ivanov, I.; Hua, J.; Lampe, J. W.; Hullar, M. A.; Chapkin, R. S.; Dougherty, E. R. The model-based study of the effectiveness of reporting lists of small feature sets using RNA-Seq data. Cancer Inform. (2017). 250. Triff, K.; McLean, M. W.; Konganti, K.; Pang, J.; Callaway, E.; Zhou, B.; Ivanov, I.; Chapkin, R. S. Assessment of histone tail modifications and transcriptional profiling during colon cancer progression reveals a global decrease in H3K4me3 activity. Biochim. Biophys. Acta Mol. Basis Dis. 1863, 1392–1402 (2017). 249. Cheng, Y.; Jin, U. H.; Davidson, L. A.; Chapkin, R. S.; Jayaraman, A.; Tamamis, P.; Orr, A.; Allred, C.; Denison, M. S.; Soshilov, A.; Weaver, E.; Safe, S. Editor’s highlight: Microbial-derived 1,4-dihydroxy-2-naphtholic acid and related compounds as aryl hydrocarbon receptor agonists/antagonists: Structure-activity relationships and receptor modeling. Toxicol. Sci. 155, 458–473 (2017). 248. Zoh, R. S.; Mallick, B.; Ivanov, I.; Baladandayuthapani, V.; Manyam, G.; Chapkin, R. S.; Lampe, J. W.; Carroll, R. J. PCAN: Probabilistic correlation analysis of two non-normal data sets. Biometrics 72, 1358–1368 (2016). 247. Navarro, S. L.; Neuhouser, M. L.; Cheng, T. D.; Tinker, L. F.; Shikany, J. M.; Snetselaar, L.; Martinez, J. A.; Kato, I.; Beresford, S. A.; Chapkin, R. S.; Lampe, J. W. The interaction between dietary fiber and fat and risk of colorectal cancer in the Women’s Health Initiative. Nutrients 8 (2016). 246. Kim, E.; Davidson, L. A.; Zoh, R. S.; Hensel, M. E.; Salinas, M. L.; Patil, B. S.; Jayapraskasha, G. K.; Callaway, E. S.; Allred, C. D.; Turner, N. D.; Weeks, B. R.; Chapkin, R. S. Rapidly cycling Lgr5+ stem cells are exquisitely sensitive to extrinsic dietary factors that modulate colon cancer risk. Cell Death Dis. 7, e2460 (2016). 245. Fan, Y. Y.; Callaway, E.; Monk, J. M.; Goldsby, J. S.; Yang, P.; Vincent, L.; Chapkin, R. S. A new model to study the role of arachidonic acid in colon cancer pathophysiology. Cancer Prev. Res. 9, 750–757 (2016). 244. Knight, J. M.; Kim, E.; Ivanov, I.; Davidson, L. A.; Goldsby, J. S.; Hullar, M. A.; Randolph, T. W.; Kaz, A. M.; Levy, L.; Lampe, J. W.; Chapkin, R. S. Comprehensive site-specific whole genome profiling of stromal and epithelial colonic gene signatures in human sigmoid colon and rectal tissue. Physiol. Genomics 48, 651–659 (2016). 243. Hou, T. Y.; McMurray, D. N.; Chapkin, R. S. Omega-3 fatty acids, lipid rafts, and T cell signaling. Eur. J. Pharmacol. 785, 2–9 (2016). 242. Hou, T. Y.; Davidson, L. A.; Kim, E.; Fan, Y. Y.; Fuentes, N. R.; Triff, K.; Chapkin, R. S. Nutrient-gene interaction in colon cancer, from the membrane to cellular physiology. Annu. Rev. Nutr. 36, 543–570 (2016). 241. DeClercq, V. C.; Goldsby, J. S.; McMurray, D. N.; Chapkin, R. S. Distinct adipose depots from mice differentially respond to a high-fat, high-salt diet. J. Nutr. 146, 1189–1196 (2016). 240. Whitfield-Cargile, C. M.; Cohen, N. D.; Chapkin, R. S.; Weeks, B. R.; Davidson, L. A.; Goldsby, J. S.; Hunt, C. L.; Steinmeyer, S. H.; Menon, R.; Suchodolski, J. S.; Jayaraman, A.; Alaniz, R. C. The microbiota-derived metabolite indole decreases mucosal inflammation and injury in a murine model of NSAID enteropathy. Gut Microbes 7, 246–261 (2016). 239. Kim, S. M.; Neuendorff, N.; Chapkin, R. S.; Earnest, D. J. Role of inflammatory signaling in the differential effects of saturated and poly-unsaturated fatty acids on peripheral circadian clocks. EBioMed. 7, 100–111 (2016). 238. Shah, M. S.; Kim, E.; Davidson, L. A.; Knight, J. M.; Zoh, R. S.; Goldsby, J. S.; Callaway, E. S.; Zhou, B.; Ivanov, I.; Chapkin, R. S. Data describing the effects of dietary bioactive agents on colonic stem cell microRNA and mRNA expression. Data Brief 6, 398–404 (2016). 237. Kim, E.; Davidson, L. A.; Zoh, R. S.; Hensel, M. E.; Patil, B. S.; Jayaprakasha, G. K.; Callaway, E. S.; Allred, C. D.; Turner, N. D.; Weeks, B. R.; Chapkin, R. S. Homeostatic responses of colonic LGR5+ stem cells following acute in vivo exposure to a genotoxic carcinogen. Carcinogenesis 37, 206–214 (2016). 236. Shah, M. S.; Kim, E.; Davidson, L. A.; Knight, J. M.; Zoh, R. S.; Goldsby, J. S.; Callaway, E. S.; Zhou, B.; Ivanov, I.; Chapkin, R. S. Comparative effects of diet and carcinogen on microRNA expression in the stem cell niche of the mouse colonic crypt. Biochim. Biophys. Acta 1862, 121–134 (2016). 235. Hou, T. Y.; Barhoumi, R.; Fan, Y. Y.; Rivera, G. M.; Hannoush, R. N.; McMurray, D. N.; Chapkin, R. S. n-3 Polyunsaturated fatty acids suppress CD4(+) T cell proliferation by altering phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P2] organization. Biochim. Biophys. Acta 1858, 85–96 (2016). 234. DeClercq, V.; McMurray, D. N.; Chapkin, R. S. Obesity promotes colonic stem cell expansion during cancer initiation. Cancer Lett. 369, 336–343 (2015). 233. Davidson, L. A.; Callaway, E. S.; Kim, E.; Weeks, B. R.; Fan, Y. Y.; Allred, C. D.; Chapkin, R. S. Targeted deletion of p53 in Lgr5-expressing intestinal stem cells promotes colon tumorgenesis in a preclinical model of colitis-associated cancer. Cancer Res. 75, 5392–5397 (2015). 232. Ying, W.; Tseng, A.; Chang, R. C.; Morin, A.; Brehm, T.; Triff, K.; Nair, V.; Zhuang, G.; Song, H.; Kanameni, S.; Wang, H.; Golding, M. C.; Bazer, F. W.; Chapkin, R. S.; Safe, S.; Zhou, B. MicroRNA-223 is a crucial mediator of PPARγ-regulated alternative macrophage activation. J. Clin. Invest. 125, 4149–4159 (2015). 231. Hong, M. Y.; Turner, N. D.; Murphy, M. E.; Carroll, R. J.; Chapkin, R. S.; Lupton, J. R. In vivo regulation of colonic cell proliferation, differentiation, apoptosis, and P27Kip1 by dietary fish oil and butyrate in rats. Cancer Prev. Res. (Phila.) 8, 1076–1083 (2015). 230. Cheng, Y.; Jin, U. H.; Allred, C. D.; Jayaraman, A.; Chapkin, R. S.; Safe, S. Aryl hydrocarbon receptor activity of tryptophan metabolites in young adult mouse colonocytes. Drug. Metab. Dispos. 43, 1536–1543 (2015). 229. Fan, Y. Y.; Davidson, L. A.; Callaway, E. S.; Wright, G. A.; Safe, S.; Chapkin, R. S. A bioassay to measure energy metabolism in mouse colonic crypts, organoids, and sorted stem cells. Am. J. Physiol. Gastrointest. Liver Physiol. 309, G1–G9 (2015). 228. Wang, M.; Li, M.; Wu, S.; Lebrilla, C. B.; Chapkin, R. S.; Ivanov, I.; Donovan, S. M. Fecal microbiota composition of breast-fed infants is correlated with human milk oligosaccharides consumed. J. Pediatr. Gastroenterol. Nutr. 60, 825– 833 (2015). 227. Triff, K.; Kim, E.; Chapkin, R. S. Chemoprotective epigenetic mechanisms in a colorectal cancer model: Modulation by n-3 PUFA in combination with fermentable fiber. Curr. Pharmacol. Rep. 1, 11–20 (2015). 226. Turk, H. F.; Chapkin, R. S. Analysis of epidermal growth factor receptor dimerization by BS³ cross-linking. Methods Mol. Biol. 1233, 25–34 (2015).

CURRENT SUPPORT NIH R01 CA244359 Chapkin, R. (PI); Karpac, J (co-PI) 2020–2025 “Targeting plasma membrane spatial dynamics to suppress aberrant Wnt signaling” NIH R35 CA197707 Chapkin, R. (PI) 2016–2023 “Molecular basis for dietary chemoprevention” NIH R01 AT010282 Safe, S (PI), Chapkin, R. (co-PI), Lee (co-PI), Jayaraman (co-PI) 2018–2022 “Dietary flavonoids-microbiota-Ah receptor interactions in the gut” NIH R01 DK107561 Donovan (PI), Chapkin, R. (co-PI) 2017–2022 “Dietary and microbial predictors of childhood obesity risk” NIH R21 CA245456 Chapkin, R. (PI), Hullar (co-PI), Lampe (co-PI) 2019–2021 “Diet and the colonic exfolioma: A novel, non-invasive approach to testing interventions in humans” NIH R01 EE025713 Chapkin, R. (PI), Safe, S. (co-PI), Jayaraman (co-PI) 2016–2021 “Role of aryl hydrocarbon receptor in microbiota-colon stem cell interactions”

COMPLETED SUPPORT (2015–present) NIH R01 CA202697 Chapkin, R. (PI), Safe, S. (co-PI), Jayaraman (co-PI) 2016–2021 “Diet-induced modifications of microbiota metabolites in colon tumorigenesis”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Grant Reviewer American Institute for Cancer Research 2019–present Deputy Director P30 Center for Translational Environmental Human Research 2019–present Editorial Board Frontiers in Immunology and Nutrition 2019–present Fellow American Association for the Advancement of Science 2018 Outstanding Investigator Award National Institutes of Health (R35) 2016

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Promotion and Tenure Committee AgriLife 2019–present Member Faculty Mentoring Committee AgriLife 2019–present

COURSES TAUGHT (2015–present) NFSC 203 Scientific Principles of Human Nutrition 3 cr. 2020 NFSC 481 Seminar 1 cr. 2020 Jae-Hyun Cho Assistant Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Columbia University with A. G. Palmer III 2006–2012 Ph.D. State University of New York with D. P. Raleigh 2006 M.S. Pohang University of Science and Technology 1999 B.S. Han-Yang University 1997

PROFESSIONAL APPOINTMENTS Assistant Professor Biochemistry and Biophysics Texas A&M University 2012–present

PEER-REVIEWED PUBLICATIONS (2015–present) 36. Shi, J.; Shen, Q.; Cho, J. H.; Hwang, W. Entropy hotspots for the binding of intrinsically disordered ligands to a receptor domain. Biophys. J. 118, 2502–2512 (2020). 35. Dubrow, A.; Lin, S.; Savage, N.; Shen, Q.; Cho, J. H. Molecular basis of the ternary interaction between NS1 of the 1918 influenza A virus, PI3K, and CRK. Viruses 23, 338 (2020). 34. Cho, J. H.; Zhao, B.; Shi, J.; Savage, N.; Shen, Q.; Byrnes, J.; Yang, L.; Hwang, W.; Li, P. Molecular recognition of a host protein by NS1 of pandemic and seasonal influenza A viruses. Proc. Natl. Acad. Sci. USA 117, 6550–6558 (2020). 33. Shen, Q.; Cho, J. H. The structure and conformation plasticity of the nonstructural protein 1 of the 1918 influenza A virus. Biochem. Biophys. Res. Commun. 518, 178–182 (2019). 32. Shen, Q.; Shi, J.; Zeng, D.; Zhao, B.; Li, P.; Hwang, W.; Cho, J. H. Molecular mechanisms of tight binding through fuzzy interactions. Biophys. J. 114, 1313–1320 (2018). 31. Shen, Q.; Bhatt, V. S.; Krieger, I.; Sacchettini, J. C.; Cho, J. H. Structure-guided design of a potent peptide inhibitor targeting the interaction between CRK and ABL kinase. MedChemComm 9, 519–524 (2018). 30. Shen, Q.; Zeng, D.; Zhao, B.; Bhatt, V. S.; Li, P.; Cho, J. H. The molecular mechanisms underlying the hijack of host protein-protein interactions by NS1 of the 1918 Spanish influenza A virus. ACS Chem. Biol. 12, 1199–1203 (2017). 29. Sato, S.; Cho, J. H.; Peran, I.; Soydaner-Azeloglu, R. G.; Raleigh, D. P. The N-terminal domain of ribosomal protein L9 folds via a diffuse and delocalized transition state. Biophys. J. 112, 1797–1806 (2017). 28. Zeng, D.; Shen, Q.; Cho, J. H. Thermodynamic contribution of backbone conformational entropy in the binding between SH3 domain and proline-rich motif. Biochem. Biophys. Res. Commun. 484, 21–26 (2017). 27. Zeng, D.; Bhatt, V. S.; Shen, Q.; Cho, J. H. Kinetic insights into the binding mechanism between the nSH3 domain of CrkII and proline-rich motifs in cAbI. Biophys. J. 111, 1843–1853 (2016). 26. Bhatt, V. S.; Zeng, D.; Krieger, I.; Sacchettini, J. C.; Cho, J. H. Binding mechanism of the N-terminal SH3 domain of CrkII and proline-rich motifs in cAbI. Biophys. J. 110, 2630–2641 (2016).

CURRENT SUPPORT Welch Foundation Cho, J. H. 2020–2023 “Biophysical bases of evading host innate immune responses by pandemic and seasonal influenza viruses” NIH #R01- GM127723 Cho, J. H. 2018–2023 “Structure and functional dynamics of virus–host protein interaction” USDA-NIFA Hatch Cho, J. H. – “Molecular mechanisms whereby a pandemic influenza A virus antagonizes host antiviral immune responses” TAMU T3 Cho, J. H. 2019 “Target oncogenic protein–protein interactions” NIH Admin. Supplement Cho, J. H. 2019 Purchase of isothermal titration calorimeter

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Ad hoc peer reviewer Various scientific journals 2012–present Poster judge The Protein Society Symposium 2017

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Admissions Committee BCBP 2020–present Member IT Oversight Committee BCBP 2019–present Member Outreach and Recruitment Committee BCBP 2019–present Member Awards Committee BCBP 2014–present Member Non-Thesis Masters Committee BCBP 2019 Member Department Head Search Committee BCBP 2018–2019 Member Graduate Recruitment and Admissions Committee BCBP 2017–2019

COURSES TAUGHT (2015–present) BICH 689 Curve Fitting with Regression Analysis 1 cr. 2018–present BICH 601 Fundamentals of Biochemistry I 3 cr. 2013–2019 BICH 624 Enzymes, Proteins, and Nucleic Acids 1 cr. 2017 BICH 404 Biochemical Calculations 2 cr. 2015

Jorge Cruz-Reyes Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral The Johns Hopkins School of Medicine 2001 Postdoctoral National Institute for Medical Research, London 1994 Ph.D. School of Hygiene and Tropical Medicine, London 1993 M.S. Biotechnology Institute, Mexico 1989 B.S. National University of Mexico 1987

PROFESSIONAL APPOINTMENTS Professor Biochemistry and Biophysics Texas A&M University 2017–present Associate Professor Biochemistry and Biophysics Texas A&M University 2007–2016 Assistant Professor Biochemistry and Biophysics Texas A&M University 2001–2007

PEER-REVIEWED PUBLICATIONS (2015–present) 43. Kumar, V.; Ivens, A.; Goodall, Z.; Meehan, J.; Doharey, P. K.; Hillhouse, A.; Hurtado, D. O.; Cai, J. J.; Zhang, X.; Schnaufer, A.; Cruz-Reyes, J. Site-specific and mRNA-specific control of accurate mRNA editing by a helicase complex in trypanosomes. RNA 076513.120 (2020). 42. Aphasizheva, I.; Alfonzo, J.; Carnes, J.; Cestari, I.; Cruz-Reyes, J.; Göringer, H. U.; Hajduk, S.; Lukeš, J.; Madison- Antenucci, S.; Maslov, D. A.; McDermott, S. M.; Ochsenreiter, T.; Read, L. K.; Salavati, R.; Schnaufer, A.; Schneider, A.; Simpson, L.; Stuart, K.; Yurchenko, V.; Zhou, Z. H.; Zíková, A.; Zhang, L.; Zimmer, S.; Aphasizhev, R. Lexis and grammar of mitochondrial RNA processing in trypanosomes. Trends Parasitol. 36, 337–355 (2020). 41. Chenna, B. C.; Li, L.; Mellott, D. M.; Zhai, X.; Siqueira-Neto, J. L.; Calvet Alvarez, C.; Bernatchez, J. A.; Desormeaux, E.; Alvarez Hernandez, E.; Gomez, J.; McKerrow, J. H.; Cruz-Reyes, J.; Meek, T. D. Peptidomimetic vinyl heterocycle inhibitors of cruzain effect anti-trypanosomal activity. J. Med. Chem. 63, 3298–3316 (2020). 40. Kumar, V.; Doharey, P. K.; Gulati, S.; Meehan, J.; Martinez, M. G.; Hughes, K.; Mooers, B. H. M.; Cruz-Reyes, J. Protein features for assembly of the RNA editing helicase 2 subcomplex (REH2C) in trypanosome holo-editosomes. PLoS One 14, e0211525 (2019). 39. Cruz-Reyes, J.; Mooers, B. H. M.; Doharey, P. K.; Meehan, J.; Gulati, S. Dynamic RNA holo-editosomes with subcomplex variants: Insights into the control of trypanosome editing. Wiley Interdiscip. Rev. RNA 9, e1502 (2018). 38. Cruz-Reyes, J.; Mooers, B. H. M.; Kumar, V.; Doharey, P. K.; Meehan, J.; Chaparro, L. Control mechanisms of the holo-editosome in trypanosomes. RNA Metabolism in Mitochondria , 125–144 (2018) 37. Cruz-Reyes, J.; Mooers, B. H.; Abu-Adas, Z.; Kumar, V.; Gulati, S. DEAH-RHA helicase Znf cofactor systems in kinetoplastid RNA editing and evolutionarily distant RNA processes. RNA Dis 3, e1336 (2016). 36. Kumar, V.; Madina, B. R.; Gulati, S.; Vashisht, A. A.; Kanyumbu, C.; Pieters, B.; Shakir, A.; Wohlschlegel, J. A.; Read, L. K.; Mooers, B. H.; Cruz-Reyes, J. REH2C helicase and GRBC subcomplexes may base pair through mRNA and small guide RNA in kinetoplastid editosomes. J. Biol. Chem. 291, 5753–5764 (2016). 35. Madina, B. R.; Kumar, V.; Mooers, B. H. ; Cruz-Reyes, J. Native variants of the MRB1 complex exhibit specialized functions in kinetoplastid RNA editing. PLoS One 10, e0123441 (2015). 34. Briggs, S. D.; Bryk, M.; Strahl, B. D.; Cheung, W. L.; Davie, J. K.; Dent, S. Y. R.; Winston, F.; Allis, C. D. Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. Genes and Development 15, 3286–3295 (2001).

CURRENT SUPPORT TAMU X-Grant 02-290386 Zhang, X. (PI); Cai, J. (PI); Ji, J.-Y. (co-PI); Patrick, K. (co-PI); Cruz- 2019–2022 Reyes, J. (co-PI); Sczepanski, J. (co-PI); Zhang, J. (co-PI); Zeng, L. (co-PI) “Genetic and epigenetic architecture of natural telomere length variation” NIH #1R01-AI127807-01 Meek, T. (PI); Cruz-Reyes, J. (co-PI) 2017–2022 “Phosphoribosyltransferases as targets to treat malaria, African trypanosomiasis and Chagas disease” NSF #1616865 Cruz-Reyes, J. (PI) (extension) 2021 2016–2019 “RNA processing in trypanosome mitochondria”

COMPLETED SUPPORT (2015–present) TAMU T3 Award 246442 Cruz-Reyes, J. (PI) 2019–2020 “Drug development against essential NTPase motor proteins in pathogenic parasites” NIH #1R21-AI127634 Meek, T. (PI); Cruz-Reyes, J. (co-PI) 2016–2018 “Novel Inhibitors of Cruzain and Trypanosoma brucei Cathepsin B as Potential Drug Candidates for the treatment of African Trypanosomiasis and Chagas Disease”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Editorial Board PLOS One 2015–2020 Reviewer TAMU Diversity Award 2016 NIH Panel Member MBG; Fellowship: Genes, Genomes, and Genetics; Pathogenic Various Eukaryotes; Forgarty, International and Cooperative Projects-1 NSF Panel Member The Genetic Mechanisms Cluster in the Division of Molecular and Various Cellular Biosciences

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Outreach and Recruitment Committee BCBP 2019–2020 Member Graduate Student Committee BCBP 2015–2019 Member International Relationship Committee BCBP 2015–2018 Member CUE Committee BCBP 2015–2018

COURSES TAUGHT (2015–present) BICH 456/656 RNA World (co-taught) 3 cr. 2016–present BICH/GENE 431 Molecular Genetics 3 cr. 2001–present BICH 491/691 Research Variable 2001–present BICH 631 Biochemical Genetics 3 cr. 2015 Sumana Datta Assistant Provost for Undergraduate Studies| Texas A&M University Professor | Department of Biochemistry and Biophysics Executive Director | LAUNCH, Texas A&M University

EDUCATION Postdoctoral Yale University with D. R. Kankel 1987–1992 Ph.D. University of California, San Diego with R. A. Firtel 1987 B.S. University of Michigan–Ann Arbor with W. Folk 1980

PROFESSIONAL APPOINTMENTS Assistant Provost Undergraduate Studies Texas A&M University 2015–present Executive Director LAUNCH Texas A&M University 2015–present Professor Biochemistry and Biophysics Texas A&M University 2015–present Executive Director Honor and Undergraduate Research Texas A&M University 2010–2015 Assistant Dean Undergraduate Research Texas A&M University 2008–2010 Visiting Professor Winship Cancer Institute Emory School of Medicine 2005–2006 Associate Professor Biochemistry and Biophysics, Center for Texas A&M University 1999–2015 Advanced Invertebrate Molecular Sciences (joint: Biology, Genetics, Neuroscience) Assistant Professor Biochemistry and Biophysics, Center for Texas A&M University 1993–1999 Advanced Invertebrate Molecular Sciences (joint: Biology, Genetics, Neuroscience)

PEER-REVIEWED PUBLICATIONS (2015–present) 22. Mathis, C.; Ramos, H.; Gonzalez, E.; Datta, S. What prevents Business faculty and students from participating in Undergraduate Research? Council on Undergraduate Research Quarterly 35, 35–41 (2015).

CURRENT SUPPORT Arnold and Mabel Beckman Datta, S. 2018–2021 Foundation “Texas A&M Beckman Scholars Program” TAMU School of Innovation Datta, S. (co-Team Leader) 2019–2021 “First Year Eats”

COMPLETED SUPPORT (2015–present) Arnold and Mabel Datta, S. 2014–2017 Beckman Foundation “Texas A&M Beckman Scholars Program”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Institutional Representative National Collegiate Honors Council 2010–present ADVANCE Diversity Champion Texas A&M University 2020 Editorial Board Honors in Higher Education 2017–2019 Division Editor Scholarship and Practice of Undergraduate Research 2012–2019

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Health and Human Services Project Based Learning Committee TAMU 2020–present Mentor ADVANCE Science Scholars Mentor TAMU 2019–present Member Office of Student Success Advisory Committee TAMU 2019–present Member Women Administrators Network Executive Committee TAMU 2017–present Member Engineering Academic and Student Affairs Steering Council on TAMU 2015–present Honors Programs for the Dwight Look College of Engineering Chair Astronaut Scholarship Foundation Nomination Committee TAMU 2012–present Vice President of Diversity Difficult Dialogs Facilitation Team TAMU 2011–present Chair Honors and Undergraduate Research Program Advisory TAMU 2010–present Committee Member Academic Operations Committee TAMU 2010–present Publisher Explorations: The Texas A&M Undergraduate Journal TAMU 2009–present Member FYE Implementation Committee TAMU 2018–2019 Member Student Success Initiative Taskforce TAMU 2018–2019 Co-Chair Executive Director for Study Abroad Program Office Search TAMU 2018 Committee Vice Chair, Chair, Past Women Administrators Network TAMU 2014–2017 Chair Member Academic Scholarship Selection Committee TAMU 2012–2017 Member Climate Survey Discussion Group TAMU 2016 Member Pilot Undergraduate Service Scholar Capstone Program TAMU 2013–2016 Convener Explorations Board TAMU 2008–2016 Member Association of Former Students Distinguished Alumni TAMU 2013–2015 Selection Committee Member ADVANCE Administrative Fellows Selection Committee TAMU 2011–2015 Member ADVANCE Scholar Committee TAMU 2010–2015

COURSES TAUGHT (2015–present) LCSE 002 Honors Freshman Learning Community 1 cr. 2012–present KINE 199 Beginning West Coast Swing Dance 1 cr. 2017–present Timothy P. Devarenne Associate Head of Undergraduate Programs, Associate Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Cornell University with G. B. Martin 2001–2006 Ph.D. University of Kentucky with J. Chappell 1995–2000 M.S. Michigan Technological University with J. H. Adler 1991–1993 B.S. Michigan Technological University with J. H. Adler 1987–1991

PROFESSIONAL APPOINTMENTS Associate Head, Biochemistry and Biophysics Texas A&M University 2018–present Undergraduate Programs Associate Professor Biochemistry and Biophysics, Molecular Texas A&M University 2012–present and Environmental Plant Science Assistant Professor Molecular and Environmental Plant Science Texas A&M University 2006–2012

PEER-REVIEWED PUBLICATIONS AND BOOK CHAPTERS (2015–present) 54. Heiss, C.; Black, I.; Ishihara, M.; Tatli, M.; Devarenne, T. P.; Azadi, P. Structure of the polysaccharide sheath from the B race of the green microalga Botryococcus braunii. Algal Research (2020, accepted). 53. Yeo, I.-C.; Devarenne, T. P. Screening for potential nuclear substrates for the plant cell death suppressor kinase Adi3 using peptide microarrays. PLoS One 15, e0234011 (2020). 52. Hsu, S.-C.; Browne, D. R.; Tatli, M.; Devarenne, T. P.; Stern, D. B. N-terminal sequences affect expression of triterpene biosynthesis enzymes in Chlamydomonas chloroplasts. Algal Research 44, 101662 (2019). 51. Su, D.; Devarenne, T. P. In vitro activity characterization of the tomato SnRK1 complex proteins. Biochim. Biophys. Acta Proteins Proteom. 1866, 857–864 (2018). 50. Kim, H. S.; Devarenne, T. P.; Han, A. Microfluidic systems for microalgal biotechnology: A review. Algal Research 30, 49–161 (2018). 49. Tatli, M.; Ishihara, M.; Heiss, C.; Browne, D. R.; Dangott, L. J.; Vitha, S.; Azadi, P.; Devarenne, T. P. Polysaccharide associated protein (PSAP) from the green microalga Botryococcus braunii is a unique extracellular matrix hydroxyproline-rich glycoprotein. Algal Research 29, 92–103 (2018). 48. Kim, H. S.; Hsu, S.-C.; Han, S.-I.; Thapa, H. R.; Guzman, A. R.; Browne, D. R.; Tatli, M.; Devarenne, T. P.; Stern, D. B.; Han, A. A high-throughput droplet microfluidics screening platform for selecting fast-growing and high lipid-producing microalgae from a mutant library. Plant Direct 1, 1–13 (2017). 47. Lozoya-Gloria, E.; Cornejo-Corona, I.; Thapa, H. R.; Browne, D. R.; Devarenne, T. P. ROS detection in Botryococcus braunii colonies with CellROX Green reagent. BioProtocol 7, e2508 (2017). 46. Thapa, H. R.; Tang, S.; Sacchettini, J. C.; Devarenne, T. P. Tetraterpene synthase substrate and product specificity in the green microalga Botryococcus braunii race L. ACS Chem. Biol. 12, 2408–2416 (2017). 45. Tatli, M.; Chun, H. J.; Camp, Jr., C. H.; Li, J.; Cicerone, M. T.; Shih, W.-C.; Laane, J.; Devarenne, T. P. Raman spectra and DFT calculations for botryococcene and methylsqualene hydrocarbons from the B race of the green microalga Botryococcus braunii. J. Mol. Struct. 1147, 427–437 (2017). 44. Browne, D. R.; Jenkins, J.; Schmutz, J.; Shu, S.; Barry, K.; Grimwood, J.; Chiniquy, J.; Sharma, A.; Niehaus, T. D.; Weiss, T. L.; Koppisch, A. T.; Fox, D. T.; Dhungana, S.; Okada, S.; Chappel, J.; Devarenne, T. P. Draft nuclear genome sequence of the liquid hydrocarbon accumulating green microalga Botryococcus braunii, race B (Showa). Genome Announc. 5, e00215–17 (2017). 43. Tatli, M.; Naik, M. T.; Okada, S.; Dangott, L. J.; Devarenne, T. P. Isolation and characterization of cyclic C33 botryococcenes and a trimethylsqualene isomer from Botryococcus braunii race B. J. Nat. Prod. 80, 953–958 (2017). 42. Kim, H. S.; Waqued, S. C.; Nodurft, D. T.; Devarenne, T. P.; Yakovlev, V.; Han, A. Raman spectroscopy compatible PDMS droplet microfluidic culture and analysis platform towards on-chip lipidomics. Analyst 142, 1054–1060 (2017). 41. Chun, H. J.; Waqued, S.; Thapa, H. R.; Han, A.; Yakovlev, V.; Laane, J.; Devarenne, T. P. Raman spectra and DFT calculations for tetraterpene hydrocarbons from the L race of the green microalga Botryococcus braunii. J. Mol. Struct. 1129, 216–221. doi: 10.1016/moistruc.2016.09.081 (2017). 40. Unkefer, C. J.; Sayre, R. T.; Magnuson, J. K.; Anderson, D. B.; Baxter, I.; Blaby, I. K.; Brown, J. K.; Carleton, M.; Cattolico, R. A.; Dale, T.; Devarenne, T. P.; Downes, C. M.; Dutcher, S. K.; Fox, D. T.; Goodenough, U.; Jaworski, J,; Holladay, J. E.; Kramer, D. M.; Koppisch, A. T.; Lipton, M. S.; Marrone, B. L.; McCormick, M.; Molnár, I.; Mott, J. B.; Ogden, K. L.; Panisko, E. A.; Pellegrini, M.; Polle, J.; Richardson, J. W.; Sabarsky, M.; Starkenburg, S. R.; Stormo, G. D.; Teshima, M.; Twary, S. N.; Unkefer, P. J.; Yuan, J. S.; Olivares, J. A. Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts. Algal Research 22, 187–215 (2017). 39. Cornejo-Corona, I.; Thapa, H. R.; Browne, D. R.; Devarenne, T. P.; Lozoya-Gloria, E. Stress responses of the oil-producing green microalga Botryococcus braunii Race B. PeerJ 4, e2748 (2016). 38. Thapa, H. R.; Naik, M. T.; Okada, S.; Takada, K.; Molnar, I.; Xu, Y.; Devarenne, T. P. A squalene synthase-like enzyme initiates production of tetraterpenoid hydrocarbons in Botryococcus braunii race L. Nat. Commun. 7, 11198 (2016). 37. Miao, M.; Niu, X.; Kud, J.; Du, X.; Avila, J.; Devarenne, T. P.; Kuhl, J.; Liu, Y.; Xiao, F. The ubiquitin ligase SEVEN IN ABSENTIA (SINA) ubiquitinates a defense-related NAC transcription factor and is involved in defense signaling. New Phytol. 211, 138–148 (2016). 36. Kim, H. S.; Guzman, A. R.; Thapa, H. R.; Devarenne, T. P.; Han, A. A droplet microfluidics platform for rapid microalgal growth and oil production analysis. Biotechnol. Bioengin. 113,1691–1701 (2016). 35. Kim, H. S.; Devarenne, T. P.; Han, A. A high-throughput microfluidic single-cell screening platform capable of selective cell extraction. Lab on a Chip 15, 2467–2475 (2015). 34. Deng, L.; Senseman, S. A.; Gentry, T. J.; Zuberer, D. A.; Camargo, E. R.; Weiss, T. L.; Devarenne T. P. Effect of selected herbicides on growth and lipid content of Nannochloris oculata. J. Aquat. Plant Manage. 53, 28–35 (2015). 33. Cornejo-Corona, I.; Thapa, H. R.; Devarenne, T. P.; Lozoya-Gloria, E. The biofuel potential of the green colonial microalga Botryococcus braunii in Microalgae and other phototrophic bacteria: Culture, processing, recovery and new products. Ed: Torres-Bustillos, L.G., Nova Science Publishers Inc., Hauppauge, NY. pp. 41–58. ISBN 978-1-63482-078-3 (2015).

COMPLETED SUPPORT (2015–present) NSF EFRI PSBR-1240478 Han, A. (PI); Devarenne, T. (co-PI); Stern, D. (co-PI) (no cost extension) 2019 2012–2016 “Microalgae lab-on-chip photobioreactor platform for genetic screening and metabolic analysis leading to scalable biofuel production” NSF-EFRI-PSBR Han, A. (PI); Devarenne, T. (co-PI); Stern, D. (co-PI) 2015–2017 “Multidisciplinary experience in engineering and microalgal bioenergy. NSF-EFRI-Research Experience and Mentoring. Supplement to NSF-EFRI-PSBR grant #1240478” TAMU Collaborative Research Grant Lozoya-Gloria, E. (PI); Devarenne, T. (co-PI) 2016–2017 Program “Characterization of the cyclin dependent kinase gene(s) involved in the interaction between the cyclin D and retinoblastoma genes, and their function related to the cell cycle of the green microalga Botryococcus braunii.” USDA-NIFA-AFRI Devarenne, T. (PI) (no cost extension) 2017 #2014-67013-21560 2013–2016 “Regulation of tomato cell death by the protein kinase Adi3 during resistance to Pseudomonas syringae.” Texas A&M Energy Institute Devarenne, T. (co-PI) 2015–2016 “Domestication of Microalgae - From Natural Diversity to Synthetic Biology” DOE-ARPA-E-PETRO Yuan, J. (PI); Devarenne, T. (co-PI) 2012–2015 #DE-AR0000203 “Synthetic crops for direct drop-in biofuel production through rerouting photosynthetic intermediates and engineering terpenoid pathways”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Editorial Board PLOS One 2014–present Executive Committee Member; Japan Society for Promotion of Science USA Alumni Association Various Treasurer; Advisory Board Member; Chair, IT Committee

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Academic Advising Advisory Board BCBP 2020–present Associate Department Head Undergraduate Programs BCBP 2019–present Co-Associate Department Head Undergraduate Programs BCBP 2018–present Member Texas A&M Energy Institute TAMU 2014–present Member TAMU Institute for Quantum Science and Engineering TAMU 2012–present Member Common Use Equipment BCBP 2014–2018 Chair Department Awards Committee BCBP 2013–2018 Chair Seminar Committee BCBP 2007–2018 Member Faculty Search Committee BCBP 2016

COURSES TAUGHT (2015–present) BICH 303 Elements of Biological Chemistry 3 cr. 2009–present BICH 675 Plant Biochemistry and Genomics (Journal Club) 1 cr. 2008–present BICH 101 Perspectives in Biochemistry & Genetics 1 cr. 2007–present BICH/GENE 491/691 Research Variable 2006–present BICH 605 Methods of Biochemical Analysis 1 cr. 2015–2016 Margaret E. Glasner Associate Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral University of California, San Francisco with P. C. Babbitt 2003–2008 Ph.D. Massachusetts Institute of Technology with D. Bartel 2003 B.S., B.M. University of Wyoming, Laramie 1995

PROFESSIONAL APPOINTMENTS Associate Professor Biochemistry and Biophysics Texas A&M University 2015–present Assistant Professor Biochemistry and Biophysics Texas A&M University 2008–2015

PEER-REVIEWED PUBLICATIONS (2015–present) 20. Glasner, M. E.; Truong, D. P.; Morse, B. C. How enzyme promiscuity and horizontal gene transfer contribute to metabolic innovation. FEBS J. 287, 1323–1342 (2020). 19. Burroughs, A. M.; Glasner, M. E.; Barry, K. P.; Taylor, E. A.; Aravind, L. Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives. J. Biol. Chem. 294, 10211–10235 (2019). 18. Odokonyero, D.; McMillan, A. W.; Ramagopal, U. A.; Toro, R.; Truong, D. P.; Zhu, M.; Lopez, M. S.; Somiari, B.; Herman, M.; Aziz, A.; Bonanno, J. B.; Hull, K. G.; Burley, S. K.; Romo, D.; Almo, S. C.; Glasner, M. E. Comparison of Alicyclobacillus acidocaldarius O-succinylbenzoate synthase to its promiscuous N-succinylamino acid racemase / O-succinylbenzoate synthase relatives. Biochemistry 57, 3676–3689 (2018). 17. Glasner, M. E. Finding enzymes in the gut metagenome. Science 355, 577–578 (2017).

CURRENT SUPPORT NIH #R01- GM124409 Glasner, M. E. 2018–2022 “Biophysics constraints on evolution of enzyme specificity” COMPLETED SUPPORT (2015–present) Welch Foundation Glasner, M. E. 2019 “Role of underground metabolism in the evolution of new metabolic pathways” NSF CAREER Glasner, M. E. 2013–2018 “Evolutionary mechanisms for recruiting promiscuous enzyme activities into new metabolic pathways”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Distinguished Achievement in Teaching Association of Former Students 2019 Ad hoc peer reviewer NIH Genome Variation and Evolution Study Section 2015, 2019 Ad hoc peer reviewer NSF Chemistry of Life Processes (Panel) 2017 Ad hoc peer reviewer Various scientific journals 2009–present

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Undergraduate Program Committee BCBP 2018–present Chair Awards Committee BCBP 2018–present Member Center for Teaching Excellence Award Selection Committee COALS 2015, 2017, 2019 Member Awards Committee BCBP 2013–2018

COURSES TAUGHT (2015–present) BICH 285 Directed Studies 5 cr. 2020 BICH/GENE 101 Perspectives in Biochemistry and Genetics 1 cr. 2016–present BICH 441 Biochemistry II 3 cr. 2010–present Vishal M. Gohil Associate Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Harvard Medical School with V. K. Mootha 2005–2008 Ph.D. Wayne State University With M. L. Greenberg 2005 M.S. The Maharaja Sayajirao University of Baroda 1997 B.S. Mohan Ial Sukhadia University 1995

PROFESSIONAL APPOINTMENTS Associate Professor Biochemistry and Biophysics Texas A&M University 2018–present Assistant Professor Biochemistry and Biophysics Texas A&M University 2012–2018 Instructor Medicine Massachusetts General Hospital 2008–2011

PEER-REVIEWED PUBLICATIONS (2015–present) 35. Gohil, V.M. Repurposing elesclomol, an investigational drug for the treatment of copper metabolism disorders. Expert Opin. Investiga. Drugs 5, 1–4 (2020). 34. Zulkifli, M.; Neff, J. K.; Timbalia, S. A.; Garza, N. M.; Chen, Y.; Watrous, J. D.; Murgia, M.; Trivedi, P. P.; Anderson, S. K.; Tomar, D.; Nilsson, R.; Madesh, M.; Jain, M.; Gohil, V. M. MCUR1 homologs Put6 and Put7 regulate mitochondrial proline metabolism in yeast. Nat. Commun. 11, 4866 (2020). 33. Ghosh, S.; Basu Ball, W.; Madaris, T. R.; Srikantan, S.; Madesh, M.; Mootha, V. K.; Gohil, V. M. An essential role for cardiolipin in the stability and function of the mitochondrial calcium uniporter. Proc. Natl. Acad. Sci. USA 29, 20200640 (2020). 32. Guthrie, L. M.; Soma, S.; Yuan, S.; Silva, A.; Zukifli, M.; Snavely, T. C.; Greene, H. F.; Nunez, E.; Lynch, B.; De Ville, C.; Shanbhag, V.; Lopez, F. R.; Acharya, A.; Petris, M. J.; Kim, B. E.; Gohil, V. M.; Sacchettini, J. C. Elesclomol alleviates Menkes pathology and mortality by escorting Cu to cuproenzymes in mice. Science 268, 620–625 (2020). 31. Iadarola, D. M.; Ball, W. B.; Trivedi, P. P.; Fu, G.; Nan, B.; Gohil, V. M. Vps39 is required for ethanolamine-stimulated elevation in mitochondrial phosphatidylethanolamine. Biochim. Biophys. Acta Mol. Cell Biol. Lipids 1865, 158655 (2020). 30. Soma, S.; Morgada, M. N.; Naik, M. T.; Boulet, A.; Roesler, A. A.; Dziuba, N.; Ghosh, A.; Yu, Q.; Lindahl, P. A.; Ames, J. B.; Leary, S. C.; Vila, A. J.; Gohil, V. M. COA6 is structurally tuned to function as a thiol-disulfide oxidoreductase in copper delivery to mitochondrial cytochrome c oxidase. Cell Rep. 29, 4114–4126.e5 (2019). 29. Ghosh, S.; Iadarola, D. M.; Basu Ball, W. B.; Gohil, V. M. Mitochondrial dysfunctions in Barth syndrome. IUBMB Life 71, 791–801 (2019). 28. Soma, S.; Latimer, A. J.; Chun, H.; Vicary, A. C.; Timbalia, S. A.; Boulet, A.; Rahn, J. J.; Chan, S. S. L.; Leary, S. C.; Kim, B. E.; Gitlin, J. D.; Gohil, V. M. Elesclomol restores mitochondrial function in genetic models of copper deficiency. Proc. Natl. Acad. Sci. USA 115, 8161–8166 (2018). 27. Basu Ball, W. B.; Baker, C. D.; Neff, J. K.; Apfel, G. L.; Lagerborg, K. A.; Zun, G.; Petrovic, U.; Jain, M.; Gohil, V. M. Ethanolamine ameliorates mitochondrial dysfunction in cardiolipin-deficient yeast cells. J. Biol. Chem. 293, 10870– 10883 (2018). 26. Basu Ball, W. B.; Neff, J. K.; Gohil, V. M. The role of nonbilayer phospholipids in mitochondrial structure and function. FEBS Lett. 592, 1273–290 (2017). 25. Baker, C. D.; Basu Ball, W.; Pryce, E. N.; Gohil, V. M. Specific requirements of non-bilayer phospholipids in mitochondrial respiratory chain function and formation. Mol. Biol. Cell 27, 2161–2171 (2016). 24. Tomar, D.; Dong, Z.; Shanmughapriya, S.; Koch, D. A.; Thomas, T.; Hoffman, N. E.; Timbalia, S. A.; Goldman, S. J.; Breves, S. L.; Corbally, D. P.; Nemani, N.; Fairweather, J. P.; Cutri, A. R.; Zhang, X.; Song, J.; Jana, F.; Huang, J.; Barrero, C.; Rabinowitz, J. E.; Luongo, T. S.; Schumacher, S. M.; Rockman, M. E.; Dietrich, A.; Merali, S.; Caplan, J.; Stathopulos, P.; Ahima, R. S.; Cheung, J. Y.; Houser, S. R.; Koch, W. J.; Patel, V.; Gohil, V. M.; Elrod, J. W.; Rajan, S.; Madesh, M. MCUR1 Is a scaffold factor for the MCU complex function and promotes mitochondrial bioenergetics. Cell Rep. 15, 1673–1685 (2016). 23. Ghosh, A.; Pratt, A. T.; Soma, S.; Theriault, S. G.; Griffin, A. T.; Trivedi, P. P.; Gohil, V. M. Mitochondrial disease genes COA6, COX6B and SCO2 have overlapping roles in COX2 biogenesis. Hum. Mol. Genet. 25, 660–671 (2016). 22. Kishi, S.; Campanholle, G.; Gohil, V. M.; Perocchi, F.; Brooks, C. R.; Morizane, R.; Sabbisetti, V.; Ichimura, T.; Mootha, V. K.; Bonventre, J. V. Meclizine preconditioning protects the kidney against ischemia–reperfusion injury. EBioMedicine 9, 1090–101 (2015).

CURRENT SUPPORT NIH #R01-GM111672-06 Gohil, V. M. 2019–2023 “Molecular Mechanisms of Copper Delivery to Mitochondrial Cytochrome c Oxidase” NIH #1R01-AG042189 Gohil, V. M. (co-PI) 2018–2023 “Epigenetics of the Aging Astrocyte: Implications for Stroke” Welch Foundation A-1810 Gohil, V. M. 2019–2022 “Phospholipid:Protein Interactions in Mitochondrial Bioenergetics” Barth Syndrome Foundation Gohil, V. M. 2020–2021 “Cardiolipin Requirement for Mitochondrial Calcium Import”

COMPLETED SUPPORT (2015–present) NIH #R01-GM111672-01 Gohil, V. M. 2014–2020 “A Genomic and Biochemical Analysis of Mitochondrial Respiratory Chain Biogenesis” Welch Foundation A-1810 Gohil, V. M. 2016–2019 “Phospholipid:Protein Interactions in Energy Transformation Reactions” American Heart Association Gohil, V. M. 2016–2018 #16GRNT31020028 “Correcting Mitochondrial Defects in Barth Syndrome Models by Targeting Phosphatidylethanolamine Metabolism” American Heart Association Gohil, V. M. 2013–2017 #13SDG17060112 “Discovery and Characterization of Novel Mitochondrial Respiratory Chain Genes” Welch Foundation A-1810 Gohil, V. M. 2013–2016 “Phospholipid–Protein Interactions in Energy Transformation Reactions”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Dean’s Outstanding Achievement Award for Teaching TAMU College of Agriculture and Life Sciences 2019 Montague Center for Teaching Excellence Scholar TAMU College of Agriculture and Life Sciences 2017

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Inclusive Excellence Committee (ICE) COAL:S 2020–present Chair Departmental Diversity Committee BCBP 2020–present Member Astronaut Fellowship applications from STEM TAMU 2020 undergraduates Member Graduate Program Committee (GPC) BCBP 2019 Member Montague-Center for Teaching Excellence Award from COALS 2018–2020 Tenure-Track Assistant Professors Member Departmental Head Search Committee BCBP 2017–2018 Member Common Use Equipment (CUE) Committee BCBP 2015–2018 Member Admission Committee (Graduate Recruitment Committee) BCBP 2015–present GRAC

COURSES TAUGHT (2015–present) BICH 689 Special Topics in Metabolism 1 cr. 2018–present BICH 441 Biochemistry II 3 cr. 2015–present BICH 605 Methods of Biochemical Analysis 3 cr. 2013–2016 BICH 602 Fundamentals of Biochemistry II 3 cr. 2014–2015 Ping He Professor | Department of Biochemistry and Biophysics Faculty of Genetics, Molecular & Environmental Plant Sciences

EDUCATION Postdoctoral Harvard Medical School 2003–2008 Ph.D. Kansas State University 2003 M.S. Chinese Academy of Sciences 1998 B.S. China Agricultural University 1993

PROFESSIONAL APPOINTMENTS Professor Biochemistry and Biophysics Texas A&M University 2020–present Faculty of Genetics Faculty of Molecular and Environmental Plant Sciences Professor Biochemistry and Biophysics Texas A&M University 2017–2020 Institute for Plant Genomics and Biotechnology Faculty of Molecular and Environmental Plant Sciences Associate Professor Biochemistry and Biophysics Texas A&M University 2013–2017 Institute for Plant Genomics and Biotechnology Faculty of Molecular and Environmental Plant Sciences Assistant Professor Biochemistry and Biophysics Texas A&M University 2009–2013 Institute for Plant Genomics and Biotechnology Faculty of Molecular and Environmental Plant Sciences

PEER-REVIEWED PUBLICATIONS (2015–present) 139. Yao, D.; Arguez, M. A.; He, P.; Bent, A. F.; Song, J. Coordinated regulation of plant immunity by poly(ADP-ribosyl)ation and K63-linked ubiquitination. Nat. Commun. (2021, under review). 138. Hou, S.; Liu, D.; Lou, D.; Liu, Z.; Han, Z.; Cai, J.; He, P.; Shan, L. Immune activation by sensing conserved signatures from plant cytokines and pathogens via the Arabidopsis MIK2 receptor kinase. Nat. Commun. (2021, under review). 137. Lahiri, A.; Zhou, L.; He, P.; Datta, A. Detecting drought regulators using stochastic inference in Bayesian networks. BMC Plant Biol. (2021, under review). 136. Ma, X.; Zhang, C.; Kim, D. Y.; Huang, Y.; He, P.; Vierstra, R. D.; Shan, L. Ubiquitylome analysis revelas a central role for the ubiquitin-proteasome system in plant innate immunity. Plant Physiol. (2021, under review). 135. de A. Manhaes, A. M. E.; Ortiz-Morea, F. A.; He, P.; Shan, L. Plant plasma membrane-resident receptors: surveillance for infections and coordination for growth and development. J. Integ. Plant Biol. (2021, under review). 134. Babilonia, K.; Wang, P.; Liu, L.; Jamieson, P.; Rodrigues, O.; Lin, W.; Clement, C. D.; Finlayson, S. A.; Nichols, R. L.; Wheeler, T. A.; Dever, J. K.; Shan, L.; He, P. A non-proteinaceous Fusarium cell wall elicitor triggers receptor-like protein-dependent immune responses in plants. New Phytol. (2021, under revision). 133. Ortiz-Morea, F. A.; He, P.; Shan, L.; Russinova, E. It takes two to tango: Molecular links between plant immunity and brassinosteroid signaling. J. Cell Sci. (2021). 132. Wang, P.; Jamieson, P.; Zhang, L.; Zhao, Z.; Shao, W.; Wu, L.; Zhou, L.; Mustafa, R.; Amin, I.; Hou, Y.; He, P.; Shan, L. Cotton wall-associated kinase GhWAK7A mediates responses to fungal wilt pathogens by modulating chitin sensory complex. Plant Cell (2021, accepted). 131. Huang, Y.; Yin, Y.; Liu, J.; Feng, B.; Ge, D.; Kong, K.; Ortiz-Morea, F. A.; Richter, J.; Hauser, M.; Wang, W.; Shan, L.; He, P. A trimerica CrRLK1L-LLG1 complex genetically modulates SUMM2-mediated autoimmunity. Nat. Commun. 11, 4859 (2020). 130. Huang, Y.; Liu, J.; Kong, L.; Yu, X.; Feng, B.; Mendes, G. C.; Zhao, B.; Yuan, P.; Ge, D.; Wang, W.-M.; Fontest, E. P. B.; Li, P.; Shan, L.; He, P. The malectin-like receptor-like kinase LETUM1 modulates NLR protein SUMM2 activation via MEKK2 scaffolding. Nat. Plants (2020). 129. Ma, X.; Lucas, A. N. C.; Leslie, E. M.; Tao, K.; Wu, Z.; Liu, J.; Xiao, Y.; Li, B.; Zhou, J.; Savatin, V. D.; Peng, J.; Tyler, B.; Heese, A.; Russinova, E.; He, P.; Shan, L. Ligand-induced multi-monoubiquitination of BIK1 regulates plant immunity. Nature 581, 199–203 (2020). 128. Yang, Y.; Liu, J.; Yin, C.; de Souza Vespoli, L.; Ge, D.; Huang, Y.; Feng, B.; Xu, G.; de A. Manhaes, A. M. E.; Dou, S.; Criswell, C.; Shan, L.; Wang, X.; He, P. RNA interference-based screen reveals concerted functions of MEKK2 and CRCK3 in plant cell death regulation. Plant Phys. 183, 331–344 (2020). 127. Yu, X.; Xu, G.; Li, B.; de Souza Vespoli, L.; Liu, H.; Moeder, W.; Chen, S.; de Oliveira, M. V. V.; de Souza, S. A.; Shao, W.; Rodrigues, B.; Ma, Y.; Chhajed, S.; Xue, S.; Berkowitz, G. A.; Yoshioka, K.; He, P.; Shan, L. The receptor kinases BAK1/SERK4 regulate Ca2+ channel-mediated cellular homeostasis for cell death containment. Curr. Biol. 29, 3778–3790 (2019). 126. Li, B.; Ferreira, M. A.; Huang, M.; Camargos, L. F.; Yu, X.; Teixeira, R. M.; Carpinetti, P. A.; Mendes, G. C.; Gouveia-Mageste, B. C.; Liu, C.; Pontes, C. S. L.; Brustolini, O. J. B.; Martins, L. G. C.; Melo, B. P.; Duarte, C. E. M.; Shan, L.; He, P.; Fontes, E. P. B. The receptor-like kinase NIK1 targets FLS2/BAK1 immune complex and inversely modulates antiviral and antibacterial immunity. Nat. Commun. 10, 4996 (2019). 125. Hou, S.; Yin, C.; He, P. Maturation and release: Peps prepare to work. Trends in Plant Sci. 24, 787–790 (2019). 124. Yu, X.; Li, B.; Jang, G. J.; Jiang, S.; Jang, J. C.; Wu, S. H.; Shan, L.; He, P. Orchestration of processing body dynamics and mRNA decay in Arabidopsis immunity. Cell Rep. 28, 2194–2205 (2019). 123. Cox, K. L.; Babilonia, K.; He, P.; Shan, L. Return of old foes – recurrence of bacterial blight and fusarium wilt of cotton. Curr. Opin. Plant Biol. 50, 95–103 (2019). 122. Liu, Z.; Jian, Y.; Chen, Y.; Kistler, H.; He, P.; Ma, Z.; Yin, Y. A phosphorylated transcription factor regulates sterol biosynthesis in Fusarium graminearum. Nat Commun. 10, 1228 (2019). 121. Zhou, J.; Wang, P.; Claus, L. A. N.; Savatin, D. V.; Xu, G.; Wu, S.; Russinova, E.; He, P.; Shan, L. Proteolytic processing of SERK3/BAK1 regulates plant immunity, development and cell death. Plant Physiol. 180, 543–558 (2018). 120. Huang, Y. Y.; Zhang, L. L.; Ma, X. F.; Zhao, Z. X.; Zhao, J. Q.; Fan, J.; Li, Y.; He, P.; Xiao, S.; Wang, W. Multiple intramolecular trafficking signals in RESISTANCE TO POWDERY MILDEW 8.2 are engaged in activation of cell death and defense. Plant J. 98, 55–70 (2019). 119. Xiong, C.; Luo, D.; Lin, A.; Zhang, C.; He, P.; Li, B.; Zhang, Q.; Hua, B.; Yuan, Z.; Li, H.; Zhang, J.; Yang, C.; Lu, Y.; Ye, Z.; Wang, T. A tomato B-box protein SIBBX20 modulates carotenoid biosynthesis by directly activating PHYTOENE SYNTHASE 1, and is targeted for 26S proteasome-mediated degradation. New Phytol. 221, 279–294 (2019). 118. Hou, S.; Jamieson, P.; He, P. The cloak, dagger, and shield: proteases in plant-pathogen interactions. Biochem. J. 475, 2491–2509 (2018). 117. Jamieson, P. A.; Shan, L.; He, P. Plant cell surface molecular cypher: receptor-like proteins and their roles in immunity and development. Plant Sci. 274, 242–251 (2018). 116. Shan, L.; He, P. Pipped at the post: pipecolic acid derivative identified as SAR regulator. Cell 173, 286–287 (2018). 115. Zhou, J.; Liu, D.; Wang, P.; Lin, W.; Chen, S.; Mishev, K.; Lu, D.; Kumar, R.; Vanhoutte, I.; He, P.; Russinova, E.; Shan, L. Regulation of Arabidopsis brassinosteroid receptor BRI1 endocytosis and intracellular degradation by the E3 ubiquitin ligase PUB12/PUB13-mediated ubiquitination. Proc. Natl. Acad. Sci. USA 115, e1906–e1915 (2018). 114. Lal, N. K.; Nagalakshmi, U.; Hurlburt, N. K.; Flores, R.; Bak, A.; Sone, P.; Ma, X.; Song, G.; Walley, J.; Shan, L.; He, P.; Casteel, C.; Fisher, A. J.; Dinesh-Kumar, S. P. The receptor-like cytoplasmic kinase BIK1 localizes to the nucleus and regulates defense hormone expression during plant innate immunity. Cell Host and Microbe 23, 485–497 (2018). 113. Mang, H.; Feng, B.; Hu, Z.; Boisson-Dernier, A.; Franck, C. M.; Meng, X.; Xu, G.; Wang, T.; Shan, L.; He, P. Differential regulation of two-tiered plant immunity and sexual reproduction by ANXUR receptor-like kinases. The Plant Cell 29, 3140–3156 (2017). 112. Li, F.; Li, M.; Wang, P.; Cox, K. L.; Duan, L.; Dever, J. K.; Shan, L.; Li, Z.; He, P. Regulation of cotton drought responses by a MAP kinase cascade-mediated phosphorylation of GhWRKY59. New Phytol. 215, 1462–1475 (2017). 111. Cox, K. L.; Meng, F.; Wilkins, K. E.; Li, F.; Wang, P.; Booher, N. J.; Chen, L. Q.; Zheng, H.; Gao, X.; Zheng, Y.; Fei, Z.; Yu, J. Z.; Isakeit, T.; Wheeler, T.; Frommer, W. B.; He, P.; Bogdanove, A. J.; Shan, L. TAL effector-mediated induction of a SWEET sucrose transporter confers susceptibility to bacterial blight of cotton. Nat. Commun. (2017). 110. Yu, X.; Feng, B.; He, P.; Shan, L. From chaos to harmony: responses and signaling upon microbial pattern recognition. Ann. Rev. Phytopath. 55, 109–137 (2017). 109. Michelmore, R. W.; Coaker, G.; Bart, R.; Beattie, G. A.; Bent, A.; Bruces, T.; Cameron, D.; Dangl, J.; Dinesh-Kumar, S.; Edwards, R.; Eves-van den Akker, S.; Gassmann, W.; Greenberg, J.; Harrison, R.; He, P.; et al. Foundational and translational research opportunities to improve plant health. Mol. Plant. Microbe Interact. (2017). 108. Yadeta, K. A.; Elmore, J. A.; Creer, A. Y.; Feng, F.; Franco, J. Y.; Rufian, J. S.; He, P.; Phinney, B.; Coaker, G. Functional analyses of extracellular cysteine residues and phosphorylation for immune responses mediated by the Arabidopsis cysteine-rich receptor-like kinase CRK28. Plant. Physiol. 173, 771–787 (2017). 107. Feng, B.; Ma, S.; Chen, S.; Zhu, N.; Zhang, S.; Yu, B.; Yu, Y.; Le, B.; Chen, X.; Dinesh-Kumar, S. P.; Shan, L.; He, P. PARylation of the forkhead-associated domain protein DAWDLE regulates plant immunity. EMBO Rep. 17, 1799–1813 (2016). 106. Ma, X.; Xu, G.; He, P.; Shan, L. SERKing coreceptors for receptors. Trends Plant Sci. 21, 1017–1033 (2016). 105. Feng, B.; Ma, S.; Chen, S.; Zhu, N.; Zhang, S.; Yu, B.; Yu, Y.; Le, B.; Chen, X.; Dinesh-Kumar, S. P.; Shan, L.; He, P. PARylation of the forkhead-associated domain protein DAWDLE regulates plant immunity. EMBO Rep. 17, 1799–1813 (2016). 104. Liu, Y.; Huang, X.; Li, M.; He, P.; Zhang, Y. Loss-of-function of Arabidopsis receptor-like kinase BIR1 activates cell death and defense responses mediated by BAK1 and SOBIR1. New Phytol. 212, 637–645 (2016). 103. Li, B.; Meng, X.; Shan, L.; He, P. Transcriptional regulation of plant pattern-triggered immunity. Cell Host and Microbe 19, 641–650 (2016). 102. de Oliveira, M. V. V.; Xu, G.; Li, B.; de Souza Vespoli, L.; Meng, X.; Chen, X.; Yu, X.; de Souza, S. A.; Intorne, A. C.; de A. Manhaes, A. M. E.; Musinsky, A. L.; Koiwa, H.; de Souza Filho, G. A.; Shan, L.; He, P. Specific control of Arabidopsis BAK1/SERK4-regulated cell death by protein glycosylation. Nat. Plants 2, 15218 (2016). 101. Zou, Y.; Chintamanani, S.; He, P.; Fukushige, H.; Yu, L.; Shao, M.; Zhu, L.; Hildebrand, D. F.; Tang, X.; Zhou, J. M. A gain-of-function mutation in Msl10 triggers cell death and wound-induced hyperaccumulation of JA in Arabidopsis. J. Integ. Plant Biol. 58, 600–609 (2016). 100. Meng, X.; Zhou, J.; Tang, J.; Li, B.; Oliveira, M. V. V.; Chai, J.; He, P.; Shan, L. Ligand-induced receptor-like kinase complex regulates floral organ abscission in Arabidopsis. Cell Rep. 14, 1330–1338 (2016). 99. Meng, X.; Chen, X.; Liu, C.; Yu, X.; Gao, X.; Torii, U. K.; He, P.; Shan, L. Differential function of Arabidopsis SERK family receptor-like kinases in stomatal patterning. Curr. Biol. 25, 2361–2372 (2015). 98. Meng, X.; Shan, L.; He, P. Stack heterotrimeric G proteins and MAPK cascades on a RACK. Mol. Plant 8, 1691–1693 (2015). 97. Zhou, J.; Lu, D.; Xu, G.; Finlayson, S. A.; He, P.; Shan, L. The dominant negative ARM domain uncovers multiple functions of plant U-box E3 ligase PUB13 in Arabidopsis immunity, flowering, and senescence. J. Exp. Botany 66, 3353–3366 (2015). 96. Li, B.; Jiang, S.; Yu, X.; Cheng, C.; Chen, S.; Cheng, Y.; Yuan, J.; Jiang, D.; He, P.; Shan, L. Phosphorylation of trihelix transcription repressor ASR3 by MPK4 negatively regulates Arabidopsis immunity. The Plant Cell 27, 839–856 (2015). 95. Feng, B.; Liu, C.; Oliveira, M. V. V.; Intorne, A. C.; Li, B.; Babilonia, K.; Filho, G. A. S.; Shan, L.; He, P. Protein poly(ADP-ribosyl)ation regulates Arabidopsis immune gene expression and defense response. PLoS Genetics 11, e1004936 (2015).

CURRENT SUPPORT USDA-NIFA He, P. (PI) 2020–2023 “Protein phosphorylation and poly(ADP-ribosyl)ation in cotton drought stress” NSF/IOS He, P. (co-PI) 2020–2023 “Molecular dissection of protein poly(ADP-ribosyl)ation in plant immunity and pathogen-induced DNA damage” NSF/MCB He, P. (co-PI) 2019–2022 “Processing-body dynamics and mRNA regulation in plants” USDA-NIFA He, P. (co-PI) 2019–2022 “Enhancing resistance in upland cotton by dissecting the disease mechanism of Fusarium oxysporum f. sp. vasinfectum race 4” The Pew Latin American Fellows Ortiz-Morea, F. A. (postdoc); He, P. 2010–2022 Program “Differential regulation of plant immunity via plasma membrane compartmentalization by malectin-like receptor-like kinases” NIH/NIGMS He, P. (PI) 2009–2022 “Differential regulation of plant innate immunity” AgriLife Strategic Research Initiative He, P. (co-PI) 2019–2021 “Fov4 in Texas cotton” TAMU Research Development Fund He, P. (co-PI) 2019–2021 “PRECISE: A PREcision genomics Core to advance Innovation Systems bioEngineering” TAMU President’s Excellence Fund He, P. (co-PI) 2018–2020 “X-Grants Program: CRISPR gene editing for healthier foods and improved crop resilience” COMPLETED SUPPORT (2015–present) AgriLife Crop Genome Editing Seed He, P. (PI) 2018–2019 Grant Program “Improving wheat resistance to powdery mildew by simulataneous editing of three homoalleles of a key immune regulator gene” AgriLife Research Crop Improvement He, P. (co-PI) 2017–2019 Program “Improve cotton disease resistance via immune gene eSNP and gene editing” NSF/IOS He, P. (PI) 2013–2019 “CAREER: Orchestrating transcriptional reprogramming by combinatorial complexity of general transcriptional regulation and specific immune responses” AgriLife Research Cotton He, P. (co-PI) 2011–2017 Improvement Program “Mining genes for Texas cotton: identify and deploy genes that confer resistance to pathogen stress” USDA-NIFA He, P. (co-PI) 2012–2016 “Cotton functional genomics in biotic and abiotic stress responses” Texas A&M Genomics Seed Grant He, P. 2014–2015 “Dissecting NLR immune signaling by next-generation sequencing-enabled fast-forward genetics”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Editorial Board Stress Biology 2021–present Editorial Board Plant Communications 2019–present Senior Editor Molecular Plant-Microbe Interactions 2016–present Chancellor Enhancing Texas A&M University 2020 Development and Generating Excellence in Scholarship (EDGES) Fellow Presidential Impact Fellow Texas A&M University 2019 Vice Chancellor’s Award for College of Agriculture and Life Sciences, Texas A&M University 2018 Excellence in Research Review Editor Frontier in Plant Physiology, Frontier in Plant-Microbe Interactions 2013–2018 Editorial Board Molecular Plant Pathology 2012–2017 Tenure and Promotion Package Various Various Reviewer Reviewer – Grant Proposals NSF, USDA, European Research Council (ERC), UK Biotechnology Various and Biological Sciences Research Council (BBSRC), The Netherlands Organisation for Scientific Research (NWO, the Dutch research council); United States-Israel Binational Agricultural Research and Development Fund (BARD), Hong Kong Research Grants Council, French National Research Agency (ANR), International Foundation for Science Sweden, National Science Foundation China (NSFC), Research Foundation-Flanders (FWO), Belgium, Swiss National Science Foundation Peer Reviewer Cell, Cell Host & Microbe, Cell Report, Current Biology, Nature, Various Nature Plants, Nature Communications, EMBO Journal, PNAS, PloS Genetics, PloS Pathogens, PloS One, Trends in Plant Science, Plant Cell, Plant Journal, Plant Physiology, Molecular Plant, Journal of Experimental Botany, Theoretical and Applied Genetics, Plant Signaling and Behavior, Molecular Plant-Microbe Interactions, Molecular Plant Pathology, Molecules and Cells, BMC Plant Biology, Biochemistry Journal, Frontier in Molecular Innate Immunity, Journal of Integrative Plant Biology, Cellular & Molecular Biology Letters, Brazilian Journal of Medical and Biological Research

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Awards Committee COALS 2019–present Member Promotion and Tenure Committee BCBP 2018–present Member Awards Committee BCBP 2013–present Member Academic Program Review Self-Study Team BCBP 2019–2020 Member Graduate Recruitment and Admissions Committee BCBP 2010–2018 Member Search Committee – Vice Chancellor and Dean COALS 2017 Member Graduate Recruitment Committee MEPS 2015–2018

COURSES TAUGHT (2015–present) BICH 631 Molecular Genetics (co-taught) 3 cr. 2020–present Biochemical Genetics 3 cr. 2010–2017 BICH 431 Molecular Genetics 3 cr. 2018–present BICH 608 Critical Analysis of the Biochemical Literature (co-taught) 2 cr. 2012–2019 Jennifer K. Herman Associate Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Harvard Medical School with D. Rucher 2007–2011 Postdoctoral Harvard Medical School with M. Goldberg 2005–2007 Ph.D. Microbiology, Indiana University 2000–2005 B.S. Biochemistry and Biology, University of North Texas 2000

PROFESSIONAL APPOINTMENTS Associate Professor Biochemistry and Biophysics Texas A&M University 2017–present Assistant Professor Biochemistry and Biophysics Texas A&M University 2011–2017

PEER-REVIEWED PUBLICATIONS (2015–present) 16. Brown, E. E.; Miller, A. K.; Krieger, I. V.; Otto, R. M.; Sacchettini, J. C.; Herman, J. K. A DNA-binding protein tunes septum placement during Bacillus subtilis sporulation. J. Bacteriol. 201, e00287-19 (2019). 15. Sperber, A. M.; Herman, J. K. Metabolism shapes the cell. J. Bacteriol. 199, e00039–17 (2017). 14. Duan, Y.; Huey, J. D.; Herman, J. K. The DnaA inhibitor SirA acts in the same pathway as Soj (ParA) to facilitate oriC segregation during Bacillus subtilis sporulation. Mol Microbiol. 102, 530–544 (2016). 13. Duan, Y.; Sperber, A. M.; Herman, J. K. YodL and YisK possess shape-modifying activities that are suppressed by mutations in Bacillus subtilis mreB and mbl. J. Bacteriol. 198, 2074–2088 (2016). 12. Miller, A. K.; Brown, E. E.; Mercado, B. T.; Herman, J. K. A DNA-binding protein defines the precise region of chromosome capture during Bacillus sporulation. Mol Microbiol. 99, 111–122 (2016). 11. Ababneh, Q. A.; Herman, J. K. A secreted factor coordinates environmental quality with Bacillus development. PLoS One. 10, e0144168 (2015). 10. Ababneh, Q. A.; Herman, J. K. CodY regulates SigD levels and activity by binding to three sites in the fla/che operon. J. Bacteriol. 197, 2999–3006 (2015). 9. Ababneh, Q. A.; Herman, J. K. RelA Inhibits Bacillus subtilis motility and chaining. J. Bacteriol. 197, 128–137 (2015).

CURRENT SUPPORT DARPA/Signature Science (subcontract) Herman, J. (PI); Gill, J. (co-PI); Young, R. (co-PI) 2019–2021 “Spore-Phage Amplified Detection (SPADe) for Subterranean Chemical Threats” COMPLETED SUPPORT (2015–present) NSF Investigator- Initiated Herman, J. (PI) 2015–2019 (MCB-1514629) “Positional Regulation of Cell Division” Bill and Melinda Gates Foundation Herman, J. (PI) 2016–2017 (06-505129) “Phagocins: Precision Tools for the Remodeling the Microbiota”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Editorial Board Journal of Bacteriology 2021–present Ad hoc peer reviewer Various scientific journals 2014–present Vice Chancellor’s Award, Excellence Texas A&M University 2020 in Teaching Session Chair, Poster Judge The International Conference on Bacilli and Gram-Positive Bacteria 2019 Session Chair, Women in Science Molecular Genetics of Bacteria and Phages Meeting 2018, 2019 Roundtable, Tenure-Track Faculty Roundtable Ad hoc reviewer NSF, Molecular and Cellular Biosciences; NIH, NIGMS-PCMB; Various Science Foundation of Ireland (Spookes Programme) Member Texas Branch ASM 2014–present

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Executive Committee BCBP 2019–present Faculty Mentor Biochemistry Graduate Association BCBP 2019–present Member Department Head Search Committee BCBP 2013–2018 Chair Website Committee BCBP 2013–2018 Member Graduate Program Committee BCBP 2012–2018

COURSES TAUGHT (2015–present) BICH 689 Application of Scientific Values in Daily Research Practice 1 cr. 2017–present BICH 431 Molecular Genetics 3 cr. 2012–present BICH 491/691 Research Variable 2012–present BICH 689 Methods of Biochemical Analysis 1 cr. 2013–2016 BICH 681 Seminar 1 cr. 2018 Magnus Höök Regents and Distinguished Professor, Neva & Wesley Chair | Institute of Biosciences and Technology Professor | Departments of Biochemistry and Biophysics, Medical Microbiology and Immunology Director | Center for Infectious and Inflammatory Diseases

EDUCATION Ph.D. University of Uppsala, Sweden 1974 B.S. University of Uppsala, Sweden 1971

PROFESSIONAL APPOINTMENTS Distinguished Professor Texas A&M University 2011–present Regents Professor Texas A&M University 2008–present Adjunct Professor Department of Infectious Diseases, UT-MD Anderson Cancer 2008–present Infection Control and Employee Health Center Professor Medical Microbiology and Immunology Texas A&M HSC 2003–present Adjunct Professor Microbiology and Molecular Genetics University of Texas Medical 1997–present School Graduate Faculty School of Biomedical Sciences University of Texas HSC 1995–present Neva and Wesley West Chair Institute of Biosciences and Technology Texas A&M University 1995–present Professor Biochemistry and Biophysics Texas A&M University 1992–present Director Center for Infectious and Inflammatory Texas A&M University 1992–present Diseases Professor Biochemistry University of Alabama at 1980–1992 Birmingham Associate Professor Swedish University of 1979–1980 Agricultural Science Assistant Professor Swedish University of 1974–1979 Agricultural Scince

PEER-REVIEWED PUBLICATIONS (2015–present) 279. Becerra-Bayonne, S. M.; Giza-Arguello, V. R.; Russell, B.; Höök, M.; Hahn, M.S. Influence of collagen-based integrin α1 and α2 mediated signaling on human mesenchymal stem cell osteogenesis in three dimensional contexts. J. Biomed. Mater. Res. A 106, 2594–2604 (2018). 278. Munoz-Pinto, D. J.; Ernst-Marino, J. D.; Becerra-Bayonne, S. M.; Giza-Arguello, V. R.; Samaveda, S.; Mammut, S.; Reichert, W. M.; Russell, B.; Höök, M.; Hahn, M. S. Evaluation of late outgrowth endothelial progenitor cell and umbilical vein endothelial cell responses to thromboresistant collagen-mimetic hydrogels. J. Biomed. Mater. Res. A 105, 1712–1724 (2017). 277. Casillas-Ituarte, N. N.; Cruz, C. H. B.; Lines, R. D.; DeBartolo, A. C.; Howard, J.; Liang, X.; Höök, M.; Viana, I. F. T.; Sierra-Hernández, M. R.; Lower, S. K. Amino acid polymorphisms in the fibronectin-binding repeats of fibronectin- binding protein A affect bond strength and fibronectin conformation. J. Biol. Chem. 292, 8797–8810 (2017). 276. Ganesh, V. K.; Liang, X.; Geoghegan, J. A.; Cohen, A. L. V.; Venugopalan, N.; Foster, T. J.; Höök, M. Lessons from the crystal structure of the S. aureus surface protein clumping factor A in complex with Tefibazumab, an inhibiting monoclonal antibody. Biomedicine 13, 328–338 (2016). 275. Liang, X.; Garcia, B. L.; Visa, L.; Prabhakaran, S.; Meena, N. A.; Potts, J. R.; Humphries, M. J.; Höök, M. Allosteric regulation of fibronectin/α5β1 interaction by fibronectin-binding MSCRAMMs. PLoS One 11, e0159118 (2016). 274. Arora, S.; Muehlemann, A. C.; Lowy, F. D.; Höök, M. A novel MSCRAMM subfamily in coagulase negative Staphylococcal species. Front. Microbiol. 7, 540 (2016). 273. Garcia, B. L.; Zhi, H.; Wager, B.; Höök, M.; Scare, J. T. Borrelia burgdorferi BBK32 inhibits the classical pathway by blocking activation of the C1 complement complex. PLoS Pathos. 12, e1005404 (2016). 272. Ko, Y. P.; Kang, M.; Ganesh, V. K.; Ravirajan, D.; Li, B.; Höök, M. Coagulase and ebb of Staphylococcus aureus have a common fibrinogen binding motif. mBio. 7, e01885-15 (2016). 271. Samarian, S. R.; La Rosa, S. L.; Singh, K. V.; Rohm, J. H.; Höök, M.; Murray, B. E. The fibronectin-binding protein FM contributes to adherence to extracellular matrix components and virulence of Enterococcus faecium. Infect. Immun. 83, 4653–4661 (2015). 270. Prasad, J. M.; Gokkun, O. V.; Raghu, H.; Thornton, S.; Mullins, E. S.; Palumbo, J. S.; Ko, Y. P.; Höök, M.; David, T.; Coughlin, S. R.; Degen, J. L.; Flick, M. J. Mice expressing a mutant form of fibrinogen that cannot support fibrin formation exhibit compromised antimicrobial host defense. Blood 126, 2047–2058 (2015). 269. Creekers, S.; Touched, T.; Browning, M. B.; Smith, C.; Rivera, J.; Höök, M.; Whitfield-Cargile, C.; Russell, B.; Cosgrave-Hernandez, E. Chronic wound dressings based on collagen-mimetic proteins. Adv. Wound Care (New Rochelle) 4, 444–456 (2015). 268. Zhi, H.; Weening, E. H.; Barbu, E. M.; Hyde, J. A.; Höök, M.; Skare, J. T. The BBA33 lipoprotein binds collagen and impacts Borrelia burgdorferi pathogenesis. Mol. Microbiol. 96, 68–83 (2015). 267. Galloway-Peña, J. R.; Liang, X.; Singh, K. V.; Yadav, P.; Chang, C.; La Rosa, S. L.; Shelburne, S.; Ton-That, H.; Höök, M.; Murray, B. E. The identification and functional characterization of WxL proteins from Enterococcus faecium reveal surface proteins involved in extracellular matrix interactions. J. Bacteriol. 197, 882–892 (2015).

CURRENT SUPPORT NIH R01-HL119648-01 Lower (PI); Höök, M (co-PI) 2019–2022 “Molecular binding reactions that initiate S. aureus infectiosn of cardiovascular implants in humans” NIH R01-AI020624-34 Höök, M. (PI) 2016–2021 “Analysis of Staphylococcus aureus host interactions”

COMPLETED SUPPORT (2015–present) NIH R21AI119821-01 Skare, J. (PI); Höök, M (co-PI) 2015–2017 “Collagen binding as a virulence mechanism in Lyme borreliosis” NIH R01 EB013297 Russell/Cosgriff-Hernandez (MPI); Höök, M (co-PI) 2012–2017 “Multilayer vascular grafts based on collagen-mimetic hydrogels”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Peer reviewer NIH and other funding organizations 1982–present Chair, Organizing Committee Immunotherapy in Infectious Diseases international symposium 2018

Tatyana I. Igumenova Associate Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Columbia University NIH Fellow, with A. G. Palmer 2005–2007 Postdoctoral University of Pennsylvania NIH Fellow, with A. J. Wand 2003–2005 Ph.D. Columbia University with A. E. McDermott 2003 M.Phil. Columbia University 2002 M.Sc. Washington State University with J. Evans 1998

PROFESSIONAL APPOINTMENTS Associate Professor Biochemistry and Biophysics Texas A&M University 2014–present Assistant Professor Biochemistry and Biophysics Texas A&M University 2008–2014

PEER-REVIEWED PUBLICATIONS (2015–present) 36. Taylor, J. T.; Mukherjee, P. K.; Puckhaber, L. S.; Dixit, K.; Igumenova, T. I.; Suh, C.; Horwitz, B. A.; Kenerley, C. M. Deletion of the Trichoderma virens NRPS, Tex7, induces accumulation of the anticancer compound heptelidic acid. Biochem. Biophys. Res. Co. (2020, accepted). 2+ 35. Katti, S.; Igumenova, T. I. Interference of pH buffer with Pb -peripheral domain interactions: obstacle or opportunity? Metallomics 12, 164–172 (2020). Journal cover. 34. Katti, S.; Nyenhuis, S. B.; Her, B.; Cafiso, D. S.; Igumenova, T. I. Partial metal ion saturation of C2 domains primes Synaptotagmin 1-membrane interactions. Biophys. J. 118, 1409–1423 (2020). 33. Cole, T. R.; Erickson, S. G.; Morales, K. A.; Sung, M.; Holzenburg, A.; Igumenova, T. I. Cd(II)- and Pb(II)-induced self-assembly of peripheral membrane domains from Protein Kinase C. Biochemistry 58, 509–513 (2019). Journal cover. 32. Katti, S.; Her, B.; Srivastava, A. K.; Taylor, A. B.; Lockless, S. W.; Igumenova, T. I. High affinity interactions of Pb2+ with Synaptotagmin I. Metallomics 10, 1211–1222 (2018). Journal cover. 31. Yang, Y.; Shu, C.; Li, P.; Igumenova, T. I. Structural basis of protein kinase Cα regulation by the C-terminal tail. Biophys. J. 114, 1590–1603 (2018). 30. Stewart, M. D.; Igumenova, T. I. Toggling of diacylglycerol affinity correlates with conformational plasticity in C1 domains. Biochemistry 56, 2637–2640 (2017). 29. Katti, S.; Nyenhuis, S. B.; Her, B.; Srivastava, A. K.; Taylor, A. B.; Hart, P. J.; Cafiso, D. S.; Igumenova, T. I. Non-native metal ion reveals the role of electrostatics in Synaptotagmin 1-membrane interactions. Biochemistry 56, 3283–3295 (2017). 28. Morales, K. A.; Yang, Y.; Cole, T. R.; Igumenova, T. I. Dynamic response of the C2 domain of protein kinase Cα to 2+ Ca binding. Biophys. J. 111, 1655–1667 (2016). 27. Igumenova, T. I. Dynamics and membrane interactions of Protein Kinase C. Biochemistry 54, 4953–4968 (2015). 26. Cole, T. R.; Igumenova, T. I. Expression and murification of the N-terminal regulatory domain of Protein Kinase C for biophysical studies. Prot. Expr. Purif. 110, 14–21 (2015). 25. Yang, Y.; Morales, K. A.; Steward, M. D.; Igumenova, T. I. Conditional membrane proteins: solution NMR studies of structure, dynamics, and function. eMagRes: Encyclopedia of Magnetic Resonance 4, 767–778 (2015). 24. Ghosh, R.; de Campos, M. K.; Huang, J.; Huh, S. K.; Orlowski, A.; Yang, Y.; Tripathi, A.; Nile, A.; Lee, H. C.; Dynowski, M.; Schafer, H.; Rog, T.; Lete, M. G.; Ahyayauch, H.; Alonso, A.; Vattulainen, I.; Igumenova, T. I.; Shaaf, G.; Bankaitis, V. A. Sec14-Nodulin proteins and the patterning of phosphoinositide landmarks for developmental control of membrane morphogenesis. Mol. Biol. Cell. 26, 1764–1781 (2015).

CURRENT SUPPORT NSF CHE-1905116 Igumenova, T. I. 2019–2022 “Mechanisms of signal transduction revealed through unique chemistry of xenobiotic metal ions” TAMU T3 Wang, Y. (PI); Igumenova, T. I. (co-PI); Ficht, A. R. 2020–2022 “Brain-On-A-Chip: Spio-Au-Mofs Decorated 3D Scaffolds for Brain Tissue Regeneration” Welch Foundation A-1784 Igumenova, T. I. 2018–2021 “Sequestration without isomerization: A novel mode of AGC kinase regulation by Pin1” TAMU T3 Igumenova, T. I. (PI); Raushel, F. (co-PI); Sacchettini, J. C. (co-PI) 2018–2020 “Fluorine-19 NMR as a probe of molecular structure and dynamics” COMPLETED SUPPORT (2015–present) NIH #R01-GM108998 Igumenova, T. I. 2014–2019 “Structural and functional studies of Protein Kinase C regulation” Welch Foundation A-1784 Igumenova, T. I. 2015–2018 “Pin1 “bites” the tail: Regulatory role of the C-terminal domain of Protein Kinase C” NSF Career CHE-1151435 Igumenova, T. I. 2012–2018 2+ “Pb as modulator of protein–membrane interactions” Welch Foundation A-1784 Igumenova, T. I. 2012–2015 “A novel interaction with Protein Kinase C enzyme”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Editorial Board member Journal of Biological Chemistry 2019–present Member NSF Site Visiting Committee, National High Magnetic Field Laboratory 2020 Ad hoc Member Tenure Case Review Committee, Texas Tech University and UT Dallas 2019, 2020 Ad hoc Reviewer NSF Molecular and Cellular Biosciences – Molecular Biophysics 2020 Session Chair Biophysical Society Meeting 2018 Ad hoc Panel Member NIH Center for Scientific Review, Special Emphasis Study Section 2016, 2017 Participant Ultra High-Field NMR/MRI Workshop/Task Force 2015 Ad hoc Reviewer NSF CAREER Program, Chemistry of Life Processes 2015 Ad hoc Peer Reviewer Various scientific journals Various

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member High-Performance Research Computing Oversight TAMU 2020–present Committee Chair Graduate Admissions Committee BCBP 2019–present Member Department Head Search Committee BCBP 2017–2019 Member Executive Committee BCBP 2017–2018 Member Graduate Program Committee BCBP 2015–2018 Faculty Director Biomolecular NMR Facility TAMU 2008–2013 2014–2018

COURSES TAUGHT (2015–present) BICH 608 Critical Analysis of the Biochemical Literature 2 cr. 2009–present BICH 689 Nuclear Magnetic Resonance Spectroscopy of Biological Molecules 1 cr. 2014–present BICH 689 Biological Nuclear Magnetic Resonance Spectroscopy 1 cr. 2015–present BICH 689 Advanced Protein–Ligand Interactions 1 cr. 2015–present BICH 624 Proteins, Enzymes, and Nucleic Acids 3 cr. 2009–present

Geoffrey Kapler Jean and Tom McMullin Professor, Genetics Head | Department of Molecular and Cellular Medicine Professor | Biochemistry and Biophysics

EDUCATION Postdoctoral University of California, San Francisco with E. Blackburn 1994 Ph.D. Harvard University with S. Berverley 1989 B.S. University of Connecticut 1979

PROFESSIONAL APPOINTMENTS Jean and Tom McMullin Genetics Texas A&M Health Science Center 2012–present Professor Head Molecular and Cellular Medicine Texas A&M University 2012–present Interim Head Molecular and Cellular Medicine Texas A&M University 2010–2011 Professor Molecular and Cellular Medicine Texas A&M University 2006–present Biochemistry and Biophysics Texas A&M University Associate Professor Biochemistry and Biophysics Texas A&M University 2002–2006 Medical Biochemistry and Genetics Texas A&M Health Science Center Chair Genetics IDP Texas A&M University 2002–2005 Assistant Professor Biochemistry and Biophysics Texas A&M University 1997-2002 Medical Biochemistry and Genetics Texas A&M Health Science Center 1994-2002

PEER-REVIEWED PUBLICATIONS (2015–present) 32. Zhao, Q.; Zhang, L.; Hai, B.; Wang, J.; Baetge, C. L.; Deveau, M. A.; Kapler, G. M.; Feng, J.Q.; Liu, F. Transient activation of the Hedgehog-Gli pathway rescues radiotherapy-induced dry mouth via recovering salivary gland resident macrophages. Cancer Res. 80, 5531–5542 (2020). 31. Feng, L.; Wang, G.; Xiong, J.; Yan, G.; Chen, K.; Chen, X.; Dui, W.; Plemens, A.; Khadr, L.; Dhanekula, A.; Mina, J.; Dang, H. Q.; Kapler, G. M.; Orias, E.; Miao, W.; Liu, Y. A germline-limited piggyBac transposase gene is required for precise excision in Tetrahymena genome rearrangement. Nucleic Acids Res 45 9481–9502 (2017). 30. Sandoval, P.Y.; Lee, P. H.; Meng, X.; Kapler, G. M. Checkpoint Activation of an Unconventional DNA Replication Program in Tetrahymena. PLoS Genet. 11, e1005405 (2015). 29. Lee, P. H.; Meng, X.; Kapler, G. M. Developmental regulation of the Tetrahymena thermophila origin recognition c8mplex. PLoS Genet. 11, e1004875 (2015).

COMPLETED SUPPORT (2015–present) NSF Kapler, G. M. 2016–2020 “Functional and bioinformatic analysis of unconventional DNA replication programs in Tetrahymena.” NSF Liu, Y; Kapler, G. M. 2014–2017 “Dissecting the role of histone lysine 27 mono-methylation in DNA replication.”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) President-elect Association of Medical and Graduate Departments of Biochemistry 2020–present Charter Member ASBME Women in Biochemistry and Molecular Biology Committee 2019–present Board of Reviewers PLOS ONE 2018–present Founding Member, Executive Tetrahymena Research Advisory Board (TetRA Board) 2011–present Committee Member, Chair Member Association of Medical and Graduate Departments of Biochemistry 2010–present (AMGDB) Board of Reviewers Current Genetics 2001–present Ad hoc Reviewer NSF Eukaryotic Genetics Study Section 1999–present Executive Committee Member American Medical and Graduate Departments in Biochemistry 2016–2021 (AMGDB) Virtual Meeting Co-Organizer NSF-supported Ciliate Molecular Biology Conference 2020 Conferences Committee Member Genetics Society of America 2017–2020 Ad hoc Member NSF Study Section, Molecular and Cellular Biosciences 2019 Coordinating Committee Member Genetics Society of America, 2016 Genetics Conference, TAGC (GSA 2013–2016 100th anniversary meeting), Orlando, FL Inna V. Krieger Research Assistant Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Los Alamos National Laboratory 2002–2005 Ph.D. Moscow State University, GosNIIgenetika Y. Maeda, G. G. Chestukhina 2001 M.S. Moscow State University, GosNIIgenetika I. A. Zalunin, V. M. Stepanov 1997 B.S. Moscow State University, GosNIIgenetika 1996

PROFESSIONAL APPOINTMENTS Research Assistant Professor Biochemistry and Biophysics Texas A&M University 2018–present Associate Research Scientist Biochemistry and Biophysics Texas A&M University 2006–present

PEER-REVIEWED PUBLICATIONS (2015–present) 24. Khan, D.; Lee, D.; Gulten, G.; Aggarwal, A.; Wofford, J.; Krieger, I.; Tripathi, A.; Patrick, J.W.; Eckert, D.M.; Laganowsky, A.; Sacchettini, J.; Lindahl, P.; Bankaitis, V.A. A Sec14-like phosphatidylinositol transfer protein paralog defines a novel class of heme-binding proteins. eLife 11, e57081 (2020). 23. Krieger, I. V.; Kuznetsov, V.; Chang, J. Y.; Zhang, J.; Moussa, S. H.; Young, R. F.; Sacchettini, J. C. The structural basis of T4 phase lysis control: DNA as the signal for lysis inhibition. J. Mol. Biol. 432, 4623–4636 (2020). 22. Crutcher, F. K.; Moran-Diez, M. E.; Krieger, I. V.; Kenerley, C. M. Effects on hyphal morphology and development by the putative copper radical oxidase glx1 in Trichoderma virens suggest a novel role as a cell wall associated enzyme. Fungal Genet. Biol. 131, 103245 (2019). 21. Brown, E. E.; Miller, A. K.; Krieger, I. V.; Otto, R. M.; Sacchettini, J. C.; Herman, J. K. A DNA-binding protein tunes septum placement during Bacillus subtilis sporulation. J. Bacteriol. 201, e00287-19 (2019). 20. Rittershaus, E. S. C.; Baek, S. H.; Krieger, I. V.; Nelson, S. J.; Cheng, Y. S.; Nambi, S.; Baker, R. E.; Leszyk, J. D.; Shaffer, S. A.; Sacchettini, J. C.; Sassetti, C. M. A lysine acetyltransferase contributes to the metabolic adaption to hypoxia in Mycobacterium tuberculosis. Cell Chem. Biol. 25, 1495–1505 (2018). 19. Ellenbarger, J. F.; Krieger, I. V.; Huang, H.-L.; Gómez-Coca, S.; Ioeger, T. R.; Sacchettini, J. C.; Wheeler, S. E.; Dunbar, K. R. Anion–π interactions in computer-aided drug design: Modeling the inhibition of malate synthase by phenyl-diketo acids. J. Chem. Inf. Model 58, 2085–2091 (2018). 18. Shen, Q.; Bhatt, V. S.; Krieger, I.; Sacchettini, J. C.; Cho, J.-H. Structure-guided design of a potent peptide inhibitor targeting the interaction between CRK and ABL kinase. Med. Chem. Commun. 9, 519–524 (2018). 17. Carey, A. F.; Rock, J. M.; Krieger, I. V.; Chase, M. R.; Fernandez-Suarez, M.; Gagneux, S.; Sacchettini, J. C.; Ioerger, T. R.; Fortune, S. M. TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities. PLoS Pathog. 14, e1006939 (2018). 16. Ly, T.; Krieger, I.; Tolkatchev, D.; Krone, C.; Moural, T.; Samatey, F. A.; Kang, C.; Kostyukova, A. S. Structural destabilization of tropomyosin induced by the cardiomyopathy-linked mutation R21H. Protein Sci. 27, 498–508 (2018). 15. Puckett, S.; Trujillo, C.; Wang, Z.; Eoh, H.; Ioerger, T. R.; Krieger, I.; Sacchettini, J.; Schnappinger, D.; Rhee, K. Y.; Ehrt, S. Glyoxylate detoxification is an essential function of malate synthase required for carbon assimilation in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 114, e2225–e2232 (2017). 14. Huang, H. L.; Krieger, I. V.; Parai, M. K.; Gawandi, V. B.; Sacchettini, J. C. Mycobacterium tuberculosis malate synthase structures with fragments reveal a portal for substrate/product exchange. J. Biol. Chem. 291, 27421–27432 (2016). 13. Bhatt, V. S.; Zeng, D.; Krieger, I.; Sacchettini, J. C.; Cho, J.-H. Binding mechanism of the N-terminal SH3 domain of CrkII and proline-rich motifs in cAbl. Biophys. J. 110, 2630–2641 (2016). Dmitry Kurouski Assistant Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Northwestern University with R. P. Van Duyne 2013–2015 Ph.D. SUNY at Albany 2008–2013 M.S. Belarusian State University 2007 B.S. Belarusian State University 1985

PROFESSIONAL APPOINTMENTS Adjunct Professor Biomedical Engineering Texas A&M University 2020–present Assistant Professor Biochemistry and Biophysics Texas A&M University 2017–present

PEER-REVIEWED PUBLICATIONS (2015–present) 72. Kurouski, D.; Dazzi, A.; Zenobi, R.; Centrone, A. Infrared and Raman chemical imaging and spectroscopy at the nanoscale. Chem. Soc. Rev. 49, 3315–3347 (2020). 71. Farber, C.; Sanchez, L.; Kurouski, D. Confirmatory non-invasive and non-destructive identification of poison ivy using a hand-held Raman spectrometer. RSC Advances 10, e21530 (2020). 70. Li, Z.; Kurouski, D. Elucidation of photo-catalytic properties of goldplatinum bimetallic nanoplates using tip-enhanced Raman. J. Phys. Chem. C 23, 12950–12854 (2020). 69. Sanchez, L.; Baltensperger, D.; Kurouski, D. Raman-based differentiation of hemp, cannabidiol-rich hemp and cannabis. Anal. Chem. 92, 7733–7737 (2020). 68. Morey, R.; Ermolenkov, A.; Payne, W. Z.; Scheuring, D. C.; Koym, J. W.; Vales, M. I.; Kurouski, D. Non-invasive identification of potato varieties and prediction of the origin of tuber cultivation using spatially offset Raman spectroscopy. Anal. Bioanal. Chem. 412, 4585–4594 (2020). 67. Zhou, L.; Kurouski, D. Structural characterization of individual α-synuclein oligomers formed at different stages of protein aggregation by atomic force microscope infrared spectroscopy. Anal. Chem. 92, 6806–6810 (2020). 66. Wang, C.-F.; O’Callahan, B.; Kurouski, D.; Krayev, A.; El-Khoury, P. The prevalence of anions at plasmonic nanojunctions: A closer look at p-nitrothiophenol. J. Phys. Chem. Lett. 11, 3809−3814 (2020). 65. Wang, R.; He, Z.; Sokolov, A.; Kurouski, D. Gap-mode tip-enhanced Raman scattering on Au nanoplates of varied thickness. J. Phys. Chem. Lett. 11, 3815−3820 (2020). 64. Farber, C.; Sanchez, L.; Rizevsky, S.; Ermolenkov, A.; McCutchen, B.; Cason, J.; Simpson, C.; Burow, M.; Kurouski, D. Raman spectroscopy enables non-invasive identification of peanut genotypes and value-added traits. Nat. Sci. Rep. 10, 7730 (2020). 63. Lee, K.-M.; Yarbrough, D.; Medhat Kozman, M.; Herrman, T. J.; Park, J.; Wang, R.; Kurouski, D. Rapid detection and prediction of chlortetracycline and oxytetracycline in animal feed using surface-enhanced Raman spectroscopy (SERS). Food Contr. 114, 1072439 (2020). 62. Sanchez, L.; Ermolenkov, A.; Tang, X.-T.; Tamborindeguy, C.; Kurouski, D. Non-invasive diagnostics of Liberibacter disease on tomatoes using a hand-held Raman spectrometer. Planta 251, 64 (2020). 61. Wang, R.; Li, J.; Rigor, J.; Large, N.; El-Khoury, P.; Rogachev, A. Y.; Kurouski, D. Direct experimental evidence of hot-carrier-driven chemical processes in Tip-Enhanced Raman Spectroscopy (TERS). J. Phys. Chem. C 124, 2238–2244 (2020). 60. Sanchez, L.; Filter, C.; Baltensperger, D.; Kurouski, D. Confirmatory non-invasive and non-destructive differentiation between hemp and cannabis using a hand-held Raman spectrometer. RSC Advances 10, 3212– 3216 (2020). 59. Rizevsky, S.; Kurouski, D. Nanoscale structural organization of insulin fibril polymorphs revealed by Atomic Force Microscope Infrared Spectroscopy (AFM-IR). ChemBioChem 21, 481–485 (2020). 58. Wang, R.; Kurouski, D. Thermal reshaping of gold microplates: Three possible routes and their transformation mechanisms. ACS Appl Mater. Interfaces 11, 41813–41820 (2019). 57. Krimmer, M.; Farber, C.; Kurouski, D. Rapid and non-invasive typing and assessment of nutrient content of maize kernels using a hand-held Raman spectrometer. ACS Omega 4, 16330–16335 (2019). 56. Sanchez, L.; Pant, S.; Irey, M.; Mandadi, K.; Kurouski, D. Detection and identification of canker and blight on orange trees using a hand-held Raman spectrometer. J. Raman Spectrosc. 50, 1875–1880 (2019). 55. Farber, C.; Shires, M.; Ong, K.; Byrne, D.; Kurouski, D. Raman spectroscopy as an early detection tool for rose rosette infection. Planta 250, 1247–1254 (2019). 54. Esparza, I.; Wang, R.; Kurouski, D. Surface-enhanced Raman analysis of underlaying colorants on re-dyed hair. Anal. Chem. 91, 7313–7318 (2019). 53. Sanchez, L.; Pant, S.; Xing, Z.; Mandadi, K.; Kurouski, D. Rapid and non-invasive diagnostics of huanglongbing and nutrient deficits on citrus trees with a hand-held Raman spectrometer. Anal. Bioanal. Chem. 411, 3125–3133 (2019). 52. Farber, C.; Li, J.; Hager, E.; Chemelewski, R.; Mullet, J.; Rogachev, A.; Kurouski, D. Complementarity of Raman and infrared spectroscopy for structural characterization of plant epicuticular waxes. ACS Omega, 4, 3700–3707 (2019). 51. Farber, C.; Wang, R.; Chemelewski, R.; Mullet, J.; Kurouski, D. Nanoscale structural organization of plant epicuticular wax probed by atomic force microscope infrared spectroscopy. Anal. Chem. 91, 2472–2479 (2019). 50. Sanchez, L.; Farber, C.; Lei, J.; Zhu-Salzman, K.; Kurouski, D. Non-invasive and non-destructive detection of cowpea bruchid within cowpea seeds with a hand-held Raman spectrometer. Anal. Chem. 91, 1733–1737 (2019). 49. Farber, C.; Mahnke, M.; Sanchez, L.; Kurouski, D. Advanced spectroscopic techniques for plant disease diagnostics. A Review. Trends Analyt. Chem. 118, 43–49 (2019). 48. Kurouski, D. Tip-enhanced Raman spectroscopy: An emergent technique for probing biology and electrochemistry at the nanoscale. Spectroscopy Magazine 33, 38–46 (2018). 47. Wang, R.; Kurouski, D. Elucidation of tip-broadening effect in Tip-Enhanced Raman Spectroscopy (TERS): A cause of artifacts or potential for 3D TERS. J. Phys. Chem. C 122, 24334–24340 (2018). 46. Egging, V.; Nguyen, J.; Kurouski, D. Detection and identification of fungal infections in intact wheat and sorghum grain using a hand-held Raman spectrometer. Anal. Chem. 90, 8616–8621 (2018). 45. Hager, E.; Farber, C.; Kurouski, D. Forensic identification of urine on cotton and polyester fabric with a hand-held Raman spectrometer. Forensic Chem 9, 44–49 (2018). 44. Farber, C.; Kurouski, D. Detection and identification of plant pathogens on maize kernels with a hand-held Raman spectrometer. Anal. Chem. 90, 3009–3012 (2018). 43. Qu, B.; Mangunuru, H.P.R.; Tcyrulnikov, S.; Rivalti, D.; Zatolochnaya, O.; Kurouski, D.; Radomkit, S.; Biswas, S.; Karyakarte, S.; Fandrick, K. R.; Sieber, J. D.; Rodriguez, S.; Desrosiers, N.-J.; Haddad, N.; Grinberg, N.; Yee, N. K.; Song, J. J.; Kozlowski, M. C.; Senanayake, C. H. Enantioselective Synthesis of α-(Hetero)aryl piperidines through asymmetric hydrogenation of pyridinium salts and its mechanistic insights. J. Org. Chem. 20, 1333–1337 (2018). 42. Sieber, J. D.; Rodriguez, S.; Frutos, R.; Buono, F.; Zhang, Y.; Li, N.; Qu, B.; Premasiri, A.; Li, Z.; Han, Z.; Xu, Y.; Bryne, D.; Haddad, N.; Lorenz, J.; Grinberg, N.; Kurouski, D.; Lee, H.; Narayanan, B.; Nummy, L.; Mulder, J.; Brown, J.; Granger, A.; Krawiec, M.; Williams, Z.; Pennino, S.; Song, J.; Hossain, A.; Yee, N.; Brusacca, C.; Roschangar, F.; Xin, Y.; Mao, Z.; Zhang, X.; Hong, Y.; Senanayake, C. H. Development of a scalable, chromatography-free synthesis of t-Bu-SMS-Phos and application to the synthesis of an important chiral CF3-alcohol derivative in high enantioselectivity using Rh-catalyzed asymmetric hydrogenation. J. Org. Chem. 83, 1448–1461 (2018). 41. Kurouski, D.; Lee, H.; Roschangar, F.; Senanayake, C. Surface-enhanced Raman spectroscopy: From concept to practical application. Spectroscopy Magazine 32, 36–44 (2018). 40. Kurouski, D. Advances of vibrational circular dichroism (VCD) in bioanalytical chemistry. A Review. Anal. Chim. Acta 990, 54–66 (2017). 39. Kurouski, D. Advances of tip-enhanced Raman spectroscopy (TERS) in electrochemistry, biochemistry, and surface science. Vibr. Spectrosc. 91, 3–15 (2017). 38. Kurouski, D.; Large, N.; Chiang, N.; Henry, A.-I.; Seideman, T.; Schatz, G. C.; Van Duyne, R. P. Unraveling near- and far-field relationship of 2D SERS substrates using wavelength-scanned surface-enhanced Raman excitation spectroscopy (WS-SERES). J. Phys. Chem. C 121, 14737–14744 (2017). 37. Desrosiers, J. N.; Wen, J.; Tcyrulnikov, S.; Biswas, S.; Qu, B.; Hie, L.; Kurouski, D.; Wu, L.; Grinberg, N.; Haddad, N.; Busacca, C. A.; Yee, N. K.; Song, J. J.; Garg, N. K.; Zhang, X.; Kozlowski, M. C.; Senanayake, C. H. Enantioselective nickel-catalyzed Mizoroki-Heck cyclizations to generate quaternary stereocenters. Org. Lett. 19, 3338–3341 (2017). 36. Li, S.-G.; Han, Z. S.; Viereck, P.; Kurouski, D.; Senanayake, C. H.; Tsantrizos, Y. S. Metal-free cycloetherification by in situ generated P-stereogenic α-diazanium intermediates: A convergent synthesis of enantiomerically pure dihydrobenzooxaphospholes. Org. Lett. 19, 894–897 (2017). 35. Li, S.-G.; Han, Z. S.; Viereck, P.; Kurouski, D.; Senanayake, C. H.; Tsantrizos, Y. S. Metal-free cycloetherification by in situ generated P-stereogenic α-diazanium intermediates: A convergent synthesis of enantiomerically pure dihydrobenzooxaphospholes. Org. Lett. 19, 894–897 (2017). 34. Qu, B.; Mangunuru, H. P. R.; Wei, H.; Fandrick, K. R.; Desrosiers, N.-J.; Sieber, J. D.; Kurouski, D.; Haddad, N., Samankumara, L. P.; Lee, H.; Savoie, J.; Ma, S.; Grinberg, N.; Sarvestani, M.; Yee, N. K.; Song, J. J.; Senanayake, C. H. Synthesis of enantioenriched 2-alkyl piperidine derivatives through asymmetric reduction of pyridinium salts. Org. Lett. 18, 4920–4923 (2016). 33. Haddad, N.; Mangunuru, H. P. R.; Fandrick, K. R.; Qu, B.; Sieber, J. D.; Rodriguez, S.; Desrosiers, N.-J.; Patel, N. D.; Lee, H.; Kurouski, D.; Grinberg, N.; Yee, N. K.; Song, J. J.; Senanayake, C. H. Reengineered BI-DIME ligand core based on computer modeling to increase selectivity in asymmetric Suzuki–Miyaura coupling for the challenging axially chiral HIV integrase inhibitor. Adv. Synth. Catal. 358, 3522–3527 (2016). 32. Sieber, J. D.; Angeles-Dunham, V. V.; Chennamadhavuni, D.; Fandrick, D. R.; Haddad, N.; Grinberg, N.; Kurouski, D.; Lee, H.; Song, J. J.; Yee, N. K.; Mattson, A. E.; Senanayake, C. H. Rhodium-catalyzed asymmetric allenylation of sulfonylimines and application to the stereospecific allylic allenylation. Adv. Synth. Catal. 358, 3062–3068 (2016). 31. Deckert-Gaudig, T.; Kurouski, D.; Hedegaard, M.; Singh, P.; Lednev, I. K.; Deckert, V. Spatially resolved spectroscopic differentiation of hydrophilic and hydrophobic domains on individual insulin amyloid fibrils. Sci. Rep. 6, 33575 (2016). 30. Breydo, L.; Kurouski, D.; Rasool, S.; Milton, S.; Wu, J. W.; Uversky, V. N.; Lednev, I. K.; Glabe, C. G. Structural differences between amyloid beta oligomers. Biochem. Biophys. Res. Commun. 477, 700–705 (2016). 29. Henry, A.-I.; Sharma, B.; Cardinal, M. F.; Kurouski, D.; Van Duyne, R. P. Surface-enhanced Raman spectroscopy biosensing: In vivo diagnostics and multimodal imaging. Anal. Chem. 88, 6638–6647 (2016). 28. Kurouski, D.; Large, N.; Chiang, N.; Greeneltch, N.; Carron, K. T.; Seideman, T.; Schatz, G. C.; Van Duyne, R. P. Unraveling near-field and far-field relationships for 3D SERS substrates – A combined experimental and theoretical analysis. Analyst 141, 1779 – 1788 (2016). 27. Jiang, N.; Kurouski, D.; Pozzi, E. A.; Chiang, M.; Hersam, M. C.; Van Duyne, R. P. Tip-enhanced Raman spectroscopy: From concepts to practical applications. Chem. Phys. Lett. 659, 16–24 (2016). 26. Kurouski, D. Supramolecular organization of amyloid fibrils in Amyloids, ed: Escamilla, A.M.F., Intech, ISBN 978-953-51-4716-9 (2016). 25. Kurouski, D.; Van Duyne, R. P.; Lednev, I. K. Exploring the structure and formation mechanism of amyloid fibrils by Raman spectroscopy: A Review. Analyst 140, 4967–4980 (2015). 24. Kurouski, D.; Mattei, M.; Van Duyne, R. P. Probing redox reactions at the nanoscale with electrochemical Tip-Enhanced Raman Spectroscopy. Nano Lett. 15, 7956–7962 (2015). 23. Shanmugasundaram, M.; Kurouski, D.; Wan, W.; Stubbs, G.; Dukor, R. K.; Nafie, L. A.; Lednev, I. K. Rapid filament supramolecular chirality reversal of HET-s (218-289) prion fibrils driven by pH elevation. J. Phys. Chem. B 119, 8521–8525 (2015). 22. Kurouski, D.; Van Duyne, R. P. In situ detection and identification of hair dyes using surface-enhanced Raman spectroscopy (SERS). Anal. Chem. 87, 2901–2906 (2015). 21. Rosario-Alomar, M.F.; Quiñones-Ruiz, T.; Kurouski, D.; Sereda, V.; Ferreira, E. B.; Jesús-Kim, L. D.; Hernández-Rivera, S.; Zagorevski, D. V.; López-Garriga, J.; Lednev, I. K. Hydrogen sulfide inhibits amyloid formation. J. Phys. Chem. B 119, 1265–1274 (2015). 20. Kurouski, D.; Handen, J. D.; Dukor, R. K.; Nafie, L. A.; Lednev, I. K. Supramolecular chirality in peptide microcrystals. Chem. Commun. 51, 89–92 (2015).

COMPLETED SUPPORT (2015–present) Merck Pharmaceuticals Kurouski, D. (PI) 2018–2019 “Coupling of Raman Spectroscopy and Hydrogen Deuterium Exchange for the Fast, Confirmatory and Site-Specific Characterization of Conformational Changes in Proteins” TAMU Crop Improvement Program Kurouski, D. (co-PI) 2017–2019 “Robotic System for Intra-Canopy Acquisition of Phenotypic and Agronomic Data.” TAMU Governor’s University Research Initiative Kurouski, D. (co-PI) 2017 (GURI) and Chancellor's Research Initiative (CRI) “Detection of plant characteristics including waxes, pathogens, volatilities. Development of libraries of chemical signatures of abiotic/biotic indicators of stress and new techniques and instruments for greenhouse/field management.”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Reviewer ACS Nano, Analyst, Journal of Physical Chemistry, ChemPhysChem, Various Sensors & Actuators

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Outreach and Recruitment Committee BCBP 2019 Member Graduate Admissions and Recruitment Committee BCBP 2017–2019

COURSES TAUGHT (2015–present) BICH 689 Optical Spectroscopy 1 cr. 2017–present BICH 410 Comprehensive Biochemistry I 3 cr. 2018–present BICH 491/691 Research Variable 2017–present Pingwei Li Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral California Institute of Technology 2003–2005 Postdoctoral Fred Hutchinson Cancer Research Institute 1998–2001 Ph.D. Peking University 1996 M.Sc. Peking University 1992 B.S. Northwest University 1989

PROFESSIONAL APPOINTMENTS Professor Biochemistry and Biophysics Texas A&M University 2017–present Associate Professor Biochemistry and Biophysics Texas A&M University 2011–2017 Assistant Professor Biochemistry and Biophysics Texas A&M University 2005–2011

PEER-REVIEWED PUBLICATIONS (2015–present) 66. Yang, K. S.; Ma, X. R.; Ma, Y.; Alugubelli, Y. R.; Scott, D. A.; Vatansever, E. C.; Drelich, A. K.; Sankaran, B.; Geng, Z. Z.; Blankenship, L. R.; Ward, H. E.; Sheng, Y. J.; Hsu, J. C.; Kratch, K. C.; Zhao, B.; Hayatshahi, H. S.; Liu, J.; Li, P.; Fierke, C.; Tseng, C.-T. K.; Xu, S.; Liu, W. R. A quick route to multiple highly potent SARS-CoV-2 main protease inhibitors. ChemMedChem (2021). 65. Zhao, B.; Xu, P.; Rowlett, C. M.; Jing, T.; Shinde, O.; Lei, Y.; West, P. A.; Liu, W. R.; Li, P. The molecular basis of tight nuclear tethering and inactivation of cGAS. Nature587, 673–677 (2020). 64. Liu, J.; Huang, Y.; Kong, L.; Yu, X.; Feng, B.; Liu, D.; Zhao, B.; Mendes, G. C.; Yuan, P.; Ge, D.; Wang, W.-M.; Fontes, E. P. B.; Li, P.; Shan, L.; He, P. The malectin-like receptor-like kinase LETUM1 modulates NLR protein SUMM2 activation via MEKK2 scaffolding. Nat. Plants 6, 1106–1115 (2020). 63. Jing, T.; Zhao, B.; Xu, P.; Gao, X.; Chi, L.; Han, H.; Sankaran, B.; Li, P. The structural basis of IRF-3 activation upon phosphorylation. J. Immunol. 205, 1886–1896 (2020). 62. Hoffpauir, C. T.; Bell, S. L.; West, K. O.; Jing, T.; Wagner, A. R.; Torres-Odio, S.; Cox, J. S.; West, A. P.; Li, P.; Patrick, K. L.; Watson, R. O. TRIM14 is a key regulator of the type I IFN response during Mycobacterium tuberculosis infection. J. Immunol. 205, 153–167 (2020). 61. Cho, J.-H.; Zhao, B.; Shi, J.; Savage, N.; Shen, Q.; Byrnes, J.; Yang, L.; Hwang, W.; Li, P. Molecular recognition of a host protein by NS1 of pandemic and seasonal influenza A viruses. Proc. Natl. Acad. Sci. USA 117, 6550–6558 (2020). 60. Zhou, X.; Yu, J.; Cheng, J.; Zhao, B.; Manyam, G. C.; Zhang, L.; Schluns, K.; Li, P.; Wang, J.; Sun, S.-C. The deubiquitinase Otub 1 controls the activation of CD8+T cells and NK cells by regulating IL-15-mediated priming. Nat. Immunol. 20, 879–889 (2019). 59. Zhao, B.; Du, F.; Xu, P.; Shu, C.; Sankaran, B.; Bell, S. L.; Liu, M.; Lei, Y.; Gao, X.; Fu, X.; Zhu, F.; Liu, Y.; Laganowsky, A. D.; Zheng, X.; Ji, J.-Y.; West, A. P.; Watson, R. O.; Li, P. A conserved PLPLRT/SD motif of STING mediates the recruitment and activation of TBK1. Nature 569, 718–722 (2019). 58. Li, X.; Deng, M.; Petrucelli, A. S.; Zhu, C.; Mo, J.; Zhang, L.; Tam, J. W.; Ariel, P.; Zhao, B.; Zhang, S.; Ke, H.; Li, P.; Dokholyan, N. V.; Duncan, J. A.; Ting, J. P.-Y. Viral DNA binding to NLRC3, an inhibitory nucleic acid sensor, unleashes STING, a cyclic dinucleotide receptor that activates type I interferon. Immunity 50, 591–599 (2019). 57. Ghosh, A.; Shao, L.; Sampath, P.; Zhao, B.; Patel, N. V.; Zhu, J.; Behl, B.; Parise, R. A.; Beumer, J. H.; O’Sullivan, R. J.; DeLuca, N. A.; Thorne, S. H.; Rathinam, V. A. K.; Li, P.; Sarkar, S. N. Oligoadenylate-synthetase-family protein OASL inhibits activity of the DNA sensor cGAS during DNA virus infection to limit interferon production. Immunity 50, 51–63 (2019). 56. Xie, X.; Jin, J.; Zhu, L.; Jie, Z.; Li, Y.; Zhao, B.; Cheng, X.; Li, P.; Sun, S.-C. Cell type-specific function of TRAF2 and TRAF3 in regulating type I IFN induction. Cell & Biosci. 9, 5 (2019). 55. Lahaye, X.; Gentili, M.; Silvin, A.; Conrad, C.; Picard, L.; Jouve, M.; Zueva, E.; Maurin, M.; Nadalin, F.; Knott, G. J.; Zhao, B.; Du, F.; Rio, M.; Amiel, J.; Fox, A. H.; Li, P.; Etienne, L.; Bond, C. S.; Colleaux, L.; Manel, N. NONO detects the nuclear HIV capsid to promote cGAS-mediated innate immune activation. Cell 175, 488–501 (2018). 54. Patrick, K. L.; Wojcechowskyj, J. A.; Bell, S. L.; Riba, M. N.; Jing, T.; Talmage, S.; Xu, P.; Cabello, A. L.; Xu, J.; Shales, M.; Jimenez-Morales, D.; Ficht, T. A.; de Figueiredo, P.; Samuel, J. E.; Li, P.; Krogan, N. J.; Watson, R. O. Quantitative yeast genetic interaction profiling of bacterial effector proteins uncovers a role for the human retromer in salmonella infection. Cell Systems 7, 323–328 (2018). 53. Wang, Z.; Ma, Z.; Castillo-Gonzalez, C.; Sun, D.; Li, Y.; Tu, B.; Zhao, B.; Li, P.; Zhang, X. SWI2/SNF2 ATPase CHR2 remodels pri-miRNA via Serrate to impede miRNA production. Nature 557, 516–521 (2018). 52. Yang, Y.; Shu, C.; Li, P.; Igumenova, T. Structural basis of protein kinase Cα regulation by the C-terminal tail. Biophys. J. 114, 1590–1603 (2018). 51. Shen, Q.; Shi, J.; Zeng, D.; Zhao, B.; Li, P.; Hwang, W.; Cho, J.-H. Molecular mechanisms of tight binding through fuzzy interactions. Biophys. J. 114, 1313–1320 (2018). 50. Guo, X.; Shu, C.; Li, H.; Pei, Y.; Woo, S.-L.; Zheng, J.; Liu, M.; Xu, H.; Botchlett, R.; Guo, T.; Cai, Y.; Gao, X.; Zhou, J.; Chen, L.; Li, Q.; Xiao, X.; Xie, L.; Zhang, K. K.; Ji, J.-Y.; Huo, Y.; Meng, F.; Alpini, G.; Li, P.; Wu, C. Cyclic GMP- AMP ameliorates diet-induced metabolic dysregulation and regulates proinflammatory responses distinctly from STING activation. Scientific Rep. 7, 6335 (2017). 49. Zhang, Z.; Hu, F.; Sung, M. W.; Shu, C.; Castillo-Gonzalez, C.; Koiwa, H.; Tang, G.; Dickman, H.; Li, P.; Zhang, X. RISC-Interacting Clearing 3'- 5' Exoribonucleases (RICEs) degrade uridylated cleavage fragments to maintain functional RISC in Arabidopsis. eLife (2017). 48. Shen, Q.; Zeng, D.; Zhao, B.; Bhatt, V. S.; Li, P.; Cho, J.-H. The molecular mechanisms underlying the hijack of host proteins by the 1918 Spanish influenza virus. ACS Chem. Biol. 12, 1199–1203 (2017). 47. Zhao, B.; Yi, G.; Du, G.; Chuang, Y.-C.; Vaughan, R. C.; Sankaran, B.; Kao, C. C.; Li, P. Structure and function of the Zika virus full-length NS5 protein. Nat. Commun. 8, 14672 (2017). 46. Zhao, B.; Shu, C.; Gao, X.; Sankaran, B.; Du, F.; Shelton, C. L.; Herr, A. B.; Ji, J.-Y.; Li, P. Structural basis for concerted recruitment and activation of IRF-3 by innate immune adaptor proteins. Proc. Natl. Acad. Sci. USA 113, e3423–e3430 (2016). 45. Li, T.; Cheng, H.; Yuan, H.; Xu, Q.; Shu, C.; Zhang, Y.; Xu, P.; Tan, J.; Rui, Y.; Li, P.; Tan, X. Antitumor activity of cGAMP via stimulation of cGAS-cGAMP-STING-IRF3 mediated innate immune response. Sci. Rep. 6, 19049 (2016). 44. Yi, G.; Wen, Y.; Shu, C.; Han, Q.; Konan, K. V.; Li, P.; Kao, C. C. The Hepatitis C virus NS4B can suppress STING accumulation to evade innate immune responses. J. Virol. 90, 254–265 (2015).

CURRENT SUPPORT NIH R01 AI145287 Li, P. (PI), Zhang, J.; Watson, R. O. 2019–2024 “The molecular basis of viral DNA sensing through the cGAS-STING pathway” NIH R01 GM132655 Hilty, C. (PI), Li, P. (co-PI) 2019–2023 “Hyperpolarization assisted structure based screening of protein–ligand interactions in live cells” NIH R01 GM127575 Liu, W. (PI), Li, P. (co-PI) 2019–2022 “Develop general methods for the synthesis of proteins with posttranslational lysine modifications”

COMPLETED SUPPORT (2015–present) NIH R21 AI140004 Watson, R. O. (PI), Li, P. (co-PI) 2018–2020 “The secreted effector SseC is a key regulator of retrograde transport during Salmonella enterica serovar Typhimurium infection” Welch Foundation A193120170325 Li, P. (PI) 2017–2020 “The structural basis of RNA synthesis by Zika virus” CPRIT RP150454 Li, P. (PI), Ji, J.-Y. (co-PI) 2015–2019 “Tumor suppression through the cGAMP/STING pathway” CST*R Pilot Grant Watson, R. O. (PI), Li, P. (co-PI) 2017 “Modulation of LRRK2-dependent cytokine production as a treatment for Parkinson’s Disease” Welch Foundation A1816 Li, P. (PI) 2013–2016 “The structural basis of microbial DNA sensing in innate immunity” TAMU and National Science Foundation of China Li, P. (PI), Tan, X. (co-PI) 2014–2015 “The antiviral and antitumor activities of cyclic GMP-AMP (cGAMP)” NIH R01 AI087741 Li, P. (PI) 2010–2015 “The structural basis of viral RNA sensing by RIG-I like receptors”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Reviewer NSF, NIAID, French National Research Agency, NIH Study Section Various MSFC, Hong Kong Research Grants Council, Austrian Science Fund, NSFC (China), RGC (Hong Kong) Peer reviewer Trends in Biological Sciences, Archives of Biochemistry and Various Biophysics, Nature Structural and Molecular Biology, Acta Crystallographica Section D: Biological Crystallography, Journal of Biological Chemistry, Journal of Molecular Cell Biology, Proceedings of the National Academy of Sciences, Journal of Molecular Biology, Nature Reviews Immunology, Current Opinion in Virology, eLife, Nature Chemical Biology, EMBO Reports, Science Signaling, Nature Communications, Nature Reviews Molecular Cell Biology, Immunity

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Seminar Committee BCBP 2018–present Member Undergraduate Program Committee BCBP 2014–present Member Graduate Recruiting and Admissions Committee BCBP 2007–2013

COURSES TAUGHT (2015–present) BICH 410 Fundamentals of Biochemistry 3 cr. 2007–present BICH 689/657 Introduction to Structural Biology 1 cr. 2006–present BICH 624 Enzymes, Proteins and Nucleic Acids 3 cr. 2015 Paul A. Lindahl Professor | Departments of Chemistry, Biochemistry and Biophysics

EDUCATION Postdoctoral University of Minnesota with E. Munck 1985–1988 Ph.D. Massachusetts Institute of Technology with W. H. Orme-Johnson 1985 B.S. North Park College 1979

PROFESSIONAL APPOINTMENTS Professor Chemistry Texas A&M University 1999–present Biochemistry and Biophysics Associate Professor Biochemistry and Biophysics Texas A&M University 1998–1999 Associate Professor Chemistry Texas A&M University 1994–1999 Assistant Professor Chemistry Texas A&M University 1988–1994

PEER-REVIEWED PUBLICATIONS (2015–present) 137. Khan, D.; Lee, D.; Gulten, G.; Aggarwal, A.; Wofford, J. J.; Krieger, I.; Tripathi, A.; Patrick, J. W.; Eckert, D. M.; Laganowsky, A. A.; Sacchettini, J.; Lindahl, P. A.; Bankaitis, V. A. A Sec14-like phosphatidylinositol transfer protein paralog defines a novel class of heme-binding proteins. eLife 9, e57081 (2020). 136. Nguyen, T. Q.; Kim, J. E.; Brawley, H. N.; Lindahl, P. A. Chromatographic detection of low-molecular-mass metal complexes in the cytosol of Saccharomyces cerevisiae. Metallomics 12, 1094–1105 (2020). 135. Soma, S.; Morgada, M. N.; Naik, M. T.; Boulet, A.; Roesler, A. A.; Dziuba, N.; Ghosh, A.; Yu, Q.; Lindahl, P. A.; Ames, J. B.; Leary, S. C.; Vila, A. J.; Gohil, V. M. COA6 is structurally tuned to function as a thiol-disulfide oxidoreductase in copper delivery to mitochondrial cytochrome c oxidase. Cell Rep. 29, 4114–4126 (2019). 134. Drake, H. F.; Day, G. S.; Vali, S. W.; Xiao, Z.; Banerjee, S.; Li, J.; Josesph, E. A.; Kuszynski, J. E.; Perry, Z. T.; Kirchon, A.; Ozdemir, O. K.; Lindahl, P. A.; Zhou, H.-C. The thermally induced decarboxylation mechanism of a mixed-oxidation state carboxylate-based iron metal-organic framework. Chem. Commun. 55, 12769–12772 (2019). 133. Dziuba, N.; Hardy, J.; Lindahl, P. A. Low-molecular-mass iron complexes in blood plasma of iron-deficient pigs do not originate directly from nutrient iron. Metallomics 11 (2019). 132. Lindahl, P. A. A comprehensive mechanistic model of iron metabolism in Saccharomyces cerevisiae. Metallomics 11, 1779–1799 (2019). 131. Soma, S.; Morgada, M. N.; Naik, M. T.; Boulet, A.; Roesler, A. A.; Dziuba, N.; Ghosh, A.; Yu, Q.; Lindahl, P. A.; Ames, J. B.; Leary, S. C.; Vila, A. J.; Gohil, V. M. COA6 is structurally tuned to function as a thiol-disulfide oxidoreductase in copper delivery to mitochondrial cytochrome c oxidase. Cell Rep. 29, 4114–4126 (2019). 130. Nguyen, T. Q.; Dziuba, N.; Lindahl, P. A. Isolated Saccharomyces cerevisiae vacuoles contain low-molecular-mass transition-metal polyphosphate complexes. Metallomics (2019). 129. Wofford, J. D.; Lindahl, P. A. A mathematical model of iron import and trafficking in wild-type and Mrs3/4ΔΔ yeast cells. BMC Sys. Biol. 13, 23 (2019). 128. Wofford, J. D.; Bolaji, N.; Dziuba, N.; Outten, F. W.; Lindahl, P. A. Evidence that a respiratory shield in Escherichia II coli protects a low molecular mass Fe pool from O2-dependent oxidation. J. Biol. Chem. 294, 50–62 (2019). 127. Dziuba, N.; Hardy, J.; Lindahl, P. A. Low-molecular-mass iron in healthy blood plasma is not predominately ferric citrate. Metallomics 10, 802–817 (2018). 126. Pandey, A.; Pain, J.; Dziuba, N.; Pandey, A. K.; Dancis, A.; Lindahl, P. A.; Pain, D. Mitochondria export sulfur species required for cytosolic tRNA thiolation. Cell Chem. Biol. 25, 738–748 (2018). 125. Moore, M. J.; Wofford, J. D.; Dancis, A.; Lindahl, P. A. Recovery of mrs3Dmrs4D Saccharomyces cerevisiae cells under iron-sufficient conditions and the role of Fe580. Biochemistry 57, 672–683 (2018). 124. Kuppuswamy, S.; Wofford, J. D.; Joseph, C.; Xie, Z.; Ali, A.; Lynch, V.; Lindahl, P. A.; Rose, M. Structures, interconversions and spectroscopy of iron carbonyl clusters with an interstitial carbide: Localized metal center reduction by overall cluster oxidation. Inorg. Chem. 56, 5998–6012 (2017). 123. Wofford, J. D.; Chakrabarti, M.; Lindahl, P. A. Mössbauer spectra of mouse hearts reveal age-dependent changes in mitochondrial and ferritin iron levels. J. Biol. Chem. 292, 5546–5554 (2017). 122. Lindahl, P. A.; Moore, M. J. Labile low-molecular-mass metal complexes in mitochondria: Trials and tribulations of a burgeoning field. Biochemistry 55, 4140–4153 (2016). 121. Wofford, J. D.; Park, J.; McCormick, S. P.; Chakraborti, M.; Lindahl, P. A. Ferric ions accumulate in the walls of metabolically inactivating Saccharomyces cerevisiae cells and are reductively mobilized during reactivation. Metallomics 8, 692–708 (2016). 120. Wofford, J. D.; Lindahl, P. A. Mitochondrial iron–sulfur-cluster activity and cytosolic iron regulate iron traffic in Saccharomyces cerevisiae. J. Biol. Chem. 290, 26968–26977 (2015). 119. Fox, N. G.; Das, D.; Chakrabarti, M.; Lindahl, P. A.; Barondeau, D. P. Frataxin accelerates [2Fe-2S] cluster formation on the human Fe-S assembly complex. Biochemistry 54, 3880–3889 (2015). 118. Fox, N. G.; Chakrabarti, M.; McCormick, S.; Lindahl, P. A.; Barondeau, D. P. The human iron-sulfur assembly complex catalyzes the synthesis of [2Fe-2S] clusters on ISCU2 that can be transferred to acceptor molecules. Biochemistry 54, 3871–3879 (2015). 117. McCormick, S.; Moore, M. J.; Lindahl, P. A. Detection of labile low-molecular-mass transition metal complexes in mitochondria. Biochemistry 54, 3442–3453 (2015). 116. Chakrabarti, M.; Nofil Barlas, M.; McCormick, S. P.; Lindahl, L. S.; Lindahl, P. A. Kinetics of iron import into developing mouse organs determined by a pup-swapping method. J. Biol. Chem. 290, 520–528 (2015).

CURRENT SUPPORT NIH MIRA Lindahl, P. A. 2018–2023 NSF Lindahl, P. A. 2019–2022 Welch Foundation Lindahl, P. A. 2019–2022 TAMU T3 Grant Lindahl, P. A. 2019

COMPLETED SUPPORT (2015–present) Welch Foundation Lindahl, P. A. 2016–2019 “Chemical characterization of low-molecular-mass metal complexes in mitochondria and blood” NIH R01 Lindahl, P. A. 2014–2018 “Iron in mitochondrial physiology and disease” Welch Foundation Lindahl, P. A. 2013–2015 “Characterization of low-molecular-mass iron and manganese complexes isolated from yeast cells” Seed money for pig studies Lindahl, P. A. (co-PI)

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Reviewer NIH study sections 2015–2016, 2018–2020 Reviewer NSF study section 2018

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Awards Committee CHEM 2015–present Member Promotion and Tenure Committee CHEM 2016–2019

COURSES TAUGHT (2015–present) CHEM 120 Fundamentals of Chemistry II 3 cr. 2020–2021 CHEM 119 Fundamentals of Chemistry I 3 cr. 2017, 2020 CHEM 222 Elements of Organic and Biological Chemistry 3 cr. 2019 CHEM 628 Coordination and Bioinorganic Chemistry 3 cr. 2016, 2018 BICH 678 Metal Ions 1 cr. 2015–2018 CHEM 627 Principles of Biological Chemistry 3 cr. 2017 CHEM 456 Chemical Biology 3 cr. 2015, 2017 Thomas D. Meek Professor | Department of Biochemistry and Biophysics

EDUCATION Ph.D. Pennsylvania State University 1981 B.S. University of Virginia 1976

PROFESSIONAL APPOINTMENTS Professor Biochemistry and Biophysics Texas A&M University 2014–present Vice President Platform Technology and Science Innovation GlaxoSmithKline Pharmaceuticals 2006–2012 Vice President Assay Development GlaxoSmithKline Pharmaceuticals 2005–2006 Vice President Assay Development and Compound Profiling GlaxoSmithKline Pharmaceuticals 2003–2005 Vice President Molecular Screening Technologies SmithKline Beecham Pharmaceuticals 1999–2001

PEER-REVIEWED PUBLICATIONS (2015–present) 73. Karhadkar, T. R.; Meek, T. D.; Gomer, R. H. Inhibiting sialidase-induced TGF-β1 activation attenuates pulmonary fibrosis in mice. J. Pharmacol. Exp. Ther. (2020). 72. Meek, T. D. Enzymes as Drug Targets, Burger's Medicinal Chemistry, Drug Discovery and Development, 8th edition, D. Abraham, Ed., J. Wiley, New York, in press (2020). 71. Chenna, B. C.; Li, L.; Mellott, D. M.; Zhai, X.; Siqueira-Neto, J. L.; Calvet Alvarez, C.; Bernatchez, J. A.; Desormeaux, E.; Alvarez Hernandez, E.; Gomez, J.; McKerrow, J. H.; Cruz-Reyes, J.; Meek, T. D. Peptidomimetic vinyl heterocyclic inhibitors of cruzain effect antitrypanosomal activity. J. Med. Chem. 63, 3298–3316 (2020). 70. Schramm, V. L.; Meek, T. D. Enhanced antibiotic discovery by PROSPECTing. Biochemistry 58, 3475–3476 (2019). 69. Ma, Y.; Li, L.; He, S.; Shang, C.; Sun, Y.; Liu, N.; Meek, T. D.; Wang, Y.; Shang, L. Application of dually activated Michael acceptor to the rational design of reversible covalent inhibitor for enterovirus 71 3C protease. J. Med. Chem. 62, 6146–6162 (2019). 68. Zhai, X.; Meek, T. D. Catalytic mechanism of cruzain from Trypanosoma cruzi as determined from solvent kinetic isotope effects of steady-state and pre-steady-state kinetics. Biochemistry 57, 3176–3190 (2018). 67. Holdgate, G. A.; Meek, T. D.; Grimley, R. L. Mechanistic enzymology in drug discovery: A fresh perspective. Nat. Rev. Drug Discov. 17, 78 (2017). 66. Pham, T. V.; Murkin, A. S.; Moynihan, M. M.; Harris, L.; Tyler, P. C.; Shetty, N.; Sacchettini, J. C.; Huang, H.-L.; Meek, T. D. Mechanism-based inactivator of isocitrate lyases 1 and 2 from Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. 114, 7617–7622 (2017). 65. Poulin, M.; Schneck, J. L.; Mattico, R. E.; McDevitt, P. J.; Huddleston, M. J.; Hoiu, W.-F.; Johnson, N. W.; Thrall, S. H.; Meek, T. D.; Schramm, V. L. Transition state for the NSD2-catalyzed methylation of histone H3 lysine 36. Proc. Natl. Acad. Sci. 113, 1197–1201 (2016).

CURRENT SUPPORT TAMU X-Grant Meek, T. D. (collaborator) 2020–2022 “A multidisciplinary platform for the identification of cancer and COVID-19 therapeutics “ NIH #1R01-AI127807-01 Meek, T. (PI); Cruz-Reyes, J. (co-PI) 2017–2022 “Phosphoribosyltransferases as targets to treat malaria, African trypanosomiasis and Chagas disease”

COMPLETED SUPPORT (2015–present) NIH R21 Meek, T. D. (PI) 2016–2018 “Novel Inhibitors of Cruzain and Trypanosoma brucei Cathepsin B as Potential Drug Candidates for the Treatment of African Trypanosomiasis and Chagas Disease”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) NSF Panel Grant reviewer 2015–present Member, Organizer Enzyme Mechanisms Conference 2015–present Secretary Division of Biological Chemistry, American Chemical Society 2016–2019 First Place BCBP Chili Cook-off 2015 NIH Panel MSFA study section Various

DEPARTMENT AND SYSTEM SERVICE (2015–present) Chair, Member RDF Advisory Committee TAMU 2015–present Chair Graduate Recruiting and Admissions Committee BCBP 2017–2019 Member Graduate Recruiting and Admission, Promotions and BCBP Various Tenure, Department Head Search, Seminar, CUE Committees

COURSES TAUGHT (2015–present) BICH 404 Biochemical Calculations 2 cr. 2015–present BICH 491/691 Research Variable 2015–present BICH 440 Biochemistry I 3 cr. 2020 BIOL 689 Biomedical Therapeutics Development 3 cr. Bryant W. Miles Senior Lecturer | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Chemistry, Texas A&M University With F. M. Raushel 1998–2001 Ph.D. Organic Chemistry, Texas A&M University 1998 B.S. Chemistry, Southern Utah State University 1988 B.S. Mathematics, Westminster College 1986

PROFESSIONAL APPOINTMENTS Senior Lecturer Biochemistry and Biophysics TAMU 2001–present Lecturer Organic Chemistry – JAMP TAMU Health Science Center Summer 2005–2019

COURSES TAUGHT (2015–present) BICH 409 Principles of Biochemistry 3 cr. 2019–present BICH 410 Comprehensive Biochemistry I 3 cr. 2000–present BICH 411 Comprehensive Biochemistry II 3 cr. 2001–present BICH 602 Fundamentals of Biochemistry II 3 cr. 2016–present

John E. Mullet Perry L. Adkisson Chair in Agricultural Biology Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Rockefeller University NIH Fellow 1980–1983 Ph.D. University of Illinois 1980 B.S. Colgate University 1976

PROFESSIONAL APPOINTMENTS Perry L. Adkisson Chair Agricultural Biology Texas A&M University 1996–present Professor Biochemistry and Biophysics Texas A&M University 1991–present Director Institute for Plant Genomics and Biotechnology Texas A&M University 1999–2005 Director Crop Biotechnology Center Texas A&M University 1993–1999 Associate Professor Biochemistry and Biophysics Texas A&M University 1986–1991 Assistant Professor Biochemistry and Biophysics Texas A&M University 1983–1986

PEER-REVIEWED PUBLICATIONS (2015–present) 207. Kebrom, T. H.; McKinley, B.; Mullet, J. E. Shade signals alter the expression of circadian clock genes in newly-formed bioenergy sorghum internodes. Plant Direct 4, e00235 (2020). 206.Gomez, F. E.; Mullet, J. E.; Muliana, A.; Nijklas, K. J.; Rooney, W. L. The genetic architecture of biomechanical traits in sorghum. Crop Sci. 60, 82–99 (2020). 205. Bagnall, G. C.; Koonjoo, N.; Altobelli, S. A.; Conradi, M. S.; Fukushima, E.; Kuethe, D. O.; Mullet, J. E.; Neely, H.; Rooney, W. L.; Stupic, K. F.; Weers, B.; Zhu, B.; Rosen, M. S.; Morgan, C. L. S. Low-field magnetic resonance imaging of roots in intact clayey and silty soils. Geoderma 370, e114356 (2020). 204. Farber, C.; Li, J.; Hager, E.; Chemelewski, R.; Mullet, J.; Y. Rogachey, A.; Kurouski, D. Complementarity of Raman and infrared spectroscopy for structural characterization of plant epicuticular waxes. ACS Omega 4, 3700–3707 (2019). 203. Farber, C.; Wang, R.; Chemelewski, R.; Mullet, J.; Kurouski, D. Nanoscale structural organization of plant epicuticular wax probed by atomic force microscope infrared spectroscopy. Anal. Chem. 91, 2472–2479 (2019). 202. Casto, A. L.; Mattison, A. J.; Olson, S. N.; Thakran, M.; Rooney, W. L.; Mullet, J. E. Maturity2, a novel regulator of flowering time in Sorghum bicolor, increases expression of SbPRR37 and SbCO in long days delaying flowering. PLoS One 14, e0212154 (2019). 201. Williams, D. L.; Ong, R. G.; Mullet, J. E.; Hodge, D. B. Integration of pretreatment with simultaneous counter-current extraction of energy sorghum for high-titer mixed sugar production. Front. Ener. Res. 6, e133 (2019). 200. Casto, A. L.; McKinley, B. A.; Yu, J. K. M.; Rooney, W. L.; Mullet, J. E. Sorghum stem aerenchyma formation is regulated by SbNAC_D during internode development. Plant Direct 2, e00085 (2018). 199. Li, M.; Yan, G.; Ghalia, A.; Maldonado-Pereira, L.; Russell, P. R.; Ding, S.-Y.; Mullet, J. E.; Hodge, D. B. Physical fractionation of sweet sorghum and energy sorghum for optimal processing in a biorefinery. Ind. Crops Prod. 124, 607– 616 (2018). 198. McKinley, B.; Casto, A. L.; Rooney, W. L.; Mullet, J. E. Developmental dynamics of stem starch accumulation in Sorghum bicolor. Plant Direct 2, e00074 (2018). 197. McKinley, B.; Olson, S.; Herb, D.; Karlen, S. D.; Lu, F.; Ralph, J.; Ronney, W.; Mullet, J. E. Variation in energy Sorghum hybrid TX08001 biomass composition and lignin chemistry during development under irrigated and non- irrigated field conditions. PLoS One 13, e0195863 (2018). 196. McCormick, R. F.; Truong, S. K.; Sreedasyam, A.; Jenkins, J.; Shu, S.; Sims, D.; Kennedy, M.; Amirebrahimi, M.; Grimwood, J.; Weers, B.; McKinley, B.; Mattison, A.; Morishige, D.; Schmutz, J.; Mullet, J. The Sorghum bicolor reference genome: Improved assembly and annotations, a transcriptome atlas, and signatures of genome organization. Plant J. 93, 338–354 (2018). 195. Awaida, H. O.; Hays, D. B.; Mullet, J. E.; Rooney, W. L.; Weers, B. D. QTL mapping and loci dissection for leaf epitcuticular wax load and canopy temperature depression and their association with QTL for staygreen in Sorghum bicolor under stress. Euphytica 213, e207 (2017). 194. Mullet, J. E. High biomass C4 grasses – filling the yield gap. Plant Sci. 261, 10–17 (2017). 193. Kebrom, T. H.; McKinley, B.; Mullet, J. E. Dynamics of gene expression during development of begetative stem internodes of bioenergy sorghum. Biotechnol. Biofuels 10, e159 (2017). 192. Hilley, J. L.; Weers, B. D.; Truong, S. K.; McCormick, R. F.; Mattison, A. J.; McKinley, B. A.; Morishige, D. T.; Mullet, J. E. Sorghum Dw2 encodes a protein kinase regulator of stem internode length. Sci. Rep. 7, e4616 (2017). 191. Truong, S. K.; McCormick, R. F.; Mullet, J. E. Bioenergy Sorghum crop model predicts VPD-Limited transpiration traits enhance biomass yield in water-limited environments. Front. Plant Sci. 8, e335 (2017). 190. McCormick, R. F.; Truong, S. K.; Mullet, J. E. 3D Sorghum reconstructions from depth images identify QTL regulating shoot architecture. Plant Physiol. 172, 823–834 (2016). 189. McKinley, B.; Rooney, W.; Wilderson, C.; Mullet, J. E. Dynamics of biomass partitioning, stem gene expression, cell wall biosynthesis, and sucrose accumulation during development of Sorghum biocolor. Plant J. 88, 662–680 (2016). 188. Hiley, J.; Truong, S. K.; Olson, S. N.; Morishige, D.; Mullet, J. E. Identification of Dw1, a regulator of sorghum stem internode length. PLoS ONE 11, e0151271 (2016). 187. Kebrom, T. H.; Mullet, J. E. Transcriptome profiling of Tiller Buds provides new insights into PhyB regulation of tillering and indeterminate growth in Sorghum. Plant Physiol. 170, 2232–2250 (2016). 186. Hayes, C. M.; Weers, B. D.; Thakran, M.; Burow, G.; Xin, Z.; Emendack, Y.; Burke, J. J.; Rooney, W. L.; Mullet, J. E. Discovery of a Dhurrin QTL in Sorghum: Co-localization of Dhurrin biosythesis and a novel stay-green QTL. Crop Sci. 56, 104–112 (2016). 185. Truong, S. K.; McCormick, R. F.; Rooney, W. L.; Mullet, J. E. Harnessing genetic variation in leaf angle to increase productivity of Sorghum bicolor. Genetics 201, 1229–1238 (2015). 184. McCormick, R. F.; Truong, S. K.; Mullet, J. E. RIG: Recalibration and interrelation of genomic sequence data with the GATK. GGG 5, 655–665 (2015). 183. Kebrom, T.; Mullet, J. E. Photosynthetic leaf area modulates tiller bud outgrowth in sorghum. Plant Cell Environ. 38, 1471–1478 (2015).

CURRENT SUPPORT DOE-ARPA-E ROOTS Rajan, N. (PI); Mullet, J. (co-PI); Rooney, W. (co-PI); Morgan, C. (co-PI); 2017–2023 Rosen, M. (co-PI); Conradi, M. (co-PI); Stupic, K. (co-PI) “LF-MRI for Field Root Imaging” DOE-GLBRC Donahue, T. (PI); Mullet, J. (co-PI); Rooney, W. (co-PI) 2012–2022 “Engineering Energy Sorghum Feedstocks” DOE-JGI Mullet, J. (PI) 2014–2020 “Community Sequencing Program”

COMPLETED SUPPORT (2015–present) ARPA-E (DOE) Rooney, W. (PI); Wettergreen, D. (co-PI); Mullet, J. (PI) 2015–2019 “Automated TERRA Phenotyping System for Genetic Improvement of Energy Crops” USDA-DOE Feedstock Mullet, J. (PI); Libault, M. (co-PI); Rooney, W. (co-PI) 2014–2017 Genomics Program “Genomics of Water Use Efficiency/Drought Tolerance in Energy Sorghum” Ceres, Inc. Mullet, J. (co-PI); Rooney, W. (co-PI); Klein, P. (co-PI) 2011–2016 “Designing Sorghum for Bioenergy” DOE-Sungrant Mallinson (PI); Bartley (co-PI); Mullet, J. (co-PI) 2013–2015 “Designing Energy Crops for Thermochemical Conversion”

DEPARTMENT AND SYSTEM SERVICE (2015–present) Chair Post-Tenure Review Committee BCBP 2019–present Member Executive Committee BCBP 2018–2020 Chair Department Head Search Committee BCBP 2018 Member Promotion and Tenure Committee COALS 2017–2018 Chair Faculty Search Committee BICH 2016–2017 Member Chairholder Review Committee COALS 2020

COURSES TAUGHT (2015–present) GENE 420 Bioethics 3 cr. 2011–present BICH 491/691 Research Variable 1987–present BICH 608 Critical Analysis of the Biochemical Literature 2 cr. 2014–2019 BICH 675 Plant Biochemistry and Genomics (Journal Club) 1 cr. 2009–2018

Vladislav M. Panin Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Waksman Institute of Microbiology, Rutgers University 1995–2001 Ph.D. Biophysics, Moscow State University 1990 B.S. Biophysics, Moscow State University 1987

PROFESSIONAL APPOINTMENTS Professor Biochemistry and Biophysics Texas A&M University 2015–present Graduate Faculty Genetics IDP Texas A&M University 2003–present Associate Professor Biochemistry and Biophysics Texas A&M University 2008–2015 Assistant Professor Biochemistry and Biophysics Texas A&M University 2001–2008

PEER-REVIEWED PUBLICATIONS (2015–present) 52. Chandel, I.; Ten Hagen, K. G.; Panin, V. Sweet rescue or surrender of the failing heart? J. Biol. Chem. 294, 12579– 12580 (2019). 51. Chandel, I.; Baker, R.; Nakamura, N.; Panin, V. Live imaging and analysis of muscle contractions in Drosophila embryo. J. Vis. Exp. 149 (2019). 50. Baker, R.; Nakamura, N.; Chandel, I.; Howell, B.; Lyalin, D.; Panin, V. M. Protein O-mannosyltransferases affect sensory axon wiring and dynamic chirality of body posture in the Drosophila embryo. J. Neurosci. 38, 1850–1865 (2018). 49. Akishina, A. A.; Vorontsova, J. E.; Cherezov, R. O.; Mertsalov, I. B.; Zatsepina, O. G.; Slezinger, M. S.; Panin, V. M.; Petruk, S.; Enikolopov, G. N.; Mazo, A.; Simonova, O. B.; Kuzin, B. A. Xenobiotic-induced activation of human aryl hydrocarbon receptor target genes in Drosophila is mediated by the epigenetic chromation modifiers. Oncotarget 8, 102934–102947 (2017). 48. Mertsalov, I. B.; Novikov, B. N.; Scott, H.; Dangott, L.; Panin, V. M. Characterization of Drosophila CMP-sialic acid synthetase activity reveals unusual enzymatic properties. Biochem. J. 473, 1905–1916 (2016). 47. Baker, R.; Panin, V. Characterizing muscle contraction strength in Drosophila embryos by intensity increase in GFP transgenically expressed in muscles. Dros. Inf. Serv. 98, 76–78 (2015).

CURRENT SUPPORT NIH #1R01-NS099409 Panin, V. (PI) 2017–2022 “Functional mechanisms underlying Dystroglycan-dependent and independent roles of protein O-mannosylation in the nervous system” TAMU-CONACYT Panin, V. (PI); Guerrero-Hernández, A. (co-PI) 2020–2021 Award 19-20-052 “Mechanisms of the Interplay between Protein Glycosylation and Ca2+ Regulation in Normal and Pathological Conditions” TAMU T3 Triads for Panin, V. (PI); Yakovlev (co-PI); Wu (co-PI) 2019–2020 Transformation Grant “Interdisciplinary study to reveal pathological mechanisms of muscular dystrophy”

COMPLETED SUPPORT (2015–present) NIH #R01-NS075534 Panin, V. (PI) 2011–2018 “The control of neural transmission by glycosylation”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Participating Investigator Consortium for Functional Glycomics (CFG) 2006–present Ad hoc peer reviewer Journal of Biological Chemistry, Glycobiology, Glycoconjugate Various Journal, PNAS Panel Member NIH Emphasis study section, MBPP study section, IMST, IRG, Glycans Various

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Undergraduate Program Committee, CryoEM Search BCBP Various Committee, Post-Tenure Review Committee, Graduate Recruitment and Admission Committee, Executive Committee, Non-Thesis MS Committee, International Outreach Committee, Awards Committee Member TAMIN Membership and Nomination Committee TAMU 2008–present Member Faculty of Neuroscience TAMU 2008–present Supervisor Microscope Imaging System BCBP 2004–present Member/Co-Chair Nomination Committee for Faculty of Genetics; Genetics TAMU 2003–present Program Advisory Committee, Genetics Executive Committee

COURSES TAUGHT (2015–present) BICH 489 Biomolecules: Glycans in Diseases, Physiology, and of Development 1.5 cr. 2015–present GENE 302H Principles of Genetics (Honors) 3 cr. 2014–present GENE 302 Principles of Genetics 3 cr. 2003–present BICH/GENE 491/691 Research Variable 2003–present William David Park Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral University of Minnesota, St. Paul with I. Rubenstein 1977–1979 Ph.D. University of Florida, Gainesville 1977 B.S. University of South Carolina, Columbia 1973

PROFESSIONAL APPOINTMENTS Professor Biochemistry and Biophysics TAMU 1991–present Associate Head of the Graduate Program Biochemistry and Biophysics TAMU 2006–2015 Associate Professor Biochemistry and Biophysics TAMU 1984–1990 Assistant Professor Horticulture Purdue University 1980–1983

PATENTS & IP DISCLOSURES Park, W. D. Disclosure TAMUS 5516 2019 2019 McClung, A. M.; Bormans, C. A.; Park, W. D. Release of Hidalgo and Cala, two higher PVP 20050051 2002 yielding long grain rice varieties having PVP 20050052 special processing quality

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Distinguished Rice Research & Education Team Award 38th Rice Technical Working Group 2020 Faculty Recognition Award TAMU 2017

DEPARTMENT & SYSTEM SERIVICE (2015–present) Panel Member Promotion and Tenure Faculty Evaluation Discussion TAMU 2020 Task Force Member Promotion and Tenure Faculty Evaluation Guidelines TAMU 2020 Member Promotion and Tenure Faculty Evaluation Guidelines BCBP 2020 Co-Chair Common-Use Equipment Committee BCBP 2020–present Chair Safety Committee and Pandemic Response Task Force BCBP 1991–present

COURSES TAUGHT (2015–present) BICH 441 Biochemistry II 3 cr. 2021 BICH/GENE 101 Perspectives in Biochemistry and Genetics 1 cr. 2020 BICH 491 Research Variable 2018–present GENE 302 Principles of Genetics 4 cr. 2013–present BICH 411 Comprehensive Biochemistry II 3 cr. 2000–present Jean-Philippe Pellois Associate Head of the Graduate Program, Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral The Rockefeller University with T. Muir 2002–2006 Ph.D. University of Houston with X. Gao 2002 M. Sc. Ecole Supérieure de Chimie Physique Electronique 1999

PROFESSIONAL APPOINTMENTS Associate Head Biochemistry and Biophysics Texas A&M University 2019–present Professor Biochemistry and Biophysics Texas A&M University 2016–present Associate Professor Biochemistry and Biophysics Texas A&M University 2012–2016 Assistant Professor Biochemistry and Biophysics, Genetics Texas A&M University 2006–2012

PEER-REVIEWED PUBLICATIONS (2015–present) 22. Brock D. J.; Kondow-McConaghy H. M.; Allen, J.; Brkljača, Z. K.; Kustigian, L.; Jiang, M.; Zhang, J.; Rye, H.; Vazdar, M.; Pellois, J.-P. Mechanism of cell penetration by permeabilization of late endosomes: Interplay between a multivalent TAT peptide and bis(monoacylglycerol)phosphate. Cell Chem. Biol. (2020, in press). 21. Allen, J.; Najjar, K.; Erazo-Oliveras, A.; Kondow-McConaghy, H. M.; Brock, D. J.; Graham, K.; Hager, E. C.; Marschall, A. L. J.; Dubel, S.; Juliano, R. L.; Pellois, J.-P. Cytosolic delivery of macromolecules in live human cells using the combined endosomal escape activities of a small molecule and cell penetrating peptides. ACS Chem. Biol. 14, 2641–2651 (2019). 20. Arora, M.; Ganugula, R.; Kumar, N.; Kaur, G.; Pellois, J.-P.; Garg, P.; Kumar, M. Next-generation noncompetitive nanosystems based on gambogic acid: In silico identification of transferrin receptor binding sites, regulatory shelf stability, and their preliminary safety in healthy rodents. ACS Appl. Bio. Mater. 2, 3540–3550 (2019). 19. Park, G.; Brock, D. J.; Pellois, J.-P.; Gabbai, F. P. Heavy pnictogenium cations as transmembrane anion transporters in vesicles and erythrocytes. Chem. 5, 2215–2227 (2019). 18. Pellois, J.-P. Efficient and innocuous live-cell delivery: Making membrane barriers disappear to enable cellular biochemistry: How better cellular delivery tools can contribute to precise and quantitative cell biology Assays. Bioessays 41, e1900031 (2019). 17. Brock, D. J.; Kondow-McConaghy, H. M.; Hager, E. C.; Pellois, J.-P. Endosomal escape and cytosolic penetration of macromolecules mediated by synthetic delivery agents. Bioconjug. Chem. 30, 29–304 (2019). 16. Fang, Y.; Lian, X.; Huang, Y.; Fu, G.; Xiao, Z.; Wang, Q.; Nan. B.; Pellois, J.-P.; Zhou, H. C. Investigating subcellular compartment targeting effect of porous coordination cages for enhancing cancer nanotherapy. Small 14, e1802709 (2018). 15. Allen, J. K.; Brock, D. J.; Kondow-McConaghy, H. M.; Pellois, J.-P. Efficient delivery of macromolecules into human cells by improving the endosomal escape activity of cell-penetrating peptides: Lessons learned from dfTAT and its analogs. Biomolecules 8 (2018). 14. Brock, D. J.; Kustigian, L.; Jiang, M.; Graham, K.; Wang, T. Y.; Erazo-Oliveras, A.; Najjar, K.; Zhang. J.; Rye, H.; Pellois, J.-P. Efficient cell delivery mediated by lipid-specific endosomal escape of supercharged branched peptides. Traffic 19, 421–435 (2018). 13. Lian, X.; Huang ,Y.; Zhu, Y.; Fang, Y.; Zhao, R.; Joseph, E.; Li. J.; Pellois, J.-P.; Zhou, H. C. Enzyme–MOF nanoreactor activates nontoxic paracetamol for cancer therapy. Angew. Chem. Int. Ed. 57, 5725–5730 (2018). 12. Stubbendieck, R. M.; Brock, D. J.; Pellois, J.-P.; Gill, J. J.; Straight, P. D. Linearmycins are lytic membrane-targeting antibiotics. J. Antibiot. 71, 372–381 (2018). 11. Najjar, K.; Erazo-Oliveras, A.; Mosior, J. W.; Whitlock, M. J.; Rostane, I.; Cinclair, J. M.; Pellois, J.-P. Unlocking endosomal entrapment with supercharged arginine-rich peptides. Bioconjugation Chem. 28, 2932–2941 (2017). 10. Lian, X.; Erazo-Oliveras, A.; Pellois, J.-P.; Zhou, H. C. High efficiency and long-term intracellular activity of an enzymatic nanofactory based on metal-organic frameworks. Nat. Commun. 8, 2075 (2017). 9. Libardo, M. D.; Wang, T. Y.; Pellois, J.-P.; Angeles-Boza, A. M. How does membrane oxidation affect cell delivery and cell killing? Trends in Biotechnology 35, 686–690 (2017). 8. Wang, T. Y.; Libardo, M. D.; Angeles-Boza, A. M.; Pellois, J.-P. Membrane oxidation in cell delivery and cell killing applications. ACS Chem. Biol. 12, 1170–1182 (2017). 7. Wang, T. Y.; Pellois, J. P. Peptide translocation through the plasma membrane of human cells: Can oxidative stress be exploited to gain better intracellular access? Commun. Integr. Bio.l 9, e1205771 (2016). 6. Najjar, K.; Erazo-Oliveras, A.; Brock, D. J.; Wang, T. Y.; Pellois, J.-P. An L- to D-amino acid conversion in an endosomolytic analog of the cell-penetrating peptide TAT influences proteolytic stability, endocytic uptake, and eEndosomal escape. J. Biol. Chem. 292, 847–861 (2017). 5. Robison, A. D.; Sun, S.; Poyton, M. F.; Johnson, G. A.; Pellois, J.-P.; Jungwirth, P.; Vazdar, M.; Cremer, P. S. Polyarginine interacts more strongly and cooperatively than polylysine with phospholipid bilayers. J. Phys. Chem. B 120, 9287–9296 (2016). 4. Erazo-Oliveras, A.; Najjar, K.; Truong, D.; Wang, T. Y.; Brock, D. J; Prater, A. R.; Pellois, J.-P. The late endosome and its anionic lipid BMP act as gateways for the efficient cytosolic access of the cell-penetrating peptide dfTAT. Cell Chem. Biol. 23, 598–607 (2016). 3. Wang, T. Y.; Sun, Y.; Muthukrishnan, N.; Erazo-Oliveras, A.; Najjar, K.; Pellois, J.-P. Membrane oxidation enables the cytosolic Entry of polyarginine cell-penetrating peptides. J. Biol. Chem. 291, 7902–7914 (2016). 2. Patterson, J. L.; Arenas-Gamboa, A. M.; Wang, T.-Y.; Hsiao, H.-C.; Howell, D. W.; Pellois, J.-P.; Bondos, S. Materials composed of the DrosophilaHox protein Ultrabithorax are biocompatible and nonimmunogenic. J. Biomed. Mater. Res. A 103, 1546–1553 (2015). 1. Najjar, K.; Erazo-Oliveras, A.; Pellois, J.-P. Delivery of proteins, peptides or cell-impermeable small molecules into live cells by incubation with the endosomolytic reagent dfTAT. J. Vis. Exp. (2015).

CURRENT SUPPORT NIH-GMS R01GM110137 Pellois, J.-P. (PI) 2019–2023 “Mechanisms and optimization of endosomal escape for cell delivery applications” NIH-GMS 1R01GM127723 Pellois, J.-P. (Co-PI); Cho, J.-H. (PI) 2018–2023 “Structure and functional dynamics of virus-host protein interactions” CPRIT Pellois, J.-P. (PI) 2019–2021 “Probing mechanisms of exosomal signaling in cancer cell-to-cell communication” COMPLETED SUPPORT (2015– present) NIH-GMS R01GM110137 Pellois, J.-P. (PI) 2015–2019 “Mechanisms and optimization of endosomal escape for cell delivery applications” STRP Pellois, J.-P.; Gabbai, F. (PI) 2019–2020 “Lewis Acidic Main Group Cations as Anion Transporters” TAMU T3 02-246439 Pellois, J.-P. (Collaborator); Cho, J.-H. (PI); Lockless, S. (PI) 2019 “Targeting oncogenic protein-protein interactions” Agrilife Research, Crop Pellois, J.-P. (Collaborator); Thomson, M. (PI) 2017–2019 Improvement Program “Integrating Association Mapping and High-Throughput CRISPR Editing into Model-based ideotype Breeding”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Collaborator Silicon Valley Advantage for Commercialization of Delivery Agents 2016–present Member Advisory Council, Feldan Bio, Inc. 2014–2019 Collaborator Lynntech, Inc. 2014–2019 Guest Editor Biomolecules, Special issue: Cell-Penetrating Peptides 2018

DEPARTMENT AND SYSTEM SERVICE (2015–present) Associate Head Graduate Program BCBP 2019–present COALS Representative Council of Principal Investigators COALS 2019–present Member Promotion and Tenure Committee COALS 2019–present Judge Undergraduate Research Scholars Symposium, LAUNCH TAMU 2019 Co-Chair Innovation and Discovery Committee, University Vision 2030 TAMU 2018–2019 Chair Graduate Recruiting and Admissions Committee BCBP 2013–2016 Reviewer Astronaut Fellowship TAMU 2014–2016 Member Development Committee, Executive Committee, Head Search BCBP Various Committee, Promotion and Tenure Committee, Graduate Recruiting and Admissions Committee, Undergraduate Program Committee Member Faculty and Staff Interaction Team, Advanced Center TAMU 2012–present

COURSES TAUGHT (2015–present) BICH 689 Oral Communication 1 cr. 2020 BICH 440 Biochemistry I 3 cr. 2007–present BICH 491/691 Research Variable 2006–present BICH 689 Membrane Biology and Biochemistry 1 cr. 2016

Stephanie Perez Lecturer | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Texas A&M University with T. D. Meek 2014–2018 Ph.D. Texas A&M University with G. Reinhart 2012 B.S. Texas Tech University 2000

PROFESSIONAL APPOINTMENTS Lecturer Biochemistry and Biophysics Texas A&M University 2013–present Lecturer Biology Blinn College 2012–2013

COURSES TAUGHT (2015–present) BICH 410 Comprehensive Biochemistry I 3 cr. 2018-present BICH 411 Comprehensive Biochemistry II 3 cr. 2018-present BICH 432 Molecular Genetics Laboratory 2 cr. 2018-present GENE 432 Molecular Genetics Laboratory 2 cr. 2018-present

Elizabeth J. Pishko Lecturer | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Structure/Function, Boston College 1995–1997 Postdoctoral Chemistry, University of Texas at Austin 1993–1995 Ph.D. Biochemistry, University of Texas at Austin with J. D. Robertus 1993 B.S. Chemistry, University of Missouri at Columbia 1988

PROFESSIONAL APPOINTMENTS Lecturer Biochemistry and Biophysics Texas A&M University 2016–present Laboratory Instructor Human Anatomy and Physiology Texas A&M University 2014–2016 Lecturer Biochemistry and Biophysics Texas A&M University 2008–2011 Senior Project Associate Pennsylvania State University 2001–2003 Lecturer Biochemistry and Biophysics Texas A&M University 2000–2001

COURSES TAUGHT (2015–present) GENE 312 Comprehensive Genetics Laboratory 1 cr. 2016–present BIOL 319 Integrated Human Anatomy and Physiology I 4 cr. 2014–2016 BIOL 320 Integrated Human Anatomy and Physiology II 4 cr. 2014–2016 Michael Polymenis Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral MGH Cancer Center, Harvard Medical School with E. Schmidt 1999 Ph.D. Tufts University with D. Stollar 1994 Pharm. D. University of Patras, Greece 1988

PROFESSIONAL APPOINTMENTS Professor Biochemistry and Biophysics Texas A&M University 2015–present Visiting Professor Biosciences University of Texas 2018 Associate Professor Biochemistry and Biophysics Texas A&M University 2005–2015 Visiting Professor Buck Institute for Research on Aging 2012 Assistant Professor Biochemistry and Biophysics Texas A&M University 1999–2005

PEER-REVIEWED PUBLICATIONS (2015–present) 53. Polymenis, M. Ribosomal proteins: Mutant phenotypes by the numbers and associated gene expression changes. Open Biol. 10, 200114 (2020). 52. Zou, K.; Zheng, J.; Rouskin, S.; Dervishi, K.; McCormick, M. A.; Sasikumar, A.; Deng, C.; Chen, Z.; Kaeberlein, M.; Brem, R. B.; Polymenis, M.; Kennedy, B. K.; Weissman, J. S.; Ouyang, Q.; Li, H. Lifespan extension by glucose restriction in budding yeast is mediated by methionine restriction and requires elevated proteasome activity. Science Adv. 6, eaba1306 (2020). 51. Maitra, N.; He, C.; Blank, H. M.; Tsuchiya, M.; Schilling, B.; Kaeberlein, M.; Aramayo, R.; Kennedy, B. K.; Polymenis, M. Translational control of one-carbon metabolism underpins ribosomal protein phenotypes in cell division and longevity. Elife 20, 9:e53127 (2020). 50. Bermudez, R. M.; Wu, P. I.; Callerame, D.; Hammer, S.; Hu, J. C.; Polymenis, M. Phenotypic associations among cell cycle genes in Saccharomyces cerevisiae. G3 10, 2345–2351 (2020). 49. Blank, H. M.; Papoulas, O.; Maitra, N.; Garge, R.; Kennedy, B. K.; Schilling, B.; Marcotte, E. M.; Polymenis, M. Abundances of transcripts, proteins, and metabolites in the cell cycle of budding yeast reveal coordinate control of lipid metabolism. Mol. Biol. Cell 31, 1069–1084 (2020). 48. Maitra, N.; Anandhakumar, J.; Blank, H. M.; Kaplan, C. D.; Polymenis, M. Perturbations of transcription and gene expression-associated processes alter distribution of cell size values in Saccharomyces cerevisiae. G3 9, 239–250 (2019). 47. Blank, H. M.; Callahan, M.; Pistikopoulos, I. P. E.; Polymenis, A. O.; Polymenis, M. Scaling of G1 duration with population doubling time by a cyclin in yeast. Genetics 210, 895–906 (2018). 46. Huang, J.; Mousley, C. J.; Dacquay, L.; Maitra, N.; Drin, G.; He, C.; Ridgway, N. D.; Tripathi, A.; Kennedy, M.; Kennedy, B. K.; Baetz, K.; Polymenis, M.; Bankaitis, V. A. A lipid transfer protein signaling axis exerts dual control of cell cycle and membrane trafficking systems. Dev. Cell 44, 378–391 (2018). 45. Polymenis, M. Proteins associated with the doubling time of the NCI-60 cancer cell lines. Cell Div. 12, 6 (2017). 44. Polymenis, M.; Kennedy, B. K. Unbalanced growth, senescence and aging. Adv. Exp. Med. Biol. 1002, 189–208 (2017). 43. Aramayo, R. ; Polymenis, M. Ribosome profiling the cell cycle: Lessons and challenges. Curr. Genet. 63, 959–964 (2017). 42. Blank, H.; Maitra, N.; Polymenis, M. Lipid biosynthesis: When the cell cycle meets protein synthesis? Cell Cycle 16, 905–906 (2017). 41. Mohler, K.; Mann, R.; Bullwinkle, T. J.; Hopkins, K.; Hwang, L.; Reynolds, N. M.; Gassaway, B.; Aerni, H. R.; Rinehart, J.; Polymenis, M.; Faull, K.; Ibba, M. Editing of misaminoacylated tRNA controls the sensitivity of amino acid stress responses in Saccharomyces cerevisiae. Nuc. Acids Res. 45, 3985–3996 (2017). 40. Blank, H. M.; Perez, R.; He, C.; Maitra, N.; Metz, R.; Hill, J.; Lin, Y.; Johnson, C. D.; Bankaitis, V. A.; Kennedy, B. K.; Aramayo, R.; Polymenis, M. Translational control of lipogenic enzymes in the cell cycle of synchronous, growing yeast cells. EMBO J 36, 487–502 (2017). 39. Polymenis, M.; Aramayo, R. Translate to divide: Control of the cell cycle by protein synthesis. Microbial Cell 2, 94–104 (2015).

CURRENT SUPPORT NIH #R01-GM123139 Polymenis, M. (PI) 2017–2021 “Coupling of Protein Synthesis with Cell Division”

COMPLETED SUPPORT (2015–present) NIH Polymenis, M. (PI) 2018–2019 #R01-GM123139-02S1 “Coupling of Protein Synthesis with Cell Division” TAMU Genomics Initiative Polymenis, M. (PI) 2014–2015 “Targets of translational control that link protein synthesis with initiation of division”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Editor-in-Chief Current Genetics 2021–present Editorial Board Microbial Cell 2014–present Editorial Board PLoS One 2009–present Associate Editor Current Genetics 2020 Grant Mail Review The European Research Council 2020 Grant Mail Review The Netherlands Organization for Scientific Research 2018 NIH Panel Member CSRS study section 2017 Grant Mail Review State of Louisiana Board of Regents 2016 NSF Panel Member ENG, BIO, HER Various Grant Mail Review Austrian Science Fund Various

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Departmental Self-Study Review Committee BCBP 2020–present Member Advisory Committee BCBP 2020–present Member Post-Tenure Review Committee BCBP 2019–present Member Undergraduate Curriculum Committee GENE 2019–present Member Executive Committee GENE 2017–present Member Promotion and Tenure Committee BCBP 2016–present Member Executive Committee BCBP 2015–2018 Member Undergraduate Program Committee BCBP 2014–2017

COURSES TAUGHT (2015–present) BICH 411 Comprehensive Biochemistry II 3 cr. 2012–present BICH/GENE 491/691 Research Variable 2000–present BICH/GENE 101 Perspectives in Biochemistry and Genetics 1 cr. 2015–2017 GENE 608 Critical Analysis of the Genetics Literature 2 cr. 2004–2017 Michelle Henderson Pozzi Senior Lecturer | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Molecular Genetics, Texas A&M University 2010–2011 Ph.D. Biochemistry and Biophysics, Texas A&M 2009 University B.S. Chemistry, Sam Houston State University 2004

PROFESSIONAL APPOINTMENTS Senior Lecturer Biochemistry and Biophysics Texas A&M University 2018–present Lecturer Biochemistry and Biophysics Texas A&M University 2010–2018

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member College of Agriculture and Life Sciences Willie Mae Harris TAMU 2020 Fellowship Review Committee Member College of Agriculture and Life Sciences No Grade Review TAMU 2019–present Panel Mentor Student Research Week-Mentor Poster Group TAMU 2016–2018 Presentation/Oral Group Presentation Mentor Teachers Scholars Launch: Capstone Mentor TAMU 2016–present Mentor Teaching as Research (TAR) Mentor; Center for the TAMU 2015 Integration of Research, Teaching Learning, Faculty Sponsor for Amanda Tindall Mentor Academy for Future Faculty (AFF) Mentor for Biochemistry BCBP 2014–present graduate students

COURSES TAUGHT (2015–present) BICH 410 Comprehensive Biochemistry I 3 cr. 2010–present BICH 411 Comprehensive Biochemistry II 3 cr. 2015–present BICH/GENE 432 Laboratory in Molecular Genetics 2 cr. 2012–2018 BICH 485 Direct Studies (Honors course Teachers Scholars Launch Capstone) 1 cr. 2020 UGST 285 Direct Studies (Honors course Teachers Scholars Launch Capstone) 1 cr. 2015 Frank M. Raushel Distinguished Professor | Department of Chemistry Powell Chair of Science Director | Center for Biological Nuclear Magnetic Resonance Professor | Biochemistry and Biophysics

EDUCATION Postdoctoral Pennsylvania State University 1980 Ph.D. University of Wisconsin-Madison 1976 B.S. St. Thomas University 1972

PROFESSIONAL APPOINTMENTS Powell Chair of Science Texas A&M University 2016–present Distinguished Professor Chemistry Texas A&M University 2010–present Director Center for Biological Nuclear Magnetic Texas A&M University 2008–present Resonance Professor Biochemistry and Biophysics Texas A&M University 1989–present Davidson Professor of Science Texas A&M University 2004–2016 Professor Chemistry Texas A&M University 1989–2010 Mercator Professor University of Regensburg 2008 Visiting Professor Enzyme Institute University of Wisconsin 1992–1993 Associate Professor Chemistry Texas A&M University 1986–1989 Biochemistry and Biophysics Assistant Professor Chemistry Texas A&M University 1980–1986

PEER-REVIEWED PUBLICATIONS (2015–present) 340. Bigley, A. N.; Narindoshvili, T.; Raushel, F. M. A Chemo-Enzymatic Synthesis of the (RP)-Isomer of the Antiviral Prodrug Remdesivir. Biochemistry 59, 3038–3043 (2020). 339. Mabanglo, M. F.; Huddleston, J. P.; Mukherjee, K.; Taylor, Z. W.; Raushel, F. M. Structure and Reaction Mechanism of YcjR, an Epimerase that Facilitates the Interconversion of D-Gulosides to D-Glucosides in Escherichia coli. Biochemistry 59, 2069–2077 (2020). 338. Huddleston, J. P.; Raushel, F. M. Functional Characterization of Cj1427, a Unique Ping-Pong Dehydrogenase Responsible for the Oxidation of GDP-D-glycero¬-α-D-manno-heptose in Campylobacter jejuni. Biochemistry 59, 1328–1337 (2020). 337. Huddleston, J. P.; Anderson, T. K.; Spencer, K. D.; Thoden, J. B.; Raushel, F. M.; Holden, H. M. Structural Analysis of Cj1427, an Essential NAD-dependent Dehydrogenase for the Biosynthesis of the Heptose Residues in the Capsular Polysaccharides of Campylobacter jejuni. Biochemistry 59, 1314–1327 (2020). 336. Bigley, A. N.; Xiang, D. F.; Narindoshvili, T.; Raushel, F. M. Stereoselective Formation of Multiple Reaction Products by the Phosphotriesterase from Sphingobium sp. TCM1. Biochemistry 59, 3893–3902 (2020). 335. Huddleston, J. P.; Raushel, F. M. Biosynthesis of GDP-D-glycero-α-D-manno-heptose for the Capsular Polysaccharide of Campylobacter jejuni. Biochemistry 58, 3893–3902 (2019). 334. Hogancamp, T.; Cory, S. M.; Barondeau, D. P.; Raushel, F. M. Structure and Chemical Reaction Mechanism of LigU, an Enzyme that Catalyzes an Allylic Rearrangement in the Bacterial Degradation of Lignin. Biochemistry 58, 3494–3503 (2019). 333. Huddleston, J. P.; Raushel, F. M. Functional Characterization of YdjH, a Sugar Kinase of Unknown Specificity in Escherichia coli K12. Biochemistry 58, 3354–3364 (2019). 332. Huddleston, J. P.; Thoden, J. B.; Dopkins, B. J.; Narindoshvili, T.; Fose, B. J.; Holden, H. M.; Raushel, F.M. Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity in Escherichia coli K12. Biochemistry 58, 3340–3353 (2019). 331. Bigley, A. N.; Desormeaux, E.; Xiang, D. F.; Bae, S. Y.; Harvey, S. P.; Raushel, F. M. Overcoming the Challenges of Enzyme Evolution to Adapt Phosphotriesterase for V-agent Decontamination. Biochemistry 58, 2039–2053 (2019). 330. Zhang, P.; Liu, E. J.; Tsao, C.; Kasten, S. A.; Boeri, M. V.; Dao, T. L.; DeBus, S. J.; Cadieux, C. L.; Otto, T. C.; Cerasoli, D. M.; Chen, Y.; Jain, P.; Sun, F.; Li, W.; Hung, H.-C.; Yuan, Z.; Ma, J.; Bigley, A. N.; Raushel F. M.; Jiang, S. Nanoscavenger Provides Long-Term Prophylactic Protection Against Nerve Agents in Rodents. Sci. Transl. Med. 11, eaau7091 (2019). 329. Hogancamp, T.; Mabanglo, M.; Raushel, F. M. Structure and Reaction Mechanism of the LigJ Hydratase: An Enzyme Critical for the Bacterial Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway. Biochemistry 57, 5841–5850 (2018). 328. Taylor, Z. W.; Brown, H. A.; Narindoshvili, T.; Wenzel, C. Q.; Szymanski, C. M.; Holden, H. M.; Raushel, F. M. Discovery of a Glutamine Kinase Required for the Biosynthesis of the O-Methyl Phosphoramidate Modifications Found in the Capsular Polysaccharides of Campylobacter jejuni. J. Am. Chem. Soc. 139, 9463–9466 (2017). 327. Mabanglo, M. F.; Xiang, D. F.; Bigley, A. N.; Raushel, F. M. Structure of a Novel Phosphotriesterase from Sphingobium sp. TCM1; A Familiar Binuclear Metal Center Embedded in a 7-Bladed β-Propeller Protein Fold. Biochemistry 55, 3963–3974 (2016). 326. Vladimirova, A.; Patskovsky, Y.; Fedorov, A. A.; Fedorov, E. V.; Bonnano, J. B.; Toro, R.; Hillerich, B.; Seidel, R.; Richards, N. G. J.; Almo, S. C.; Raushel, F. M. Substrate Distortion and the Catalytic Reaction Mechanism of 5-Carboxyvanillate Decarboxylase J. Am. Chem. Soc. 138, 826–836 (2016). 325. Bigley, A. N.; Mabanglo, M.; Harvey, S. P. ; Raushel, F. M. Variants of Phosphotriesterase for the Enhanced Detoxification of Chemical Warfare Agent VR. Biochemistry 54, 5502–5512 (2015).

CURRENT SUPPORT NIH GM 122825 Raushel, F. M. 2017-2021 “Novel Biochemical Pathways for the Metabolism of Carbohydrates in the Human Microbiome” COMPLETED SUPPORT (2015–present) Robert A. Welch Raushel, F. M. 2017–2020 Foundation (A-840) “Enzyme Reaction Mechanisms” NIH (GM116894) Raushel, F. M. 2017–2020 “Enzymatic Hydrolysis of Organophosphate Esters”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Editorial Board Archives of Biochemistry & Biophysics 2005–present Editorial Advisory Board Biochemistry 2000–2017 Gordon Hammes Lectureship ACS Biochemistry 2015 Editorial Board Bioorganic Chemistry 1998–present Mollie Megan Reynolds Senior Lecturer | Department of Biochemistry and Biophysics

EDUCATION Ph.D. Genetics, Texas A&M University with M. Belfort 2003–2010 B.S. Genetics, Texas A&M University 1994–1999

PROFESSIONAL APPOINTMENTS Senior Lecturer Biochemistry and Biophysics Texas A&M University 2016–present Lecturer Biochemistry and Biophysics Texas A&M University 2009–2016

DEPARTMENT AND SYSTEM SERVICE (2015–present) Instructor/Mentor First-Year Program AGLS 2020 Member Hiring Committee for Lab (GENE) TAMU 2016 Mentor Academy of Future Faculty (Genetics Graduate Students/Teaching Assistants) TAMU 2016

COURSES TAUGHT (2015–present) GENE 301 Comprehensive Genetics 3 cr. 2016–present GENE 312 Comprehensive Genetics Laboratory 1 cr. 2015–2016 GENE 301 Comprehensive Genetics (Lab) 1 cr. 2009-2015 GENE 302 Principles of Genetics (Lab) 1 cr. 2009–2015 Hays S. Rye Associate Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Yale University Medical School with A. Horwich 1995–2000 Ph.D. University of California at Berkeley with A. Glazer 1995 B.A. Rice University with F. Rudolph 1989

PROFESSIONAL APPOINTMENTS Associate Professor Biochemistry and Biophysics Texas A&M University 2009–present Assistant Professor Molecular Biology Princeton University 2000–2009

PEER-REVIEWED PUBLICATIONS (2015–present) 35. Shoup, D.; Thapa, R.; Puchalla, J.; Rye, H. S. Development and applications of multi-color burst analysis spectroscopy. Biophys. J. (2020, in revision). 34. Naqvi, M.; Avellandeda, M. J.; Roth, A.; Koers, E.; Sunderlikova, V.; Kramer, G.; Rye, H. S.; Tans, S. J. GroEL-mediated acceleration of protein folding by enhanced collapse (2020, under review). 33. Brock, D.; Kondow-McConaghy, H.; Allen, J.; Brkljača, Z.; Kustigian, L.; Jiang, M.; Zhang, J.; Rye, H. S.; Vazdar, M.; Pellois, J.-P. Mechanism of cell penetration by permeabilization of late endosomes: Interplay between a multivalent TAT peptide and bis(monoacylglycerol)phosphate. Cell Chem. Biol. 27, 1–12 (2018). 32. Brock, D. J.; Kustigian, L.; Jiang, M.; Graham, K.; Wang, T.-Y.; Erazo-Oliveras, A.; Najjar, K.; Zhang, J.; Rye, H.; Pellois, J.-P. Efficient cell delivery mediated by lipid-specific endosomal escape of supercharged branched peptides. Traffic 19, 421–435 (2018). 31. Weaver, J.; Puchalla, J.; Rye, H. S. GroEL actively stimulates folding of the endogenous substrate protein PepQ. Nat. Commun. 8, 15934 (2017). 30. Brooks, A.; Shoup, D.; Kustigian, L.; Puchalla, J.; Carr, C. M.; Rye, H. S. Single particle fluorescence burst analysis of Epsin induced membrane fission. PLoS One 10, e0119563 (2015).

CURRENT SUPPORT NIH #1R01-GM134063 Rye, H. S. 2019–2023 “Mechanism of protein aggregate recognition and disassembly by molecular chaperones” NIH #1R01-GM11405 Rye, H. S. 2015–2021 “Mechanism of Membrane Fission at the Recycling Endosome” NIH Admin. Supplement Rye, H. S. 2018–2019 #1R01-GM114405 NIH Admin. Supplement Rye, H. S. 2016 #1R01-GM114405 NIH #2R01-GM114405 Rye, H. S. 2010–2015 “Mechanism of protein folding intermediate disaggregation by molecular chaperones” (renewal)

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Review Editor Frontiers in Molecular Biosciences 2014–present Ad hoc peer reviewer Various scientific journals 2000–present Ad hoc peer reviewer NIH Membrane Biology and Protein Processing 2015, 2017

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Facilities Renovation Committee BCBP 2020–present Member COVID Safety Committee BCBP 2020–present Chair Biophysics Graduate Program Development Committee BCBP 2020–present Member Departmental Executive Committee BCBP 2019–present Chair Outreach and Recruitment Committee BCBP 2019–2020 Member University Vision 2030 Steering Committee TAMU 2016–2020 Member University Radiation Safety Committee TAMU 2015–2019 Member Common Use Equipment Committee BCBP 2014–2019 Member Department Head Search Committee BCBP 2017–2018 Member Graduate Admissions Committee BCBP 2010–2017 Member Faculty Search Committee BCBP 2016

COURSES TAUGHT (2015–present) BICH 603 Biochemistry and Biophysics 3 cr. 2010–present BICH 674 Protein Structure, Function and Folding (Journal Club) 1 cr. 2010–present BICH 491/691 Research Variable 2009–present BICH 681 Seminar 1 cr. 2019 BICH 624 Enzymes, Proteins and Nucleic Acids 3 cr. 2017 BICH 489 Special Topics in Physics Biochemistry 1 cr. 2015–2016

James Sacchettini Professor | Department of Biochemistry and Biophysics R. J. Wolfe-Welch Endowed Chair in Science

EDUCATION Ph.D. Washington University with J. Gordon and L. Banaszak 1987 B.S. St. Louis University 1980

PROFESSIONAL APPOINTMENTS Director Center for Structural Biology Texas A&M University 2001–present Professor Biochemistry and Biophysics Texas A&M University 1997–present Chemistry Wolfe-Welch Chair The Robert A Welch Foundation Texas A&M University 1996–present Professor Albert B. Alkek Institute of Biosciences Texas A&M University 1998–2014 and Technology Assistant Professor Biochemistry Albert Einstein College of 1990–1996 Medicine Research Assistant Professor Biochemistry and Molecular Biophysics Washington University School 1987–1989 of Medicine

PEER-REVIEWED PUBLICATIONS (2015–present) 325. Burke, C.; Jankute, M.; Moynihan, P.; Gonzalez Del Rio, R.; Li, X.; Esquivias, J.; Lelièvre, J.; Cox, J. A. G.; Sacchettini, J.; Besra, G. S. Development of a novel secondary phenotypic screen to identify hits within the mycobacterial protein synthesis pipeline. FASEB Bioadv. 2, 600–612 (2020). 324. Rifat, D.; Li, S. Y.; Ioerger, T.; Shah, K.; Lanoix, J. P.; Lee, J.; Bashiri, G.; Sacchettini, J.; Nuermberger, E. Mutations in fbiD (Rv2983) as a novel determinant of resistance to pretomanid and delamanid in Mycobacterium tuberculosis. Antimicrob. Agents Chemother. AAC.01948-20 (2020). 323. Ingram, S. N.; Robbins, A. B.; Gillenwater, S. J.; Gresham, V.; Sacchettini, J. C.; Moreno, M. R. A low-cost, novel endoscopic repeated-access port for small animal research. MethodsX 7, 101049 (2020). 322. Khan, D.; Lee, D.; Gulten, G.; Aggarwal, A.; Wofford, J.; Krieger, I.; Tripathi, A.; Patrick, J. W.; Eckert, D. M.; Laganowsky, A.; Sacchettini, J.; Lindahl, P.; Bankaitis, V. A. A Sec14-like phosphatidylinositol transfer protein paralog defines a novel class of heme-binding proteins. Elife 9, e57081 (2020). 321. Lopez Quezada, L.; Smith, R.; Lupoli, T. J.; Edoo, Z.; Li, X.; Gold, B.; Roberts, J.; Ling, Y.; Park, S. W.; Nguyen, Q.; Schoenen, F. J.; Li, K.; Hugonnet, J. E.; Arthur, M.; Sacchettini, J. C.; Nathan, C.; Aubé, J. Activity-based protein profiling reveals that cephalosporins selectively active on non-replicating Mycobacterium tuberculosis bind multiple protein families and spare peptidoglycan transpeptidases. Front Microbiol. 11, 1248 (2020). 320. Krieger, I. V.; Kuznetsov, V.; Chang, J. Y.; Zhang, J.; Moussa, S. H.; Young, R. F.; Sacchettini, J. C. The structural basis of T4 phage lysis control: DNA as the signal for lysis inhibition. J. Mol. Biol. 432, 4623–4636 (2020). 319. Guthrie, L. M.; Soma, S.; Yuan, S.; Silva, A.; Zulkifli, M.; Snavely, T. C.; Greene, H. F.; Nunez, E.; Lynch, B.; De Ville, C.; Shanbhag, V.; Lopez, F. R.; Acharya, A.; Petris, M. J.; Kim, B. E.; Gohil, V. M.; Sacchettini, J. C. Elesclomol alleviates Menkes pathology and mortality by escorting Cu to cuproenzymes in mice. Science 368, 620– 625 (2020). 318. Jansen, R. S.; Mandyoli, L.; Hughes, R.; Wakabayashi, S.; Pinkham, J. T.; Selbach, B.; Guinn, K. M.; Rubin, E. J.; Sacchettini, J. C.; Rhee, K. Y. Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis. Nat. Commun. 11, 1960 (2020). 317. Taira, J.; Umei, T.; Inoue, K.; Kitamura, M.; Berenger, F.; Sacchettini, J. C.; Sakamoto, H.; Aoki, S. Improvement of the novel inhibitor for Mycobacterium enoyl-acyl carrier protein reductase (InhA): a structure-activity relationship study of KES4 assisted by in silico structure-based drug screening. J. Antibiot. 73, 372–381 (2020). 316. Sun, Q.; Li, X.; Perez, L. M.; Shi, W.; Zhang, Y.; Sacchettini, J. C. The molecular basis of pyrazinamide activity on Mycobacterium tuberculosis PanD. Nat. Commun. 11, 339 (2020). 315. Mosior, J.; Bourland, R.; Soma, S.; Nathan, C.; Sacchettini, J. Structural insights into phosphopantetheinyl hydrolase PptH from Mycobacterium tuberculosis. Protein Sci. 29, 744–757 (2020). 314. Tang, S.; Hicks, N. D.; Cheng, Y. S.; Silva, A.; Fortune, S. M.; Sacchettini, J. C. Structural and functional insight into the Mycobacterium tuberculosis protein PrpR reveals a novel type of transcription factor. Nucleic Acids Res. 47, 9934– 9949 (2019). 313. Dragset, M. S.; Ioerger, T. R.; Zhang, Y. J.; Mærk, M.; Ginbot, Z.; Sacchettini, J. C.; Flo, T. H.; Rubin, E. J.; Steigedal, M. Genome-wide phenotypic profiling identifies and categorizes genes required for mycobacterial low iron fitness. Sci. Rep. 9, 11394 (2019). 312. Carey, A. F.; Rock, J. M.; Krieger, I. V.; Chase, M. R.; Fernandez-Suarez, M.; Gagneux, S.; Sacchettini, J. C.; Ioerger, T. R.; Fortune, S. M. Correction: TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities. PLoS Pathog. 15, e1007846 (2019). 311. Brown, E. E.; Miller, A. K.; Krieger, I. V.; Otto, R. M.; Sacchettini, J. C.; Herman, J. K. A DNA-binding protein tunes septum placement during Bacillus subtilis sporulation. J. Bacteriol. 201, e00287-19 (2019). 310. Farhat, M. R.; Freschi, L.; Calderon, R.; Ioerger, T.; Snyder, M.; Meehan, C. J.; de Jong, B.; Rigouts, L.; Sloutsky, A.; Kaur, D.; Sunyaev, S.; van Soolingen, D.; Shendure, J.; Sacchettini, J.; Murray, M. GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions. Nat. Commun. 10, 2128 (2019). 309. Crespo, R. A.; Dang, Q.; Zhou, N. E.; Guthrie, L. M.; Snavely, T. C.; Dong, W.; Loesch, K. A.; Suzuki, T.; You, L.; Wang, W.; O’Malley, T.; Parish, T.; Olsen, D. B.; Sacchettini, J. C. Structure-guided drug design of 6-substituted adenosine analogues as potent inhibitors of Mycobacterium tuberculosis adenosine kinase. J. Med. Chem. 62, 4483– 4499 (2019). 308. Dixit, A.; Freschi, L.; Vargas, R.; Calderon, R.; Sacchettini, J.; Drobniewski, F.; Galea, J. T.; Contreras, C.; Yataco, R.; Zhang, Z.; Lecca, L.; Kolokotronis, S. O.; Mathema, B.; Farhat, M. R. Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting. Sci. Rep. 9, 5602 (2019). 307. Chen, Q.; Shah, K. N.; Zhang, F.; Salazar, A. J.; Shah, P. N.; Li, R.; Sacchettini, J. C.; Wooley, K. L.; Cannon, C. L. Minocycline and silver dual-loaded polyphosphoester-based nanoparticles for treatment of resistant Pseudomonas aeruginosa. Mol. Pharm. 16, 1606–1619 (2019). 306. Salazar, A. J.; Sherekar, M.; Tsai, J.; Sacchettini, J. C. R pyocin tail fiber structure reveals a receptor-binding domain with a lectin fold. PLoS One. 14, e0211432 (2019). 305. Ballinger, E.; Mosior, J.; Hartman, T.; Burns-Huang, K.; Gold, B.; Morris, R.; Goullieux, L.; Blanc, I.; Vaubourgeix, J.; Lagrange, S.; Fraisse, L.; Sans, S.; Couturier, C.; Bacqué, E.; Rhee, K.; Scarry, S. M.; Aube, J.; Yang, G.; Ouerfelli, O.; Schnappinger, D.; Ioerger, T. R.; Engelhart, C. A.; McConnell, J. A.; McAulay, K.; Fay, A.; Roubert, C.; Sacchettini, J*.; Nathan, C.* Opposing reactions in coenzyme A metabolism sensitize Mycobacterium tuberculosis to enzyme inhibition. Science 363, eaau8959 (2019). * Corresponding authors 304. Miller, B. K.; Hughes, R.; Ligon, L. S.; Rigel, N. W.; Malik, S.; Anjuwon-Foster, B. R.; Sacchettini, J. C.; Braunstein, M. Mycobacterium tuberculosis SatS is a chaperone for the SecA2 protein export pathway. Elife 8, e40063 (2019). 303. Daniel-Wayman, S.; Abate, G.; Barber, D. L.; Bermudez, L. E.; Coler, R. N.; Cynamon, M. H.; Daley, C. L.; Davidson, R. M.; Dick, T.; Floto, R. A.; Henkle, E.; Holland, S. M.; Jackson, M.; Lee, R. E.; Nuermberger, E. L.; Olivier, K. N.; Ordway, D. J.; Prevots, D. R.; Sacchettini, J. C.; Salfinger, M.; Sassetti, C. M.; Sizemore, C. F.; Winthrop, K. L.; Zelazny, A. M. Advancing translational science for pulmonary nontuberculous mycobacterial infections. A Road Map for Research. Am. J. Respir. Crit. Care Med. 199, 947–951 (2019). 302. Xia, Y.; Zhou, Y.; Carter, D. S.; McNeil, M. B.; Choi, W.; Halladay, J.; Berry, P. W.; Mao, W.; Hernandez, V.; O’Malley, T.; Korkegian, A.; Sunde, B.; Flint, L.; Woolhiser, L. K.; Scherman, M. S.; Gruppo, V.; Hastings, C.; Robertson, G. T.; Ioerger, T. R.; Sacchettini, J.; Tonge, P. J.; Lenaerts, A. J.; Parish, T.; Alley, M. Discovery of a cofactor-independent inhibitor of Mycobacterium tuberculosis InhA. Life Sci. Alliance 1, e201800025 (2018). 301. Ritterhaus, E. C.; Baek, S. H.; Krieger, I. V.; Nelson, S. J.; Cheng, Y. S.; Nambi, S.; Baker, R. E.; Leszyk, J. D.; Shaffer, S. A.; Sacchettini, J. C.; Sassetti, C. M. A lysine acetyltransferase contributes to the metabolic adaptation to hypoxia in Mycobacterium tuberculosis. Cell Chem. Biol. 25, 1495–1505 (2018). 300. Melief, E.; Kokoczka, R.; Files, M.; Bailey, M. A.; Alling, T.; Li, H.; Ahn, J.; Misquith, A.; Korkegian, A.; Roberts, D.; Sacchettini, J.; Parish, T. Construction of an overexpression library for Mycobacterium tuberculosis. Biol. Methods Protoc. 3, bpy009 (2018). 299. Ellenbarger, J. F.; Krieger, I. V.; Huang, H. L.; Gómez-Coca, S.; Ioerger, T. R.; Sacchettini, J. C.; Wheeler, S. E.; Dunbar, K. R. Anion-π interactions in computer-aided drug design: Modeling the inhibition of malate synthase by phenyl-diketo acids. J. Chem. Inf. Model 58, 2085–2091 (2018). 298. Shen, Q.; Bhatt, V. S.; Krieger, I.; Sacchettini, J. C.; Cho, J.-H. Structure-guided design of a potent peptide inhibitor targeting the interaction between CRK and ABL kinase. MedChemComm. 9, 519–524 (2018). 297. Blanc, L.; Sarathy, J. P.; Alvarez Cabrera, N.; O’Brien, P.; Dias-Freedman, I.; Mina, M.; Sacchettini, J.; Savic, R. M.; Gengenbacher, M.; Podell, B. K.; Prideaux, B.; Ioerger, T.; Dick, T.; Dartois, V. Impact of immunopathology on the antituberculous activity of pyrazinamide. J. Exp. Med. 215, 1975–1986 (2018). 296. Singh, S. B.; Odingo, J.; Bailey, M. A.; Sunde, B.; Korkegian, A.; O’Malley, T.; Ovechkina, Y.; Ioerger, T. R.; Sacchettini, J. C.; Young, K.; Olsen, D. B.; Parish, T. Identification of cyclic hexapeptides natural products with inhibitory potency against Mycobacterium tuberculosis. BMC Res. Notes 11, 416 (2018). 295. Ganley, J. G.; Carr, G.; Ioerger, T. R.; Sacchettini, J. C.; Clardy, J.; Derbyshire, E. R. Discovery of antimicrobial pipodepsipeptides produced by a Serratia sp. within mosquito microbiomes. ChemBioChem 19, 1590–1594 (2018). 294. Tiwari, D.; Park, S. W.; Essawy, M. M.; Dawadi, S.; Mason, A.; Nandakumar, M.; Zimmerman, M.; Mina, M.; Ho, H. P.; Engelhart, C. A.; Ioerger, T.; Sacchettini, J. C.; Rhee, K.; Ehrt, S.; Aldrich, C. C.; Dartois, V.; Schnappinger, D. Targeting protein biotinylation enhances tuberculosis chemotherapy. Sci. Transl. Med. 10, eaal1803 (2018). 293. Korkegian, A.; O’Malley, T.; Xia, Y.; Zhou, Y.; Carter, D. S.; Sunde, B.; Flint, L.; Thompson, D.; Ioerger, T. R.; Sacchettini, J.; Alley, M. R. K.; Parish, T. The 7-phenyl benzoxaborole series is active against Mycobacterium tuberculosis. 108, 96–98 (2018). 292. Murugesan, D.; Ray, P. C.; Bayliss, T.; Prosser, G. A.; Harrison, J. R.; Green, K.; Soares de Melo, C.; Feng, T. S.; Street, L. J.; Chibale, K.; Warner, D. F.; Mizrahi, V.; Epemolu, O.; Scullion, P.; Ellis, L.; Riley, J.; Shishikura, Y.; Ferguson, L.; Osuna-Cabello, M.; Read, K. D.; Green, S. R.; Lamprecht, D. A.; Finin, P. M.; Steyn, A. J. C.; Ioerger, T. R.; Sacchettini, J.; Rhee, K. Y.; Arora, K.; Barry, C. E. III; Wyatt, P. G.; Boshoff, H. I. M. 2-Mercapto- quinazolinones as inhibitors of type II NADH dehydrogenase and Mycobacterium tuberculosis: Structure-activity relationships, mechanism of action and absorption, distribution, metabolism, and excretion characterization. ACS Infec. Dis. 4, 954–969 (2018). 291. Carey, A. F.; Rock, J. M.; Krieger, I. V.; Chase, M. R.; Fernandez-Suarez, M.; Gagneux, S.; Sacchettini, J. C.; Ioerger, T. R.; Fortune, S. M. TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities. PLoS Pathog. 14, e1006939 (2018). 290. Negri, A.; Javidnia, P.; Mu, R.; Zhang, X.; Vendome, J.; Gold, B.; Roberts, J.; Barman, D.; Ioerger, T.; Sacchettini, J. C.; Jiang, X.; Burns-Huang, K.; Warrier, T.; Ling, Y.; Warren, J. D.; Oren, D. A.; Beuming, T.; Wang, H.; Wu, J.; Li, H.; Rhee, K. Y.; Nathan, C. F.; Liu, G.; Somersan-Karakaya, S. Identification of a mycothiol-dependent nitroreductase from Mycobacterium tuberculosis. ACS Infect. Dis. (2018). 289. Lehmann, J.; Cheng, T. Y.; Aggarwal, A.; Park, A. S.; Zeiler, E.; Raju, R. M.; Akopian, T.; Kandror, O.; Bach, N. C.; Sacchettini, J. C.; Moody, D. B.; Rubin, E. J.; Sieber, S. A. An antibacterial β-lactone kills Mycobacterium tuberculosis by infiltrating mycolic acid biosynthesis. Angew. Chem. Int. Ed. 57, 348–535 (2018). 288. Chandrasekera, N. S.; Berube, B. J.; Shetye, G.; Chettiar, S.; O’Malley, T.; Manning, A.; Flint, L.; Awasthi, D.; Ioerger, T. R.; Sacchettini, J.; Masquelin, T.; Hipskind, P. A.; Odingo, J.; Parish, T. Improved phenoxyalkylbenzimidazoles with activity against Mycobacterium tuberculosis appear to target QcrB. ACS Infect. Dis. 3, 898–916 (2017). 287. Yang, K.; Chang, J. Y.; Cui, Z.; Li, X.; Meng, R.; Duan, L.; Thongchol, J.; Jakana, J.; Huwe, C. M.; Sacchettini, J. C.; Zhang, J. Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis. Nucleic Acids Res. 45, 10884–10894 (2017). 286. Taira, J.; Morita, K.; Kawashima, S.; Umei, T.; Baba, H.; Maruoka, T.; Komatsu, H.; Sakamoto, H.; Sacchettini, J. C.; Aoki, S. Identification of a novel class of small compounds with anti-tuberculosis activity by in silico structure-based drug screening. J. Antibiot. 70, 1057–1064 (2017). 285. Yadon, A. N.; Maharaj, K.; Adamson, J. H.; Lai, Y. P.; Sacchettini, J. C.; Ioerger, T. R.; Rubin, E. J.; Pym, A. S. A comprehensive characterization of PncA polymorphisms that confer resistance to pyrazinamide. Nat. Commun. 8, 588 (2017). 284. Thapa, H. R.; Tang, S.; Sacchettini, J. C.; Devarenne, T. P. Tetraterpene synthase substrate and product specificity in the green microalga Botryococcus braunii Race L. ACS Chem. Biol. 12, 2408–2416 (2017). 283. Pham, T. V.; Murkin, A. S.; Moynihan, M. M.; Harris, L.; Tyler, P. C.; Shetty, N.; Sacchettini, J. C.; Huang, H. L.; Meek, T. D. Mechanism-based inactivator of isocitrate lyases 1 and 2 from Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 114, 7617–7622 (2017). 282. Patel, N.; O’Malley, T.; Zhang, Y. K.; Xia, Y.; Sunde, B.; Flint, L.; Korkegian, A.; Ioerger, T. R.; Sacchettini, J.; Alley, M. R. K.; Parish, T. A novel 6-benzyl ether benzoxaborole is active against Mycobacterium tuberculosis in vitro. Antimicrob. Agents Chemother. 61 (2017). 281. Aggarwal, A.; Parai, M. K.; Shetty, N.; Wallis, D.; Woolhiser, L.; Hastings, C.; Dutta, N. K.; Galaviz, S.; Dhakal, R. C.; Shrestha, R.; Wakabayashi, S.; Walpole, C.; Matthews, D.; Floyd, D.; Scullion, P.; Riley, J.; Epemolu, O.; Norval, S.; Snavely, T.; Robertson, G. T.; Rubin, E. J.; Ioerger, T. R.; Siregel, F. A.; van der Merwe, R.; van Helden, P. D.; Keller, P.; Böttger, E. C.; Karakousis, P. C.; Lenaerts, A. J.; Sacchettini, J. C. Development of a Nnovel lead that targets M. tuberculosis polyketide synthase 13. Cell 170, 249–259 (2017). 280. Perkowski, E. F.; Zulauf, K. E.; Weerakoon, D.; Hayden, J. D.; Ioerger, T. R.; Oreper, G.; Gomez, S. M.; Sacchettini, J. C.; Braunstein, M. Erratum for Perkowski et al., The EXIT strategy: An approach for identifying bacterial proteins exported during host infection. MBio. 8 (2017). 279. Perkowski, E. F.; Zulauf, K. E.; Weerakoon, D.; Hayden, J. D.; Ioerger, T. R.; Oreper, G.; Gomez, S. M.; Sacchettini, J. C.; Braunstein, M. The EXIT strategy: An approach for identifying bacterial proteins exported during host infection. MBio. 8 (2017). 278. Puckett, S.; Trujillo, C.; Wang, Z.; Eoh, H.; Ioerger, T. R.; Krieger, I.; Sacchettini, J.; Schnappinger, D.; Rhee, K. Y.; Ehrt, S. Glyoxylate detoxification is an essential function of malate synthase required for carbon assimilation in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 114, e2225–e2232 (2017). 277. Gomez, J. E.; Kaufmann-Malaga, B. B.; Wivagg, C. N.; Kim, P. B.; Silvis, M. R.; Renedo, N.; Ieorger, R. T.; Ahmand, R.; Livny, J.; Fishbein, S.; Sacchettini, J. C.; Carr, S. A.; Hung, D. T. Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment. Elife 6 (2017). 276. Zhu, M.; Harshbarger, W. D.; Robles, O.; Krysiak, J.; Hull, K. G.; Cho, S. W.; Richardson, R. D.; Yang, Y.; Garcia, A.; Spiegelman, L.; Ramirez, B.; Wilson, C. T.; Yau, J. A.; Moore, J. T.; Walker, C. B.; Sacchetini, J. C.; Liu, W. R.; Sieber, S. A.; Smith, J. W.; Romo, D. A strategy for dual inhibition of the proteasome and fatty acid synthase with belactosin C-orlistat hybrids. Bioorg. Med. Chem. (2017). 275. Park, Y.; Pacitto, A.; Bayliss, T.; Cleghorn, L. A.; Wang, Z.; Hartman, T.; Arora, K.; Ioerger, T. R.; Sacchettini, J.; Rizzi, M.; Donini, S.; Blundell, T. L.; Ascher, D. B .; Rhee, K.; Breda, A.; Zhou, N.; Dartois, V.; Jonnala, S. R.; Via, L. E.; Mizrahi, V.; Epemolu, O.; Stojanovski, L.; Simeons, F.; Osuna-Cabello, M.; Ellis, L.; MacKenzie, C. J.; Smith, A. R.; Davis, S. H.; Murugesan, D.; Buchanan, K. I.; Turner, P. A.; Huggett, M.; Zuccotto, F.; Rebollo-Lopez, M. J.; Lafuente-Monasterio, M. J.; Sanz, O.; Diaz, G. S.; Lelièvre, J.; Ballell, L.; Selenski, C.; Axtman, M.; Ghidelli-Disse, S.; Pflaumer, H.; Bösche, M.; Drewes, G.; Freiberg, G. M.; Kurnick, M. D.; Srikumaran, M.; Kempf, D. J.; Green, S. R.; Ray, P. C.; Read, K.; Wyatt, P.; Barry, C. E. III; Boshoff, H. I. Essential but not vulnerable: Indazole sulfonamides targeting inosine monophosphate dehydrogenase as potential leads against Mycobacterium tuberculosis. ACS Infect. Dis. 3, 18–33 (2017). 274. Huang, H. L.; Kireger, I. V.; Parai, M. K.; Gawandi, V. B.; Sacchettini, J. C. Mycobacterium tuberculosis malate synthase structures with fragments reveal a portal for substrate/product exchange. J. Biol. Chem. 291, 27421–27432 (2016). 273. Palencia, A.; Li, X.; Bu, W.; Choi, W.; Ding, C. Z.; Easom, E. E.; Feng, L.; Hernandez, V.; Houston, P.; Liu, L.; Meewan, M.; Mohan, M.; Rock, F. L.; Sexton, H.; Zhang, S.; Zhou, Y.; Wan, B.; Wang, Y.; Franzblau, S. G.; Woolhiser, L.; Gruppo, V.; Lenaerts, A. J.; O’Malley, T.; Parish, T.; Cooper, C. B.; Waters, M. G.; Ma, Z.; Ioerger, T. R.; Sacchettini, J. C.; Rullas, J.; Angulo-Barturen, I.; Pérez-Herrán, E.; Mendoza, A.; Barros, D.; Cusack, S.; Plattner, J. J.; Alley, M. R. Discovery of novel oral protein synthesis inhibitors of Mycobacterium tuberculosis that target leucyl-tRNA synthetase. Antimicrob. Agents Chemother. 60, 6271–6280 (2016). 272. Martinez-Hoyos, M.; Perez-Herran, E.; Gulten, G.; Encinas, L.; Alvarez-Gomez, D.; Alvarez, E.; Ferrer-Bazaga, S.; Garcia-Perez, A.; Ortega, F.; Angulo-Barturen, I.; Rullas-Trincado, J.; Blanco, Ruano, D.; Torres, P.; Castaneda, P.; Huss, S.; Fernandez Menendez, R.; Gonzalez Del Valle, S.; Ballell, L.; Barros, D.; Modha, S.; Dhar, N.; Signorino- Gelo, F.; McKinney, J. D.; Garcia-Bustos, J. F.; Lavandera, J. L.; Sacchettini, J. C.; Jimenez, M. S.; Martin-Casabona, N.; Castro-Pichel, J.; Mendoza-Losana, A. Antitubercular dugs for an old target: GSK693 as a promising InhA direct inhibitor. EBioMedicine 291–301 (2016). 271. Bhatt, V. S.; Zeng, D.; Krieger, I.; Sacchettini, J. C.; Cho, J.-H. Binding mechanism of the N-terminal SH3 domain of CrKII and proline-rich motifs in cAbl. Biophys. J. 2630–2341 (2016). 270. Almeida, D.; Ioerger, T.; Tyagi, S.; Li, S. Y.; Mdluli, K.; Andries, K.; Grosset, J.; Sacchettini, J.; Nuermberger, E. Mutations in pepQ confer low-level resistance to Bedaquiline and Clofazimine in Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 4590–4599 (2016). 269. Guardia, A.; Gulten, G.; Fernandez, R.; Gomez, J.; Wang, F.; Convery, M.; Blanco, D.; Martinez, M.; Perez-Herran, E.; Alonso, M.; Ortega, F.; Rullas, J.; Calvo, D.; Mata, L.; Young, R.; Sacchetini, J. C.; Mendoza-Losana, A.; Remuinan, M.; Ballell Pages, L.; Castro-Pichel, J. N-Benzyl-4-((heteroaryl)methyl)benzamides: A new class of direct NADH-dependent 2-trans enoyl-acyl carrier protein reductase (InhA) inhibitors with antitubercular activity. ChemMedChem 11, 687–701 (2016). 268. Bageshwar, U. K.; VerPlank, L.; Baker, D.; Dong, W.; Hamsanthan, S.; Whitaker, N.; Sacchettini, J. C.; Musser, S. M. High-throughput screen for Escherichia coli twin arginine translocation (Tat) inhibitors. PLoS One 11, e0149659 (2016). 267. Cheng, Y. S.; Sacchettini, J. C. Structural insights into Mycobacterium tuberculosis Rv2671 protein as a dihydrofolate reductase functional analogue contributing to para-aminosalicylic acid resistance. Biochemistry 55, 1107–1119 (2016). 266. Martinot, A. J.; Farrow, M.; Bai, L.; Layre, E.; Cheng, T. Y.; Tsai, J. H.; Iqbal, J.; Annand, J. W.; Sullivan, Z. A.; Hussain, M. M.; Sacchettini, J.; Moody, D. B.; Seeliger, J. C.; Rubin, E. J. Mycobacterial metabolic syndrome: LprG and Rv1410 regulate triacylglyceride levels, growth rate and virulence in Mycobacterium tuberculosis. PLoS Pathog. 12, e1005351 (2016). 265. Swanson, S.; Ioerger, T. R.; Rigel, N. W.; Miller, B. K.; Braunstein, M.; Sacchettini, J. C. Structural similarities and differences between two functionally distinct SecA proteins, Mycobacterium tuberculosis SecA1 and SecA2. J. Bacteriol. 198, 720–730 (2015). 264. Lanoix, J. P.; Ioerger, T.; Ormond, A.; Kaya, F.; Sacchettini, J.; Dartois, V.; Nuermberger, E. Selective inactivity of pyrazinamide against tuberculosis in C3HeB/FeJ mice is best explained by neutral pH of caseum. Antimicrob. Agents Chemother. 60, 735–742 (2015). 263. Maksymiuk, C.; Ioerger, T.; Balakrishnan, A.; Bryk, R.; Rhee, K.; Sacchettini, J.; Nathan, C. Comparison of transposon and deletion mutants in Mycobacterium tuberculosis: The case of Rv1248c, encoding 2-hydroxy-3- oxoadipate synthase. Tuberculosis (Edinb) 95, 689–694 (2015). 262. Hong, W.; Wang, Y.; Chang, Z.; Yang, Y.; Pu, J.; Sun, T.; Kaur, S.; Sacchettini, J. C.; Jung, H.; Lin Wong, W.; Fah Yap, L.; Fong Ngeow, Y.; Paterson, I. C.; Wang, H. The identification of novel Mycobacterium tuberculosis DHFR inhibitors and the investigation of their binding preferences by using molecular modeling. Sci. Rep. 5, 15328 (2015). 261. Kieser, K. J.; Baranowski, C.; Chao, M. C.; Long, J. E.; Sassetti, C. M.; Waldor, M. K.; Sacchettini, J. C.; Ioerger, T. R.; Rubin, E. J. Peptidoglycan synthesis in Mycobacterium tuberculosis is organized into networks with varying drug susceptibility. Proc. Natl. Acad. Sci. USA 112, 13087–13092 (2015). 260. Li, X.; Sun, Q.; Jiang, C.; Yang, K.; Hung, L. W.; Zhang, J.; Sacchettini, J. C. Structure of ribosomal silencing factor bound to Mycobacterium tuberculosis ribosome. Structure 23, 1858–1865 (2015). 259. Loesch, K.; Galaviz, S.; Hamoui, Z.; Clanton, R.; Akabani, G.; Deveau, M.; DeJesus, M.; Ioerger, T.; Sacchettini, J. C.; Wallis, D. Functional genomics screening utilizing mutant mouse embryonic stem cells identifies novel radiation- response genes. PLoS One 10, e0120534 (2015). 258. Kanetaka, H.; Koseki, Y.; Taira, J.; Umei, T.; Komatsu, H.; Sakamoto, H.; Gulten, G.; Sacchettini, J. C.; Kitamura, M.; Aoki, S. Discovery of InhA inhibitors with anti-mycobacterial activity through a matched molecular pair approach. Eur. J. Med. Chem. 94, 378–385 (2015). 257. Wallis, D.; Loesch, K.; Galaviz, S.; Sun, Q.; DeJesus, M.; Ioerger, T.; Sacchettini, J. C. High-throughput differentiation and screening of a library of mutant stem cell clones defines new host-based genes involved in rabies virus infection. Stem Cells 33, 2509–2522 (2015). 256. Dragset, M. S.; Poce, G.; Alfonso, S.; Padilla-Benavides, T.; Ioerger, T. R.; Kaneko, T.; Sacchettini, J. C.; Biava, M.; Parish, T.; Arguello, J. M.; Steigedal, M.; Rubin, E. J. A novel antimycobacterial compound acts as an intracellular iron chelator. Antimicrob. Agents Chemother. (2015). 255. Harshbarger, W.; Miller, C.; Diedrich, C.; Sacchettini, J. Crystal structure of the human 20S proteasome in complex with Carfilzomib. Structure 23, 418–424 (2015).

CURRENT SUPPORT NIH 1P01AI143575 Erht (PI); Sacchettini, J. C. (co-PI) 2020–2025 “Pathway analysis of tuberculosis” NIH 1R01AI149727-01 Braunstein (PI); Sacchettini, J. C. (co-PI) 2020-2024 “A novel protein export chaperone of mycobacterium tuberculosis” NIH/NIAID P01AI0095208 Sacchettini, J. C. (PI) 2018–2023 “Structure-based discovery of critical vulnerabilities of mycobacteria” Bill & Melinda Gates Sacchettini, J. C. (PI) 2019–2022 Foundation INV002178 “Target identification for tuberculosis drug discovery” DOD PR160865 Rubin (PI); Sacchettini, J. C. (co-PI) 2017–2021 “Chemigenomic drug discovery for tuberculosis” Welch Foundation A-0015 Sacchettini, J. C. (PI) 1996-present

COMPLETED SUPPORT (2015–present) NIH U19AI109755 Murrary (PI); Sacchettini, J. C. (co-PI) 2014-2020 “Integrated discovery and development of innovative TB diagnostics” Bill & Melinda Gates Sacchettini, J. C. (PI) 2010-2019 Foundation OPP1024055 “Target identification for tuberculosis drug discovery” NIH U19AI107774 Rubin (PI); Sacchettini, J. C. (co-PI) 2013-2018 “Decoding the roles of critical genes of unknown function in M. tuberculosis”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Dean’s Outstanding Achievement Award College of Agriculture and Life Sciences, TAMU 2018 Research Director’s Superior Grantmanship College of Agriculture and Life Sciences, TAMU 2020 Award

COURSES TAUGHT (2015–present) BICH 654 Structural Biochem 3 2015-present BICH 655 Crystallolgraphy Methods 3 2015-present BICH 677 Chem Gene & Drug Discvry 1 2015-present BICH 681 Seminar 1 2015-present Stephen H. Safe University Distinguished Professor | Veterinary Physiology and Pharmacology, Biochemistry and Biophysics Sid Kyle Chair in Toxicology

EDUCATION Postdoctoral Harvard University 1967 Postdoctoral Oxford University 1966 D. Phil. Oxford University 1965 M. Sc. Queen’s University 1963 B. Sc. Queen’s University 1962

PROFESSIONAL APPOINTMENTS Sid Kyle Chair Toxicology Texas A&M University 1992–present Distinguished Professor Veterinary Physiology and Pharmacology Texas A&M University 1984–present Biochemistry and Biophysics Director Center for Environmental and Genetic Texas A&M HSC 2002–2015 Medicine Adjunct Professor University of Guelph 1985–1991 Chester J. Reed Chair Toxicology Texas A&M University 1983–1989 Professor University of Guelph 1977–1981 Associate Professor University of Guelph 1973–1977

PEER-REVIEWED PUBLICATIONS (2015–present) 815. Chatterjee, S.; Walsh, E. N.; Yan, A. L.; Giese, K. P.; Safe, S.; Abel, T. Pharmacological activation of Nr4a rescues age-associated memory decline. Neurobiol. Aging 85, 140–144 (2020). 814. Han, H.; Davidson, L. A.; Fan, Y. Y.; Goldsby, J. S.; Yoon, G.; Jin, U. H.; Wright, G. A.; Landrock, K. K.; Weeks, B. R.; Wright, R. C.; Allred, C. D.; Jayaraman, A.; Ivanov, I.; Roper, J.; Safe, S. H.; Chapkin, R. S. Loss of aryl hydrocarbon receptor potentiates FoxM1 signaling to enhance self-renewal of colonic stem and progenitor cells. EMBO J. 39, e104319 (2020). 813. Jin, U. H.; Michelhaugh, S. K.; Polin, L. A.; Shrestha, R.; Mittal, S.; Safe, S. Omeprazole inhibits glioblastoma cell invasion and tumor growth. Cancers (Basel). 12 (2020). 812. Karki, K.; Li, X.; Jin, U. H.; Mohankumar, K.; Zarei, M.; Michelhaugh, S. K.; Mittal, S.; Tjalkens, R.; Safe, S. Nuclear receptor 4A2 (NR4A2) is a druggable target for glioblastomas. J. Neurooncol. 146, 25–39 (2020). 811. Park, H.; Jin, U. H.; Karki, K.; Allred, C.; Davidson, L. A.; Chapkin, R. S.; Orr, A. A.; Nowshad, F.; Jayaraman, A>; Tamamis, P.; Safe, S. Hydroxylated chalcones as aryl hydrocarbon receptor agonists: Structure-activity effects. Toxicol. Sci. (2020). 810. Park, H.; Jin, U. H.; Karki, K.; Jayaraman, A.; Allred, C.; Michelhaugh, S. K.; Mittal, S.; Chapkin, R. S.; Safe, S. Dopamine is an aryl hydrocarbon receptor agonist. Biochem. J. 477, 3899–3910 (2020). 809. Safe, S.; Jayaraman, A.; Chapkin, R. S. Ah receptor ligands and their impacts on gut resilience: Structure-activity effects. Crit. Rev. Toxicol. 50, 463–473 (2020). 808. Safe, S.; Jin, U. H.; Park, H.; Chapkin, R. S.; Jayaraman, A. Aryl Hydrocarbon Receptor (AHR) ligands as selective AHR modulators (SAhRMs). Int. J. Mol. Sci. 21 (2020). 807. Safe, S.; Karki, K. The paradoxical roles of orphan nuclear receptor 4A (NR4A) in cancer. Mol. Cancer Res. 19, 180–191 (2020). 806. Shrestha, R.; Mohankumar, K.; Jin, U. H.; Martin, G. G.; Safe, S. The histone methyltransferase gene G9a is regulated by nuclear receptor 4a1 (Nr4a1) in Alveolar Rhabdomyosarcoma cells. Mol. Cancer Ther. (2020). 805. Shrestha, R.; Mohankumar, K.; Safe, S. Bis-indole derived nuclear receptor 4A1 (NR4A1) antagonists inhibit TGFbeta-induced invasion of embryonal rhabdomyosarcoma cells. Am. J. Cancer Res. 10, 2495–2509 (2020). 804. Yang, F.; DeLuca, J. A. A.; Menon, R.; Garcia-Vilarato, E.; Callaway, E.; Landrock, K. K.; Lee, K.; Safe, S. H.; Chapkin, R. S.; Allred, C. D.; Jayaraman, A. Effect of diet and intestinal AhR expression on fecal microbiome and metabolomic profiles. Microb. Cell Fact. 19, 219 (2020). 803. Garcia-Villatoro, E. L.; DeLuca, J. A. A.; Callaway, E. S.; Allred, K. F.; Davidson, L. A.; Hensel, M. E.; Menon, R.; Ivanov, I.; Safe, S. H.; Jayaraman, A.; Chapkin, R. S.; Allred, C. D. Effects of high-fat diet and intestinal aryl hydrocarbon receptor deletion on colon carcinogenesis. Am. J. Physiol. Gastrointest. Liver Physiol. 318, G451–G463 (2020). 802. Karki, K.; Wright, G. A.; Mohankumar, K.; Jin, U. H.; Zhang, X. H.; Safe, S. A bis-indole-derived NR4A1 antagonist induces PD-L1 degradation and enhances antitumor immunity. Cancer Res. 80, 1011–1023 (2020). 801. Kumaravel, S.; Singh, S.; Roy, S.; Venkatasamy, L.; White, T. K.; Sinha, S.; Glaser, S. S.; Safe, S. H.; Chakraborty, S. CXCL11-CXCR3 axis mediates tumor lymphatic cross talk and inflammation-induced tumor, promoting pathways in head and neck cancers. Am. J. Pathol. 190, 900–915 (2020). 800. Mohankumar, K.; Li, X.; Sung, N.; Cho, Y. J.; Han, S. J.; Safe, S. Bis-indole-dervied nuclear receptor 4A1 (NR4A1, Nur 77) ligands as inhibitors of endometriosis. Endocrinol. 161 (2020). 799. Nottingham, E.; Sekar, V.; Mondal, A.; Safe, S.; Rishi, A. K.; Singh, M. The role of self-nanoemulsifying drug delivery systems of CDODA-Me in sensitizing Erlotinib-resistant non-small cell lung cancer. J. Pharm. Sci. 109, 1867–1882 (2020). 798. Wu, C. S.; Wei, Q.; Wang, H.; Kim, D. M.; Balderas, M.; Wu, G.; Lawler, J.; Safe, S.; Guo, S.; Devaraj, S.; Chen, Z.; Sun, Y. Protective effects of Ghrelin on fasting-induced muscle atrophy in aging mice. J. Gerontol. A. Biol. Sci. Med. Sci. 75, 621–630 (2020). 797. Dolciami, D.; Ballarotto, M.; Gargaro, M.; Lopez-Cara, L. C.; Fallarino, F.; Macchiarulo, A.; Targeting aryl hydrocarbon receptor for next-generation immunotherapies: Selective modulators (SAhRMs) versus rapidly metabolized ligands (RMAhRLs). Eur. J. Med. Chem. 185, 111842 (2020). 796. Chatterjee, S.; Walsh, E. N.; Yan, A. L.; Giese, K. P.; Safe, S.; Abel, T. Pharmacological activation of Nr4a rescues age-associated memory decline. Neurobiol. Aging 85, 140–144 (2020). 795. Karki, K.; Li, X.; Jin, U. H.; Mohankumar, K.; Zarei, M.; Michelhaugh, S. K.; Mittal, S.; Tjalkens, R.; Safe, S. Nuclear receptor 4A2 (NR4A2) is a druggable target for glioblastomas. J. Neurooncol. 146, 25–39 (2020). 747. Yoon, K.; Chen, C. C.; Orr, A. A.; Barreto, P. N.; Tamamis, P.; Safe, S. Activation of COUP-TFI by a novel diindolulmethane derivative. Cells 8 (2019). 746. Wang, M.; Safe, S.; Hearon, S. E.; Philipps, T. D. Strong adsorption of Polychlorinated Biphenyls by processed montmorillonite clays: Potential applications as toxin enterosorbents during disasters and floods. Environ. Pollut. 255, 113210 (2019). 745. Park, H.; Jin, U. H.; Orr, A. A.; Echegaray, S. P.; Davidson, L. A.; Allred, C. D.; Chapkin, R. S.; Jayaraman, A.; Lee, K.; Tamamis, P.; Safe, S. Isoflavones as Ah receptor agonists in colon-derived cell lines: Structure-activity relationships. Chem. Res. Toxicol. 32, 2353–2364 (2019). 744. Mohankumar, K.; Li, X.; Sridharan, S.; Karki, K.; Safe, S. Nuclear receptor 4A1 (NR4A1) antagonists induce ROS-dependent inhibition of mTOR signaling in endometrial cancer. Gynecol. Oncol. 154, 218–227 (2019). 743. Li, X.; Tjalkens, R. B.; Srestha, R.; Safe, S. Structure-dependent activation of gene expression by bis-indole and quinoline-derived activators of nuclear receptor 4A2. Chem. Biol. Drug 94, 1711–1720 (2019). 742. Kasiappan, R.; Jutooru, I.; Mohankumar, K.; Karki, K.; Lacey, A.; Safe, S. Reactive oxygen species (ROS)-indicing triterpenoid inhibits rhabdomyosarcoma cell and tumor growth through targeting Sp transcription factors. Mol. Cancer Res. 17, 794–805 (2019). 741. Karki, K.; Li, X.; Jin, U. H.; Mohankumar, K.; Zarei, M.; Michelhaugh, S. K.; Mittal, S.; Tjalkens, R.; Safe, S. Nuclear receptor 4A2 (NR4A2) is a druggable target for glioblastomas. J. Neurooncol. (2019). 740. Jung, Y. S.; Lee, H. S.; Cho, H. R.; Kim, K. J.; Kim, J. H.; Safe, S.; Lee, S. O. Dual targeting of Nur77 and AMPKalpha by isoalantolactone inhibits adipogenesis in vitro and decreases body fat mass in vivo. Int. J. Obes. 43, 952–962 (2019). 739. Jin, U. H.; Karki, K.; Cheng, Y.; Michelhaugh, S. K.; Mittal, S.; Safe, S. The aryl hydrocarbon receptor is a tumor suppressor-like gene in glioblastoma. J. Biol. Chem. 294, 11342–11353 (2019). 738. Hedrick, E.; Mohankumar, K.; Lacey, A.; Safe, S. Inhibition of NR4A1 promotes ROS accumulation and IL24-dependent growth arrest in rhabdomyosarcoma. Mol. Cancer Res. 17, 2221–2232 (2019). 737. Hedrick, E.; Li, X.; Cheng, Y.; Lacey, A.; Mohankumar, K.; Zarei, M.; Safe, S. Potent inhibition of breast cancer by bis-indole-derived nuclear receptor 4A1 (NR4A1) antagonists. Breast Cancer Res. Treat. 177, 29–40 (2019). 736. Chatterjee, S.; Walsh, E. N.; Yan, A. L.; Giese, K. P.; Safe, S.; Abel, T. Pharmacological activation of Nr4a rescues age-associated memory decline. Neurobiol. Aging (2019). 735. Wu, C. S.; Wei, Q.; Wang, H.; Kim, D. M.; Balderas, M.; Wu, G.; Lawler, J. Safe, S.; Guo, S.; Devaraj, S.; Chen, Z.; Sun, Y. Protective effects of ghrelin on fasting-induced muscle atrophy in aging mice. J. Gerontol. A Biol. Sci. Med. Sci. (2018). 734. Safe, S.; Abbruzzese, J. L.; Abdelrahim, M.; Hedrick, E. Specificity protein transcription factors and cancer: opportunities for drug development. Cancer Pres. Res. 11, 371–382 (2018). 733. Safe, S.; Nair, V.; Karki, K. K. Metformin-induced anticancer activities: recent insights. Biol. Chem. 399, 321–335 (2018). 732. Popichak, K. A.; Hammond, S. L.; Moreno, J. A.; Afzali, M. F.; Backos, D. S.; Slayden, R. D.; Safe, S.; Tjalkens, R. B. Compensatory expression of Nur77 and Nurr1 regulates NF-κB-dependent inflammatory signaling in astrocytes. Mol. Pharmacol. 94, 1174–1186 (2018). 731. Mohankumar, K.; Lee, J.; Wu, C. S.; Sun, Y.; Safe, S. Bis-indole-derived NR4A1 ligands and metformin exhibit NR4A1-dependent glucose metabolism and uptake in C2C12 cells. Endocrinol. 159, 1950–1963 (2018). 730. Lacey, A.; Hedrick, E.; Cheng, Y.; Mohankumar, K.; Warren, M.; Safe, S. Interleukin-24 (IL-24) is suppressed by PAX3-FOXO1 and is a novel therapy for rhabdomyosarcoma. Mol. Cancer Ther. 17, 2756–2766 (2018). 729. Karki, K.; Harashchandra, S.; Safe, S. Bortezomib targets Sp transcription factors in cancer cells. Mol. Pharmacol. 94, 1187–1196 (2018). 728. Jin, U. H.; Park, H.; Li, X.; Davidson, L. A.; Allred, C.; Patil, B.; Jayaprakasha, G.; Orr, A. A.; Mao, L.; Chapkin, R. S.; Jayaraman, A.; Tamamis, P.; Safe, S. Structure-dependent modulation of aryl hydrocarbon receptor-mediated activities by flavones. Toxicol. Sci. 164, 205–217 (2018). 727. Jin, U. H.; Karki, K.; Kim, S. B.; Safe, S. Inhibition of pancreatic cancer Panc1 cell migration by omeprazole is dependent on aryl hydrocarbon receptor activation of JNK. Biochem. Biophys. Res. Commun. 501, 751–757 (2018). 726. Hedrick, E.; Mohankumar, K.; Safe, S. TGFβ-induced lung cancer cell migration is NR4A1-dependent. Mol. Cancer Res. (2018). 725. Hammond, S. L.; Popichak, K. A.; Li, X.; Hunt, L. G.; Richman, E. H.; Damale, P.; Chong, E.; Backos, D. S.; Safe, S.; Tjalkens, R. B. The Nurr1 ligand, 1,1-bis(3'-indolyl)-1-(p-chlorophenyl)methane, modulates glial reactivity and is neuroprotective in MPTP-induced parkinsonism. J. Pharmacol. Exp. Ther. 365, 636–651 (2018). 724. Draz, H.; Goldberg, A. A.; Tomlinson Guns, E. S.; Fazli, L.; Safe, S.; Sanderson, J. T. Autophagy inhibition improves the chemotherapeutic efficacy of cruciferous vegetable-derived diindolylmethane in a murine prostate cancer xenograft model. Invest. New Drugs. 36, 718–725 (2018). 723. Choudhary, M.; Safe, S.; Malek, G. Suppression of aberrant choroidal neovascularization through activation of the aryl hydrocarbon receptor. Biochim. Biophys. Acta 1864, 1583–1593 (2018). 722. Cheng, Y.; Imanirad, P.; Jutooru, I.; Hedrick, E.; Jin, U. H.; Leal de Aruajo, J.; Rodrigues-Hoffman, A.; Morpurgo, B.; Glovko, A.; Safe, S. Role of metastasis-associated lung adenocarcinoma transcript-1 (MALAT-1) in pancreatic cancer. PLoS One 13, e0192264 (2018). 721. Afzali, M. F.; Popichak, K. A.; Burton, L. H.; Klochak, A. L.; Wilson, W. J.; Safe, S.; Tjalkens, R. B.; Legare, M. E. A novel diindolylmethane analog, 1,1-bis(3'-indolyl)-1-(p-chlorophenyl)methane, inhibits the tumor necrosis factor-induced inflammatory response in primary murine synovial fibroblasts through a Nurr1-dependent mechanism. Mol. Immunol. 101, 46–54 (2018). 720. Taoka, R.; Jinesh, G. G.; Xue, W.; Safe, S.; Kamat, A. M. CF3DODA-Me induces apoptosis, degrades Sp1, and blocks the transformation phase of the blebbishield emergency program. Apoptosis 22, 719–729 (2017). 719. Safe, S.; Cheng, Y.; Jin, U. H. The aryl hydrocarbon receptor (AhR) as a drug target for cancer chemotherapy. Curr. Opin. Toxicol. 2, 24–29 (2017). 718. Safe, S. Carbidopa: A selective Ah receptor modulator (SAhRM). Biochem. J. 474, 3763–3765 (2017). 717. Li, Y.; Wang, F.; Lu, L.; Zhu, F.; Huang, S.; Nomie, K.; Zhang, L.; Yang, D. T.; Huang, W.; Kahl, B. S.; Safe, S.; Wang, M.; Rui, L. NR4A1 inhibition synergizes with ibrutinib in killing mantle cell lymphoma cells. Blood Cancer J. 7, 632 (2017). 716. Lee, H. S.; Safe, S.; Lee, S. O. Inactivation of the orphan nuclear receptor NR4A1 contributes to apoptosis induction by fangchinoline in pancreatic cancer cells. Toxicol. Appl. Pharmacol. 332, 32–39 (2017). 715. Lacey, A.; Rodrigues-Hoffman, A.; Safe, S. PAX3-FOXO1A expression in rhabdomyosarcoma is driven by the targetable nuclear receptor NR4A1. Cancer Res. 77, 732–741 (2017). 714. Kolluri, S. K.; Jin, U. H.; Safe, S. Role of the aryl hydrocarbon receptor in carcinogenesis and potential as an anticancer drug target. Arch. Toxicol. 91, 2497–2513 (2017). 713. Karki, K.; Hedrick, E.; Kasiappan, R.; Jin, U. H.; Safe, S. Piperlongumine induces reactive oxygen species (ROS)-dependent downregulation of specificity protein transcription factors. Cancer Prev. Res. 10, 467–477 (2017). 712. Jin, U. H.; Cheng, Y.; Park, H.; Davidson, L. A.; Callaway, E. S.; Chapkin, R. S.; Jayaraman, A.; Asante, A.; Allred, C.; Weaver, E. A.; Safe, S. Short chain fatty acids enhance aryl hydrocarbon (Ah) responsiveness in mouse colonocytes and Caco-2 human colon cancer cells. Sci. Rep. 7, 10163 (2017). 711. Jin, U. H.; Cheng, Y.; Zhou, B.; Safe, S. Bardoxolone methyl and a related triterpenoid downregulate cMyc expression in leukemia cells. Mol. Pharmacol. 9, 438–450 (2017). 710. Hedrick, E.; Safe, S. Transforming growth factor β/NR4A1 inducible breast cancer cell migration and epithelial to mesenchymal transition is p38α (MAPK14) dependent. Mol. Cell. Biol. 37, e00306–e00317 (2017). 709. Hedrick, E.; Li, X.; Safe, S. Penfluridol represses integrin expression in breast cancer through induction of reactive oxygen species and downregulation of Sp transcription factors. Mol. Cancer Ther. 16, 205–216 (2017). 708. Hedrick, E.; Lee, S. O.; Safe, S. The nuclear orphan receptor NR4A1 regulation β1-integrin expression in pancreatic and colon cancer cells and can be targeted by NR4A1 antagonists. Mol. Carcinog. 56, 2066–2075 (2017). 707. Draz, H.; Goldberg, A. A.; Titorenko, V. I.; Tomlinson Guns, E. S.; Safe, S.; Sanderson, J. T. Diindolylmethane and its halogenated derivatives induce protective autophagy in human prostate cancer cells via induction of the oncogenic protein AEG-1 and activation of AMP-activated protein kinase (AMPK). Cell Signal 40, 172–182 (2017). 706. Cheng, Y.; Jin, U. H.; Davidson, L. A.; Chapkin, R. S.; Jayaraman, A.; Tamamis, P.; Orr, A.; Allred, C.; Denison, M. S.; Soshilov, A.; Weaver, E.; Safe, S. Microbial-derived 1,4-dihydroxy-2-naphthoic acid and related compounds as aryl hydrocarbon receptor agonists/antagonists: structure-activity relationships and receptor modeling. Toxicol. Sci. 155, 458–473 (2017). 705. Bridi, M. S.; Hawk, J. D.; Chatterjee, S.; Safe, S.; Abel, T. Pharmacological activators of the NR4A1 nuclear receptors enhance LTP in a CREB/CBP-dependent fashion. Neuropsychopharmacology 42, 1243–1253 (2017). 704. Ying, W.; Tseng, A.; Chang, R. C.; Wang, H.; Lin, Y. L.; Kanameni, S.; Brehm, T.; Morin, A.; Jones, B.; Splawn, T.; Criscitiello, M.; Golding, M. C.; Baser, F. W.; Safe, S.; Zhou, B. miR-150 regulates obesity-associated insulin resistance by controlling B cell function. Sci. Rep. 6, 20176 (2016). 703. Takeuchi, H.; Taoka, R.; Mmeje, C. O.; Jinesh, G. G.; Safe, S.; Kamat, A. M. CDODA-Me decreases specificity protein transcription factors and induces apoptosis in bladder cancer cells through induction of reactive oxygen species. Urol. Oncol. 34, 337.e11–e18 (2016). 702. Safe, S.; Kasiappan, R. Natural products as mechanism-based anticancer agents: Sp transcription factors as targets. Phytotherapy Res. 30, 1723–1732 (2016). 701. Safe, S.; Jin, U. H.; Morpurgo, B.; Abudayyeh, A.; Singh, M.; Tjalkens, R. B. Nuclear receptor 4A (NR4A) family – orphans no more. J. Steroid Biochem. Mol. Biol. 157, 48–60 (2016). 700. Moore, R. A.; Fritz, W. A.; Schneider, A. J.; Lin, T. M.; Branam, A. M.; Safe, S.; Peterson, R. E. 2,3,7,8-Tetrachlorodibenzo-p-dioxin has both pro-carcinogenic and anti-carcinogenic effects on neuroendocrine prostate carcinoma formation in TRAMP mice. Toxicol. Appl. Pharmacol. 305, 424–249 (2016). 699. Lacey, A.; Hedrick, E.; Li, X.; Patel, K.; Doddapaneni, R.; Singh, M.; Safe, S. Nuclear receptor 4A1 (NR4A1) as a drug target for treating rhabsomyosarcoma (RMS). Oncotarget. 7, 31257–31269 (2016). 698. Kasiappan, R.; Jutooru, I.; Karki, K.; Hedrick, E.; Safe, S. Benzyl isothiocyanate (BITC) induces reactive oxygen species-dependent repression of STAT3 protein by downregulation of specificity proteins in pancreatic cancer. J. Biol. Chem. 291, 27122–27133 (2016). 697. Hedrick, E.; Lee, S. O.; Doddapaneni, R.; Singh, M.; Safe, S. NR4A1 antagonists inhibit β1-integrin-dependent breast cancer cell migration. Mol. Cell. Biol. 36, 1383–1394 (2016). 696. Hedrick, E.; Cheng, Y.; Jin, U. H.; Kim, K.; Safe, S. Specificity protein (Sp) transcription factors Sp1, Sp3 and Sp4 are non-oncogene addiction genes in cancer cells. Oncotarget. 7, 22245–22256 (2016). 695. Goldberg, A. A.; Draz, H.; Montes-Grajales, D.; Olivero-Verbel, J.; Safe, S. H.; Sanderson, J. T. Erratum: 3,3'-Diindolylmethane (DIM) and its ring-substituted halogenated analogs (ring DIMs) induce differential mechanisms of survival and death in androgen-dependent and -independent prostate cancer cells. Genes Cancer 7, 59 (2016). 694. Delgado, E.; Boisen, M. M.; Laskey, R.; Chen, R.; Song, C.; Sallit, J.; Yochum, Z. A.; Andersen, C. L.; Sikora, M. J.; Wagner, J.; Safe, S.; Elishaev, E.; Lee, A.; Edwards, R. P.; Haluska, P.; Tseng, G.; Schurdak, M.; Oesterreich, S. High expression of orphan nuclear receptor NR4A1 in a subset of ovarian tumors with worse outcome. Gynecol. Oncol. 141, 348–356 (2016). 693. Boakye, C. H.; Patel, K.; Patel, A. R.; Faria, H. A.; Zucolotto, V.; Safe, S.; Singh, M. Lipid-based oral delivery systems for skin deposition of a potential chemopreventive DIM derivative: characterization and evaluation. Drug Deliv. Transl. Res. 6, 526–539 (2016). 692. Boakye, C. H.; Patel, K.; Doddapaneni, R.; Bagde, A.; Behl, G.; Chowdhury, N.; Safe, S.; Singh, M. Ultra-flexible nanocarriers for enhanced topical delivery of a highly lipophilic antioxidative molecule for skin cancer chemoprevention. Colloids Surf. B Biointerfaces 143, 156–167 (2016). 691. Ying, W.; Tseng, A.; Chang, R. C.; Morin, A.; Brehm, T.; Triff, K.; Nair, V.; Zhuang, G.; Song, H.; Kanameni, S.; Wang, H.; Golding, M. C.; Bazer, F. W.; Chapkin, R. S.; Safe, S.; Zhou, B. MicroRNA-223 is a crucial mediator of PPARγ-regulated alternative macrophage activation. J. Clin. Invest. 125, 4149–4159 (2015). 690. Safe, S. Targeting apoptosis pathways in cancer – Letter. Cancer Prev. Res. 8, 338 (2015). 689. Safe, S. MicroRNA-specificity protein (Sp) transcription factor interactions and significance in carcinogenesis. Curr. Pharmacol. Rep. 1, 73–78 (2015). 688. Riddell, N.; Jin, U. H.; Safe, S. H.; Cheng, Y.; Chittim, B.; Konstantinov, A.; Parette, R.; Pena-Abaurrea, M.; Reiner, E. J.; Poirier, D.; Stefanac, T.; McAlees, A.; McCrindle, R. Characterization and biological potency of mono- to tetra-halogenated carbazoles. Environ. Sci. Technol. 49, 10658–10666 (2015). 687. Phillips, T. D.; Richardson, M.; Cheng, Y. S.; He, L.; McDonald, T. J.; Cizmas, L. H.; Safe, S.; Donnelly, K. C.; Wang, F.; Moorthy, B.; Zhou, G. D. Mechanistic relationships between hepatic genotoxicity and carcinogenicity in male B6C3F1 mice treated with polycyclic aromatic hydrocarbon mixtures. Arch. Toxicol. 89, 697–977 (2015). 686. Patel, A. R.; Godugu, C.; Wilson, H.; Safe, S.; Singh, M. Evaluation of spray BIO-Max DIM-P in dogs for oral bioavailability and in Nu/nu mice bearing orthotopic/metastatic lung tumor models for anticancer activity. Pharm. Res. 32, 2292–2300 (2015). 685. Patel, A. R.; Doddapaneni, R.; Andey, T.; Wilson, H.; Safe, S.; Singh, M. Evaluation of self-emulsified DIM-14 in dogs for oral bioavailability and in Nu/nu mice bearing stem cell lung tumor models for anticancer activity. J. Control Release 213, 18–26 (2015). 684. Li, X.; Pathi, S. S.; Safe, S. Sulindac slfide inhibits colon cancer cell growth and downregulates specificity protein transcription factors. BMC Cancer 15, 974 (2015). 683. Jin, U. H.; Kim, S. B.; Safe, S. Omeprazole inhibits pancreatic cancer cell invasion through a nongenomic aryl hydrocarbon receptor pathway. Chem. Res. Toxicol. 28, 907–918 (2015). 682. Hedrick, E.; Lee, S. O.; Kim, G.; Abdelrahim, M.; Jin, U. H.; Safe, S.; Abudayyeh, A. Nuclear receptor 4A1 (NR4A1) as a drug target for renal cell adenocarcinoma. PLoS One 10, e0128308 (2015). 681. Hedrick, E.; Lee, S. O.; Doddapaneni, R.; Singh, M.; Safe, S. Nuclear receptor 4A1 (NR4A1) as a drug target for breast cancer chemotherapy. Endocr. Relat. Cancer 22, 831–840 (2015). 680. Hedrick, E.; Crose, L.; Linardic, C. M.; Safe, S. Histone deacetylase inhibitors inhibit rhabdomyosarcoma by reactive oxygen species-dependent targeting of specificity protein transcription factors. Mol. Cancer Ther. 14, 2143–2153 (2015). 679. Hammond, S. L.; Safe, S.; Tjalkens, R. B. A novel synthetic activator of Nurr1 induces dopaminergic gene expression and protects against 6-hydroxydopamine neurotoxicity in vitro. Neurosci. Lett. 607, 83–89 (2015). 678. Goldberg, A. A.; Draz, H.; Montes-Grajales, D.; Oliverso-Verbel, J.; Safe, S. H.; Sanderson, J. T. 3,3'-Diindolylmethane (DIM) and its ring-substituted halogenated analogs (ring-DIMs) induce differential mechanisms of survival and death in androgen-dependent and -independent prostate cancer cells. Genes Cancer 6, 265–280 (2015). 677. Gandhy, S. U.; Imanirad, P.; Jin, U. H.; Nair, V.; Hedrick, E.; Cheng, Y.; Corton, J. C.; Kim, K.; Safe, S. Specificity protein (Sp) transcription factors and metformin regulate expression of the long non-coding RNA HULC. Oncotarget 6, 26359–26372 (2015). 676. Fan, Y. Y.; Davidson, L. A.; Callaway, E. S.; Wright, G. A.; Safe, S.; Chapkin, R. S. A bioassay to measure energy metabolism in mouse colonic crypts, organoids and sorted stem cells. Am. J. Physiol. Gastrointest. Liver Physiol. 309, G1–G9 (2015). 675. De Miranda, B. R.; Popichak, K. A.; Hammond, S. L.; Miller, J. A.; Safe, S.; Tjalkens, R. B. Novel para-phenyl substituted diindolylmethanes protect against MPTP neurotoxicity and suppress glial activation in a mouse model of Parkinson's disease. Toxicol. Sci. 143, 360–373 (2015). 674. De Miranda, B. R.; Popichak, K. A.; Hammond, S. L.; Jorgensen, B. A.; Phillips, A. T.; Safe, S.; Tjalkens, R. B. The Nurr1 activator 1,1-bis(3'-indolyl)-1-(p-chlorophenyl)methane blocks inflammatory gene expression in BV-2 microglial cells by inhibiting NFκB. Mol. Pharmacol. 87, 1021–1034 (2015). 673. Das Gupta, S.; Sae-Tan, S.; Wahler, J.; So, J. Y.; Bak, M. J.; Cheng, L. C.; Lee, M. J.; Lin, Y.; Shih, W. J.; Shull, J. D.; Safe, S.; Yang, C. S.; Suh, N. Dietary gamma-tocopherol rich mixture inhibits estrogen-induced mammary tumorigenesis by modulating estrogen netabolism, antioxidant response and PPARgamma. Cancer Prev. Res. (Phila) 8, 807–816 (2015). 672. Cheng, Y.; Jutooru, I.; Chadalapaka, G.; Corton, J. C.; Safe, S. The long non-coding RNA HOTTIP enhances pancreatic cancer cell proliferation, survival and migration. Oncotarget 6, 10840–10852 (2015). 671. Cheng, Y.; Jin, U. H.; Allred, C. D.; Jayaraman, A.; Chapkin, R. S.; Safe, S. Aryl hydrocarbon receptor activity of tryptophan metabolites in young adult mouse colonocytes. Drug Metab. Dispos. 43, 1536–1543 (2015). 670. Boakye, C. H.; Shah, P. P.; Doddapaneni, R.; Patel, A. R.; Safe, S.; Singh, M. Enhanced percutaneous delivery of 1,1-bis(3'-indolyl)-1-(p-chlorophenyl)methane for skin cancer chemoprevention. J. Biomed. Nanotechnol. 11, 1269–1281 (2015).

CURRENT SUPPORT NIEHS R01-ES025713 Chapkin, R. (PI), Jayaraman (PI), Safe, S. H. (PI) 2016–2021 “Role of aryl hydrocarbon receptor in microbiota-colon stem cell interactions” NCI R01-CA202697 Chapkin, R. (PI), Allred (PI), Safe, S. H. (PI) 2016–2021 “Diet-induced modiciations of microbiota metabolites in colon tumorigenesis” COMPLETED SUPPORT (2015–present) Robert J. and Helen C. Safe, S. H. (PI) 2017–2020 Kleberg Foundation “A novel approach for targeting pediatric sarcoma” CPRIT RP160589 Chapkin, R. (PI), Safe, S. H. (co-PI) 2016–2019 “Aryl hydrocarbon receptor mediated modulation of colorectal cancer by microbiota metabolites” NIEHS R21-ES025839 Safe, S. H. (PI) 2015–2017 “Cytosolic Ah receptor: Mechanism of action” Eli Lilly – Sponsored Safe, S. H. (PI) 2016–2017 “NR4A receptors as targets for C-DIMs”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Member Continuing Education Committee, Society of Toxicology 2009–present Scientific Advisory Board Meharry Medical University – Vanderbilt University 2007–present Scientific Advisory Board Plantacor 2004–present External Advisory Board Environmental Health Center, University of Texas 1995–present Consultant Science Advisory Board of Environmental Protection Agency (EPA) 1984–present International Advisory Board Dioxin Symposia 1980–present Award for Distinguished Texas A&M University Association of Former Students 2020 Membership Member Senior Scholars Executive Committee 2017–2020 Merit Award Society of Toxicology 2019 Member National Academy of Inventors 2019 Phillipe Shubik Award Toxicology Forum 2017 Excellence in Innovation Award Texas A&M Technology and Commercialization 2016 Honorary Doctorate Degree Queen’s University 2016 Associate Editor BioMed Research International Various Editorial Board Biomedical Genetics and Genomics; Cancers; Clinical Pharmacology: Various Advances and Applications; Clinics in Oncology; International Journal of Chronic Diseases and Therapy; Journal Cancers; Journal of Biological Chemistry; Journal of Women's Cancer; Breast Cancer: Targets and Therapy; Nutrition and Dietary Supplements; Reactive Oxygen Species

DEPARTMENT AND SYSTEM SERVICE (2015–present) Advisory Board Institute for Advanced Study TAMU 2012–present Member Promotion and Tenure Committee CVMBS 2012–present Chair Promotion and Tenure Committee VTPP 2012–present Chair, Executive Committee Faculty of Toxicology TAMU 1989–present Libo Shan Christine Richardson Professor of Agriculture | Department of Biochemistry and Biophysics Faculty of Molecular and Environmental Plant Sciences

EDUCATION Postdoctoral Harvard Medical School 2003–2008 Ph.D. Kansas State University 2003 M.S. Chinese Academy of Sciences 1998 B.S. Beijing Normal University 1995

PROFESSIONAL APPOINTMENTS Christine Richardson Biochemistry and Biophysics Texas A&M University 2020–present Professor of Agriculture Molecular and Environmental Plant Sciences Christine Richardson Institute for Plan Genomics & Biotechnology Texas A&M University 2018–2020 Professor of Agriculture Plant Pathology and Microbiology Molecular and Environmental Plant Sciences Director Institute for Plant Genomics and AgriLife Research 2018–2020 Interim Director Biotechnology 2017–2018 Professor Institute for Plan Genomics & Biotechnology Texas A&M University 2016–2018 Plant Pathology and Microbiology Molecular and Environmental Plant Sciences Associate Professor Institute for Plan Genomics & Biotechnology Texas A&M University 2013–2016 Plant Pathology and Microbiology Molecular and Environmental Plant Sciences Assistant Professor Institute for Plan Genomics & Biotechnology Texas A&M University 2009–2013 Plant Pathology and Microbiology Molecular and Environmental Plant Sciences Biochemistry and Biophysics Texas A&M University

PEER-REVIEWED PUBLICATIONS (2015–present) 106. Wang, P.; Jamieson, P.; Zhang, L.; Zhao, Z.; Shao, W.; Wu, L.; Zhou, L.; Mustafa, R.; Amin, I.; Hou, Y.; He, P.; Shan, L. Cotton wall-associated kinase GhWAK7A mediates responses to fungal wilt pathogens by modulating chitin sensory complex. Plant Cell (2021, accepted). 105. Babilonia, K.; Wang, P.; Liu, L.; Jamieson, P.; Rodrigues, O.; Lin, W.; Clement, C. D.; Finlayson, S. A.; Nichols, R. L.; Wheeler, T. A.; Dever, J. K.; Shan, L.; He, P. A non-proteinaceous Fusarium cell wall elicitor triggers receptor-like protein-dependent immune responses in plants. New Phytol. (2021, under revision). 104. Hou, S.; Liu, D.; Lou, D.; Liu, Z.; Han, Z.; Cai, J.; He, P.; Shan, L. Immune activation by sensing conserved signatures from plant cytokines and pathogens via the Arabidopsis MIK2 receptor kinase. Nat. Commun. (2021, under review). 103. Ma, X.; Zhang, C.; Kim, D. Y.; Huang, Y.; He, P.; Vierstra, R. D.; Shan, L. Ubiquitylome analysis revelas a central role for the ubiquitin-proteasome system in plant innate immunity. Plant Physiol. (2021, under review). 102. de A. Manhaes, A. M. E.; Ortiz-Morea, F. A.; He, P.; Shan, L. Plant plasma membrane-resident receptors: surveillance for infections and coordination for growth and development. J. Integ. Plant Biol. (2021, under review). 101. Ortiz-Morea, F. A.; He, P.; Shan, L.; Russinova, E. It takes two to tango: Molecular links between plant immunity and brassinosteroid signaling. J. Cell Sci. (2021). 100. Huang, Y.; Yin, Y.; Liu, J.; Feng, B.; Ge, D.; Kong, K.; Hauser, M.; Wang, W.; Shan, L.; He, P. LETUM malectin-like receptor-like kinases complex with coreceptor LLG1 and regulate NLR protein SUMM2 activation. Nat. Commun. (2020). 99. Huang, Y.; Liu, J.; Kong, L.; Yu, X.; Feng, B.; Mendes, G. C.; Zhao, B.; Yuan, P.; Ge, D.; Wang, W.-M.; Fontest, E. P. B.; Li, P.; Shan, L.; He, P. The malectin-like receptor-like kinase LETUM1 modulates NLR protein SUMM2 activation via MEKK2 scaffolding. Nat. Plants (2020). 98. Ma, X.; Lucas, A. N. C.; Leslie, E. M.; Tao, K.; Wu, Z.; Liu, J.; Xiao, Y.; Li, B.; Zhou, J.; Savatin, V. D.; Peng, J.; Tyler, B.; Heese, A.; Russinova, E.; He, P.; Shan, L. Ligand-induced multi-monoubiquitination of BIK1 regulates plant immunity. Nature 581, 199–203 (2020). 97. Liu, J.; Li, J.; Shan, L. SERKs. Curr. Biol. 30, PR293–R294 (2020). 96. Ley, J. G.; Gross, R.; Mendoza-Herrera, A.; Tang, X.; Babilonia, K.; Shan, L.; Kuhl, J. C.; Dibble, M. S.; Diang, F.; Tamborindeguy. Lso-HPE1, an effector of ‘Cadidatus Liberibacter solanacearum,’ can repress plant immune response. Phytopath. (2020). 95. Yang, Y.; Liu, J.; Yin, C.; de Souza Vespoli, L.; Ge, D.; Huang, Y.; Feng, B.; Xu, G.; de A. Manhaes, A. M. E.; Dou, S.; Criswell, C.; Shan, L.; Wang, X.; He, P. RNA interference-based screen reveals concerted functions of MEKK2 and CRCK3 in plant cell death regulation. Plant Phys. 183, 331–344 (2020). 94. Yu, X.; Xu, G.; Li, B.; de Souza Vespoli, L.; Liu, H.; Moeder, W.; Chen, S.; de Oliveira, M. V. V.; de Souza, S. A.; Shao, W.; Rodrigues, B.; Ma, Y.; Chhajed, S.; Xue, S.; Berkowitz, G. A.; Yoshioka, K.; He, P.; Shan, L. The receptor kinases BAK1/SERK4 regulate Ca2+ channel-mediated cellular homeostasis for cell death containment. Curr. Biol. 29, 3778–3790 (2019). 93. Li, B.; Ferreira, M. A.; Huang, M.; Camargos, L. F.; Yu, X.; Teixeira, R. M.; Carpinetti, P. A.; Mendes, G. C.; Gouveia-Mageste, B. C.; Liu, C.; Pontes, C. S. L.; Brustolini, O. J. B.; Martins, L. G. C.; Melo, B. P.; Duarte, C. E. M.; Shan, L.; He, P.; Fontes, E. P. B. The receptor-like kinase NIK1 targets FLS2/BAK1 immune complex and inversely modulates antiviral and antibacterial immunity. Nat. Commun. 10, 4996 (2019). 92. Yu, X.; Li, B.; Jang, G. J.; Jiang, S.; Jang, J. C.; Wu, S. H.; Shan, L.; He, P. Orchestration of processing body dynamics and mRNA decay in Arabidopsis immunity. Cell Rep. 28, 2194–2205 (2019). 91. Mu, C.; Zhou, L.; Shan, L.; Li, F.; Li, Z. Phosphatase GhDsPTP3a interacts with annexin protein GhANN8b to reversely regulate salt tolerance in cotton (Gossypium spp.) New Phytol. 223, 1856–1872 (2019). 90. Xiong, C.; Luo, D.; Lin, A.; Zhang, C.; Shan, L.; He, P.; Li, B.; Zhang, Q.; Hua, B.; Yuan, Z.; Li, H.; Zhang, J.; Yang, C.; Lu, Y.; Ye, Z.; Wang, T. A tomato B-box protein SIBBX20 modulates carotenoid biosynthesis by directly activating PHYTOENE SYNTHASE 1, and is targeted for 26S proteasome-mediated degradation. New Phytol. 221, 279–294 (2019). 89. Wan, W.; Zhang, L.; Pruitt, R.; Zaidem, M.; Brugman, R.; Ma, X.; Krol, E.; Perraki, A.; Kilian, J.; Grossmann, G.; Stahl, M.; Shan, L.; Zipfel, C.; van Kan, J.; Hedrich, R.; Weigel, D.; Gust, A.; Nuernberger, T. Comparing Arabidopsis receptor kinase and receptor protein-mediated immune signaling reveals BIK1-dependent differences. New Phytol. 221, 2080–2095 (2019). 88. Chen, C.; Yang, S.; Liu, Y.; Jamieson, P.; Shan, L.; Chu, K. Accumulation and phytotoxicity of perfluorooctanic acid and 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)propanoate in Arabidopsis thaliana and Nicotiana benthamiana. Environ. Poll. 259, 113817 (2019). 87. Cox, K. L.; Babilonia, K.; He, P.; Shan, L. Return of old foes – recurrence of bacterial blight and fusarium wilt of cotton. Curr. Opin. Plant Biol. 50, 95–103 (2019). 86. Zhou, J.; Wang, P.; Claus, L. A. N.; Savatin, D. V.; Xu, G.; Wu, S.; Russinova, E.; He, P.; Shan, L. Proteolytic processing of SERK3/BAK1 regulates plant immunity, development and cell death. Plant Physiol. 180, 543–558 (2018). 85. Jamieson, P. A.; Shan, L.; He, P. Plant cell surface molecular cypher: receptor-like proteins and their roles in immunity and development. Plant Sci. 274, 242–251 (2018). 84. Shan, L.; He, P. Pipped at the post: pipecolic acid derivative identified as SAR regulator. Cell 173, 286–287 (2018). 83. Lal, N. K.; Nagalakshmi, U.; Hurlburt, N. K.; Flores, R.; Bak, A.; Sone, P.; Ma, X.; Song, G.; Walley, J.; Shan, L.; He, P.; Casteel, C.; Fisher, A. J.; Dinesh-Kumar, S. P. The receptor-like cytoplasmic kinase BIK1 localizes to the nucleus and regulates defense hormone expression during plant innate immunity. Cell Host and Microbe 23, 485–497 (2018). 82. Huang, Y.; Jamieson, P.; Shan, L. The APEX approaches: a unified LRR-RK network revealed. Trends in Plant Sci. 23, 372–374 (2018). 81. Zhou, J.; Liu, D.; Wang, P.; Lin, W.; Chen, S.; Mishev, K.; Lu, D.; Kumar, R.; Vanhoutte, I.; He, P.; Russinova, E.; Shan, L. Regulation of Arabidopsis brassinosteroid receptor BRI1 endocytosis and intracellular degradation by the E3 ubiquitin ligase PUB12/PUB13-mediated ubiquitination. Proc. Natl. Acad. Sci. USA 115, e1906–e1915 (2018). 80. Fan, J.; Bai, P.; Xiong, Y.; Ning, Y.; Zhang, C.; Wang, R.; Meng, X.; Zhou, J.; Wang, M.; Park, C. H.; Bellizzi, M.; Jeon, J. S.; Shan, L.; Wang, G.-L. The monocot-specific receptor-like kinase SDS2 modulated by the E3 ligase SPL11 controls cell death and immunity via receptor-like cytoplasmic kinases in rice. Cell Host & Microbe 23, 498–510 (2018). 79. Gao, F. Y.; DeFalco, T. A.; Moeder, W.; Li, B.; Gong, Y. C.; Liu, X. M.; Taniguchi, M.; Lumba, S.; Toh, S.; Shan, L.; Ellis, B.; Desveaux, D.; Yoshioka, K. Arabidopsis ETHYLENE RESPONSE FACTOR 8 (ERF8) has dual functions in ABA signaling and immunity. BMC Plant Biol. 18, 211 (2018). 78. He, Y.; Zhou, J.; Shan, L.; Meng, X. Plant cell surface receptor-mediated signaling – a common theme amid diversity. J. Cell Sci. 131, jcs209353 (2018). 77. Yu, X.; Feng, B.; He, P.; Shan, L. From chaos to harmony: responses and signaling upon microbial pattern recognition. Ann. Rev. Phytopath. 55, 109–137 (2017). 76. Cox, K. L.; Meng, F.; Wilkins, K. E.; Li, F.; Wang, P.; Booher, N. J.; Chen, L. Q.; Zheng, H.; Gao, X.; Zheng, Y.; Fei, Z.; Yu, J. Z.; Isakeit, T.; Wheeler, T.; Frommer, W. B.; He, P.; Bogdanove, A. J.; Shan, L. TAL effector-mediated induction of a SWEET sucrose transporter confers susceptibility to bacterial blight of cotton. Nat. Commun. (2017). 75. Mang, H.; Feng, B.; Hu, Z.; Boisson-Dernier, A.; Franck, C. M.; Meng, X.; Xu, G.; Wang, T.; Shan, L.; He, P. Differential regulation of two-tiered plant immunity and sexual reproduction by ANXUR receptor-like kinases. The Plant Cell 29, 3140–3156 (2017). 74. Li, F.; Li, M.; Wang, P.; Cox, K. L.; Duan, L.; Dever, J. K.; Shan, L.; Li, Z.; He, P. Regulation of cotton drought responses by a MAP kinase cascade-mediated phosphorylation of GhWRKY59. New Phytol. 215, 1462–1475 (2017). 73. Ma, X.; Xu, G.; He, P.; Shan, L. SERKing coreceptors for receptors. Trends Plant Sci. 21, 1017–1033 (2016). 72. Meng, X.; Zhou, J.; Tang, J.; Li, B.; Oliveira, M. V. V.; Chai, J.; He, P.; Shan, L. Ligand-induced receptor-like kinase complex regulates floral organ abscission in Arabidopsis. Cell Rep. 14, 1330–1338 (2016). 71. Feng, B.; Ma, S.; Chen, S.; Zhu, N.; Zhang, S.; Yu, B.; Yu, Y.; Le, B.; Chen, X.; Dinesh-Kumar, S. P.; Shan, L.; He, P. PARylation of the forkhead-associated domain protein DAWDLE regulates plant immunity. EMBO Rep. 17, 1799–1813 (2016). 70. Feng, B.; Liu, C.; Shan, L.; He, P. ADP-ribosylation takes control in plant-bacterium interactions. PLoS Pathog. 12, 31005941 (2016). 69. Li, B.; Meng, X.; Shan, L.; He, P. Transcriptional regulation of plant pattern-triggered immunity. Cell Host and Microbe 19, 641–650 (2016). 68. de Oliveira, M. V. V.; Xu, G.; Li, B.; de Souza Vespoli, L.; Meng, X.; Chen, X.; Yu, X.; de Souza, S. A.; Intorne, A. C.; de A. Manhaes, A. M. E.; Musinsky, A. L.; Koiwa, H.; de Souza Filho, G. A.; Shan, L.; He, P. Specific control of Arabidopsis BAK1/SERK4-regulated cell death by protein glycosylation. Nat. Plants 2, 15218 (2016). 67. Meng, X.; Chen, X.; Liu, C.; Yu, X.; Gao, X.; Torii, U. K.; He, P.; Shan, L. Differential function of Arabidopsis SERK family receptor-like kinases in stomatal patterning. Curr. Biol. 25, 2361–2372 (2015). 66. Li, B.; Jiang, S.; Yu, X.; Cheng, C.; Chen, S.; Cheng, Y.; Yuan, J.; Jiang, D.; He, P.; Shan, L. Phosphorylation of trihelix transcription repressor ASR3 by MPK4 negatively regulates Arabidopsis immunity. The Plant Cell 27, 839–856 (2015). 65. Meng, X.; Shan, L.; He, P. Stack heterotrimeric G proteins and MAPK cascades on a RACK. Mol. Plant 8, 1691–1693 (2015). 64. Zhou, J.; Lu, D.; Xu, G.; Finlayson, S. A.; He, P.; Shan, L. The dominant negative ARM domain uncovers multiple functions of plant U-box E3 ligase PUB13 in Arabidopsis immunity, flowering, and senescence. J. Exp. Botany 66, 3353–3366 (2015).

CURRENT SUPPORT USDA NIFA Shan, L. (co-PI) 2020–2023 “Protein phosphorylation and poly(ADP-riboyl)ation in cotton drought stress” NSF Shan, L. (co-PI) 2019–2022 “Fate of per- and polyfluoroalkyl substances (PFASs) in soils affected by plant and rhizosphere microbial community” USDA NIFA Shan, L. (PI) 2019–2022 “Enhancing resistance in upland cotton by dissecting the disease mechanism of Fusarium oxysporum f. sp. Vasinfectum race 4” NSF-MCB Shan, L. (co-PI) 2019–2022 “Processing-body dynamics and mRNA regulation in plants” Research Development Fund, TAMU Shan, L. (PI) 2019–2021 “A PREcision genomics Core to advance Innovation Systems bioEngineering (PRECISE)” AgriLife Research Strategic Research Shan, L. (co-PI) 2019–2021 Initiative “Fov4 in Texas cotton” USDA NIFA Shan, L. (PI) 2018–2021 “Cotton resistance and susceptibility to bacterial blight” Welch Foundation Shan, L. (PI) 2012–2021 “Biochemical and regulatory constraints of immune sensors” NIH R01 Shan, L. (PI) 2011–2021 “Phosphorylation and ubiquitination of immune sensory complexes in innate immune signaling”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Chancellor Enhancing Development and Texas A&M University 2020 Generating Excellence in Scholarship (EDGES) Fellow Standing Member NIH Cellular Signaling and Regulatory Systems Study Section 2019–2024 Associate Editor PLoS Pathogens 2019–present Guest Editor 2016–2019 Guest Editor Plant Cell 2018–present Editorial Board The Arabidopsis Book 2013–present Dorothy Elaine Shippen University Distinguished Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral University of California, Berkeley; San Francisco with E. Blackburn 1987–1991 Ph.D. Biology, University of Alabama 1987 B.S. Biology, Auburn University 1982

PROFESSIONAL APPOINTMENTS Distinguished Professor Executive Committee Texas A&M University 2019–present Interim Head Biochemistry and Biophysics Texas A&M University 2018–2019 Chair Genetics IDP Texas A&M University 2016–2018 Professor Biochemistry and Biophysics Texas A&M University 2002–2019 Associate Professor Biochemistry and Biophysics Texas A&M University 1997–2002 Assistant Professor Biochemistry and Biophysics Texas A&M University 1991–1997

PEER-REVIEWED PUBLICATIONS (2015–present) 72. Choi, J. Y.; Abdulkina, L. R.;Yin, J.; Chastukhina, I. B.; Lovell, J. T.; Inna, A.; Agabekian, I. A.; Young, P. G.; Razzaque, S.; Shippen, D. E.; Juenger, T. E.; Shakirov, E. V.; Purugganan, M. D. Natural variation in plant telomere length is associated with flowering time. In revision for Plant Cell. 71. Bose, S.; Suescún, V.; Song, J.; Castillo-González, C.; Aklilu, B. B.; Branham, E.; Lynch, R.; Shippen, D. E. tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana. Plant Cell Reports 39, 1669–1685 (2020). 70. Aklilu, B.; Peurois, F.; Saintome, C.; Culligan, K. M.; Kobbe, D.; Smithson, C.; Chung, M.; Cattoor, M.; Lynch, R.; Sampson, L.; Fatora, J.; Shippen, D. E. Functional diversification of Replication Protein A paralogs and telomere length maintenance in Arabidopsis. Genetics 215, 989–1002 (2020). 69. Montgomery, S. A.; Tanizawa, Y.; Galik, B.; Wang, N.; Ito, T. A.; Mochizuki, T.; Akimcheva, S.; Bowman, J.; Cognat, V.; Drouard, L.; Ekker, H.; Houng, S.-F.; Kohchi, T.; Lin, S.-S.; Liu, D. L-Y.; Nakamura, Y.; Valeeva, L. R.; Shakirov, E. V.; Shippen, D. E.; Wei, W.-L.; Yagura, M.; Yamoaka, S.; Yamato, K. T.; Liu, C.; Berger, F. Chromatin organization in early land plants reveals an ancestral association between H3K27me3, transposons, and constitutive heterochromatin. Current Biology 30, 573–588 (2020). 68. Kobayashi, C.; Nigmatullina, L. R.; Chastukhina, I. B.; Lovell, J. T.; Suescún, A. V.; Aklilu, B.; Valeeva, L. R.; Nyamsuren, C.; Aglyamova, G. V.; Sharipova, M. R.; Shippen, D. E.; Juenger, T. E.; Shakirov, E. V. Components of the ribosome biogenesis pathway underlie establishment of telomere length set point in Arabidopsis. Nat. Commun. 10, 5479 (2019). 67. Song, J.; Logeswaran, D.; Castillo-González, C.; Li, Y.; Bose, S.; Aklilu, B.; Ma, Z.; Polkhovsky, A.; Chen, J. J.-L.; Shippen, D. E. The conserved structure of plant telomerase RNA provides the missing link for an evolutionary pathway from ciliates to humans. PNAS USA 49,24542–24550 (2019). 66. Kobayashi, C.; Castillo-González C.; Surovtseva Y.; Canal, E.; Nelson, A. D. L.; Shippen, D. E. Recent emergence and extinction of the Protection of Telomeres 1c gene in Arabidopsis thaliana. Plant Cell Reports 38, 1081–1097 (2019). 65. Watson, J. M.; Trieb, J.*; Schirato-Trostl, M.*; Renfrew, K.; Mandakova, T.; Lysak, M.; Shippen, D. E.; Riha, K. A hypomorphic allele of telomerase reverse transcriptase uncovers the minimal functional length of telomeres in Arabidopsis. BioRxiv (2019). 64. Xie, X.; Shippen, D. E. DDM1 guards against telomere truncation in Arabidopsis. Plant Cell Rep. 37, 501–513 (2018). 63. Schaller, M. D.; McDowell, G.; Porter, A.; Shippen, D. E.; Friedman, K. L.; Gentry, M. S.; Serio, T. R.; Sundquist, W. I. What’s in a name? eLife 6, e32437 (2017). 62. Lee, J. R.; Zhang, J.; Yang, K.; Lee, S. Y.; Xie, X.; Shippen, D. E. Dynamic interactions of Arabidopsis TEN1: stabilizing telomeres in response to heat stress. Plant Cell 28, 2212–2224 (2016). 61. Arora, A.; Beilstein, M. A.; Shippen, D. E. Evolution of Arabidopsis Protection of Telomeres 1 alters nucleic acid recognition and telomerase regulation. Nucleic Acids Research 44, 9821–9830 (2016). 60. Xu, H.; Nelson, A. D. L. and Shippen, D. E. A transposable element within the Non-canonical telomerase RNA of Arabidopsis thaliana modulates telomerase in response to DNA damage. PLoS Genetics 11, e1005281 (2015). 59. Beilstein, M. A.; Renfrew, K. B.; Song, X.; Shakirov, E. V. and Shippen, D. E. Evolution of the telomerase-associated protein POT1a in Arabidopsis thaliana is characterized by positive selection to reinforce protein-protein interaction. Molecular Biology and Evolution 32, 1329 –1341 (2015). 58. González-García, M. P.; Pavelescu, I.; Canela, A.; Sevillano, J.; Leehy, K. A.; Nelson, A. D. L.; Shippen, D. E.; Blasco, M.; Caño-Delgado, A. Single-Cell Telomere-Length Quantification Couples Telomere Length to Meristem Activity and Stem Cell Development in Arabidopsis. Cell Reports 11, 977–989 (2015).

CURRENT SUPPORT NIH #R01-GM065383 Shippen, D. (PI) 2020–2024 “Telomere structure and function in Arabidopsis” NIH #T32 GM125748 Shippen, D. (Co-PI); Butler-Perry, K. (PI) 2020 – 2025 “IMSD at Texas A&M University: Initiative for maximizing student diversity in biomedical sciences” NIH #R01-GM12702-01 Shippen, D. (PI) 2018 –2022 “Genetic and epigenetic architecture of natural telomere length variation” NSF #MCB 1517817 Shippen,D. (PI) 2015–2021 “REU Regulation of TER2, the non-canonical telomerase RNA in Arabidopsis”

COMPLETED SUPPORT (2015–present) CRDF Global Shippen, D. E. (PI) 2018–2019 “A role for NOP2 in the control of telomere length” NSF #MCB-1052018 Shippen, D. E. (PI) 2018–2019 “Negative regulation of telomerase in Arabidopsis” NIH RO1 GM065383 Shippen, D. E. (PI) 2015–2020 “Telomere structure and function in Arabidopsis” NIH R01-GM065383 Shippen, D. E. (PI) 2015–2016 “Telomere structure and function in Arabidopsis” NSF #MCB-1052018 Shippen, D. E. (PI) 2011–2016 “Regulation of TER2, the non-canonical telomerase RNA in Arabidopsis” CPRIT RP130639 Shippen, D. E. (PI); Fuchs-Young, R. (Co-PI) 2010–2015 “A role for non-coding RNA in telomerase inhibition”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) TAMU Regents Professor Award 2020 EMBO, Co-Organizer Plant DNA Repair and Recombination (postponed due to COVID-19) 2020 ASBMB William Rose Award for Outstanding Contributions to Biochemical 2019 Research and Commitment to Training Younger Scientists TAMU Dean’s Outstanding Achievement Award in Administration 2015 ASBMB Public Affairs Advisory Committee, American Society for Biochemistry 2015–present and Molecular Biology TAMU Association of Former Students Distinguished Achievement Award for 2015 Graduate Mentoring NIH, CDF-1, CDF-2, NDT, MGC Study section reviewer 2000–present

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member President’s Commission on Diversity, Equity and Inclusion TAMU 2020–present Member Executive Committee, University Distinguished Professors TAMU 2019–present Member Biological Sciences Strategic Planning Committee TAMU 2019 Interim Head Department of Biochemistry and Biophysics BCBP 2018–2019 Chair Interdisciplinary Graduate Program in Genetics TAMU 2016–2018 Member American Association of Biochemistry and Molecular TAMU 2015–present Biology Public Affairs Advisory Committee Member Executive Committee MD-PhD Program TAMU 2012–2015

COURSES TAUGHT (2015–present) BICH/GENE 631 Biochemical Genetics (co-taught) 3 cr. 2020 BICH/GENE 101 Perspectives in Biochemistry and Genetics 1 cr. 2019 BICH 681 Seminar 1 cr. 2019 GENE 302 Principles of Genetics 1 cr. 2012–present BICH 689 Building Scientific Relationships 1 cr. 2010–2018 BICH 673 Gene Expression (Journal Club) 1 cr. 2007–2012 BICH 491/691 Research Variable 1991–present Patrick J. Stover Vice Chancellor and Dean | College of Agriculture and Life Sciences University Distinguished Professor | Biochemistry and Biophysics Director | Texas A&M AgriLife Research

EDUCATION Postdoctoral University of California at Berkeley with B. Shane 1992–1994 Postdoctoral Medical College of Virginia with V. Schirch 1990–1991 Ph.D. Medical College of Virginia with V. Schirch 1993 B.S. Saint Joseph’s University 1986

PROFESSIONAL APPOINTMENTS Vice Chancellor and Dean College of Agriculture and Life Sciences Texas A&M University 2018–present University Distinguished Biochemistry and Biophysics Texas A&M University 2018–present Professor Director Texas A&M AgriLife Research Texas A&M University 2018–present Adjunct Professor Biomedical Sciences Cornell University 2000–present Director Collaborating Centre on Implementation World Health Organization 2015–2018 Research in Nutrition and Global Policy Director Nutritional Sciences Cornell University 2005–2018 Professor Nutritional Sciences Cornell University 2005–2018 Associate Professor Nutritional Sciences Cornell University 2000–2005 Assistant Professor Nutritional Sciences Cornell University 1994–2000

PEER-REVIEWED PUBLICATIONS (2015–present) 31. Misselbeck, K.; Marchetti, L.; Priami, C.; Stover, P. J.; Field, M. S. The 5-formyltetrahydrofolate futile cycle reduces pathway stochasticity in an extended hybrid-stochastic model of folate-mediated one-carbon metabolism. Sci Rep. 9, 4322 (2019). 30. Alonzo, J. R.; Venkataraman, C.; Field, M. S.; Stover, P. J. The mitochondrial inner membrane protein MPV17 prevents uracil accumulation in mitochondrial DNA. J. Biol. Chem. 293, 20285–20294 (2019). 29. Chon, J.; Field, M. S.; Stover, P. J. Deoxyuracil in DNA and disease: Genomic signal or managed situation? DNA Repair (Amst). 77, 36–44 (2019). 28. Tiani K. A.; Stover, P. J.; Field, M. S. The role of brain barriers in maintaining brain vitamin levels. Annu. Rev. Nutr. 39, 147–173 (2019). 27. James, W. P. T.; Johnson, R. J.; Speakman, J. R.; Wallace, D. C.; Frühbeck, G.; Iversen, P. O.; Stover, P. J. Nutrition and its role in human evolution. J. Intern Med. 285, 533–549 (2019). 26. Lan, X.; Field, M. S.; Stover, P. J. Cell cycle regulation of folate-mediated one-carbon metabolism. Wiley Interdiscip. Rev. Syst. Biol. Med. 10, e1426 (2018). 25. Balling, R.; Stover, P. J. Introduction. Annu. Rev. Nutr. (2018). 24. Lan, X.; Field, M. S.; Stover, P. J. Cell cycle regulation of folate-mediated one-carbon metabolism. Wiley Interdiscip. Rev. Syst. Biol. Med. 10, e1426 (2018). 23. Stover, P. J.; James, W. P. T.; Krook, A.; Garza, C. Emerging concepts on the role of epigenetics in the relationships between nutrition and health. J. Intern. Med. 284, 37–49 (2018). 22. Field, M. S.; Lan, X.; Stover, D. M.; Stover, P. J. Dietary uridine decreases tumorigenesis in the ApcMin/+ model of intestinal cancer. Curr. Dev. Nutr. 13, nzy013 (2018). 21. Field, M. S.; Kamynina, E.; Chon, J.; Stover, P. J. Nuclear folate metabolism. Annu. Rev. Nutr. 38, 219–243 (2018). 20. Dixit, R.; Nettem, S.; Madan, S. S.; Soe, H. H. K.; Abas, A. B.; Vance, L. D.; Stover, P. J. Folate supplementation in people with sickle cell disease. Cochrane Database Syst. Rev. 16, CD011130 (2018). 19. Stover, P. J.; Durga, J.; Field M. S. Folate nutrition and blood-brain barrier dysfunction. Curr. Opin. Biotech. 9, 146– 152 (2017). 18. Hootman, K. C.; Trezzi, J. P.; Kraemer, L.; Burwell, L. S.; Dong, X.; Guertin, K. A.; Jaeger, C.; Stover, P. J.; Hiller, K.; Cassano, P. A. Erythritol is a pentose-phosphate pathway metabolite and associated with adiposity gain in young adults. Proc. Natl. Acad. Sci. 114, E4233–E4240 (2017). 17. Chon, J.; Stover, P. J.; Field, M. S. Targeting nuclear thymidylate biosynthesis. Mol. Aspects Med. 53, 48–56 (2017). 16. Kamynina, E.; Stover, P. J. The roles of sumo in metabolic regulation. Adv. Exp. Med. Biol. 963, 143–168 (2017). 15. Palmer, A. M.; Kamynina, E.; Field, M. S.; Stover, P. J. Folate rescues vitamin B12 depletion-induced inhibition of nuclear thymidylate biosynthesis and genome instability. Proc. Natl. Acad. Sci. 114, E4095–E4102 (2017). 14. Misselbeck, K.; Marchetti, L.; Field, M. S.; Scotti, M.; Priami, C.; Stover P. J. A hybrid stochastic model of folate- mediated one-carbon metabolism: Effect of the common C677T MTHFR variant on de novo thymidylate biosynthesis. Sci. Rep. 7, 797 (2017). 13. Bae, S.; Chon, J.; Field, M. S.; Stover, P. J. Alcohol dehydrogenase 5 is a source of formate for de novo purine biosynthesis in HepG2 cells. J. Nutr. 147, 499–505 (2017). 12. Kamynina, E.; Lachenauer, E. R.; DiRisio, A. C.; Liebenthal, R. P.; Field, M. S.; Stover, P. J. Arsenic trioxide targets MTHFD1 and SUMO-dependent nuclear de novo thymidylate biosynthesis. Proc. Natl. Acad. Sci. 21, E2319–E2326 (2017). 11. Field, M. S.; Stover, P. J.; Kisliuk, R. Thymidylate Synthesis in eLS. John Wiley & Sons, Ltd: Chichester (2016). 10. Dixit, R.; Nettem, S.; Madan, S. S.; Soe, H. H.; Abas, A. B.; Vance, L. D.; Stover, P. J. Folate supplementation in people with sickle cell disease. Cochrane Database Syst. Rev. 2, CD011130 (2016). 9. Field, M. S.; Kamynina E.; Watkins, D.; Rosenblatt, D. S.; Stover, P. J. MTHFD1 regulates nuclear de novo thymidylate biosynthesis and genome stability. Biochimie 126, 27-30 (2016). 8. MacFarlane, A.; Stover, P. J. Gastrointestinal Disorders: Overview. Encyclopedia of Public Health. International Encyclopedia of Public Health Second Edition, vol. 3 pp. 9–19 (2016). 7. Field, M. S.; Kamynina, E.; Watkins, D.; Rosenblatt, D. S.; Stover, P. J. New insights into the metabolic and nutritional determinants of severe combined immunodeficiency rare diseases. 3, e1112479 eCollection (2015). 6. Bailey, L. B.; Stover, P. J.; McNulty, H.; Fenech, M. F.; Gregory, J. F. III; Mills, J. L.; Pfeiffer, C. M.; Fazili, Z.; Zhang, M.; Ueland, P. M.; Molloy, A. M.; Caudill, M. A.; Shane, B.; Berry, R. J.; Bailey, R. L.; Hausman, D. B.; Raghavan, R.; Raiten, D. J. Biomarkers of nutrition for development–Folate Review. J. Nutr. 145, 1636S–1680S (2015). 5. MacFarlane, A. J.; Behan, N. A.; Field, M. S.; Williams, A.; Stover, P. J.; Yauk, C. L. Dietary folic acid protects against genotoxicity in the red blood cells of mice. Mutat. Res. 779, 105–111 (2015). 4. Finkelstein, J. L.; Layden, A. J.; Stover, P. J. Vitamin B-12 and perinatal health. Adv. Nutr. 15, 552–563 (2015). 3. Stover, P. J.; Field, M. S. Vitamin B6. Adv. Nutr. 6, 132–133 (2015). 2. Martiniova, L.; Field, M. S.; Finkelstein, J. L.; Perry, C. A.; Stover, P. J. Maternal dietary uridine causes, and deoxyuridine prevents, neural tube closure defects in a mouse model of folate-responsive neural tube defects. Amer. J. Clin. Nutr. 101, 860–869 (2015). 1. Field, M. S.; Kamynina, E.; Watkins, D.; Rosenblatt, D. D.; Stover, P. J. Human mutations in methylenetetrahydrofolate dehydrogenase 1 impair nuclear de novo thymidylate biosynthesis. Proc. Natl. Acad. Sci. 112, 400–405 (2015).

CURRENT SUPPORT NIH #R37-DK58144 Stover, P. J. 2012–2022 “Homeostatic Regulation of Folate Metabolism” USDA Agricultural Research Service Stover, P. J. 2018–2021 “Responsive Agriculture and Food Systems to Promote Health and Quality of Life across the Life Span”

COMPLETED SUPPORT (2015–present) NIH #R01-HD059120 Stover, P. J. 2014–2020 “Gene-Nutrient Interactions in Neural Tube Defects” NIH T32-DK007158 Stover, P. J. 2017–2022 (expired 2018) “Nutrition Training”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Advisory Board Aegean Conferences 2019–present Advisory Board International Import Center on Food Nutrition and Human Health 2017–present External Advisory Committee Fred Hutchinson Cancer Center, Cancer Prevention Training: 2016–present Epidemiology, Nutrition, Genetics and Survivorship Chair, Board Member Marabou Foundation Scientific Advisory Committee 2015–present Editor Annual Reviews of Nutrition 2014–present Associate Editor Frontiers in Genetics present Member Integrated Biomarker and Signaling-Pathways Approaches for 2020 Understanding Operational Performance Panel, NASA Member FAO Director General’s Roundtable on the Future of Food 2019 Member American Society for Nutrition Fellows Selection Panel 2019 Elected Member TAMU Chapter of Phi Kappa Phi 2019 Scientific Advisory Committee Biofotis 2015–2019 Scientific Advisory Committee Supporters of Agricultural Research (SoAR) Foundation 2015–2019 Co-Organizer Precision Nutrition in Public Health and Medicine, Aegean Conference 2018 Series Organizer Cornell University Responsible Conduct of Research Symposium 2018 Scientific Advisory Committee Chobani 2015–2018 Chair NIH, Nutrition Research Task Force Thought Leaders Panel 2017 Chair ARS/USDA, Retrospective Review Panel 2017 National Academies of Redesigning the Process for Establishing the Dietary Guidelines for 2017 Sciences Reports Americans National Academies of Optimizing the Process for Establishing the Dietary Guidelines for 2017 Sciences Reports Americans, The Selection Process Board of Directors American Society for Nutritional Sciences 2011–2017 Elected Member National Academy of Sciences 2016 Member, Consensus Study NAS, The Development of Guiding Principles for the Inclusion of Chronic 2016 Disease Endpoints in Future Dietary Reference Intakes Chair NIH, Iron Screening and Supplementation of Iron-Replete Pregnant 2016 Women and Young Children Member NIDCR/NIH, Gene-Environment Interaction in Oralfacial Clefting 2016 Member Johnson Space Center, Evaluation of the Current Understanding of the 2016 Role of Nutrition in Space, to Define Nutritional Requirements for Future Space Exploration Missions Panel Member Medical Research Council, Nutrition and Human Health Research 2016 President American Society for Nutrition 2015–2016 Member Committee to Establish a Cochrane Nutrition Field 2015 Organizer New York Academic of Sciences, Conference on Distinctive Nutritional 2015 Requirements Member NIH/RTI, Nutrition and Dietary Supplements Committee: PhenX 2014–2015 Consensus Measures for Phenotypes and Exposures Member, Expert Panel NIH/ILSI/USDA/ASNS, Achieving a Transparent, Actionable Framework 2014–2015 for Public-Private Partnerships Member, Expert Panel NTP/NIH, Identifying Research Needs for Assessing Safe Use of High 2014–2015 Intakes of Folic Acid Organizer WHO/Cochrane Collaboration/Cornell University Summer Institute for 2014–2015 Systematic Reviews in Nutrition for Global Policy Making Member NAS, Framework for Assessing the Health, Environmental, and Social 2013–2015 Effects of the Food System Member Undernutrition Group, Scientific Steering Committee, The Sackler Institute 2011–2015 for Nutrition Science Treasurer Association of Nutrition Departments and Chairs 1996–2015 Ad hoc Peer Reviewer Journals: Science, Nature, JAMA Internal Medicine, The Journal of Various Biological Chemistry, Structure, Gene, Biochemistry, Journal of Clinical Nutrition, Analytical Biochemistry, BBA, Blood, Journal of Molecular Biology, Brain Research, Journal of Nutrition, Analytical Chemistry, Pharmacogenomics, Molecular Genetics and Metabolism, Proceedings of the National Academy of Sciences, Mammalian Genome, Carcinogenesis Ad hoc Reviewer Granting Agencies: Canadian Cancer Society, NSERC/CRSNG, NIH, Various Health Research Council of New Zealand, NASA, USDA,

Paul Straight Associate Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Harvard Medical School With R. Kolter 2008 Ph.D. Molecular/Cellular Biology, University of Colorado, Boulder 2000 B.S. Biochemistry, Lewis & Clark College 1992

PROFESSIONAL APPOINTMENTS Associate Professor Biochemistry and Biophysics Texas A&M University 2014–present Assistant Professor Biochemistry and Biophysics Texas A&M University 2008–2014 Instructor Genetics IDP Harvard Medical School/MIT/Broad Institute 2007–2008

PEER-REVIEWED PUBLICATIONS (2015–present) 9. Zhang, C.; Straight, P. D. Antibiotic discovery through microbial interactions. Curr. Opin. Microbiol. 51, 64–71 (2019). 8. Liu, Y.; Kyle, S.; Straight, P. D. Antibiotic stimulation of a Bacillus subtilis migratory response. mSphere 3, e00586-17 (2018). 7. Stubbendieck, R. M.; Brock, D. J.; Pellois, J.-P.; Gill, J. J.; Straight, P. D. Linearmycins are lytic membrane-targeting antibiotics. J. Antibiot. 71, 372–381 (2018). 6. Stubbendieck, R. M.; Straight, P. D. Linearmycins activate a two-component signaling system involved in bacterial competition and biofilm morphology. J. Bacteriol. 199, e00186-17 (2017). 5. Goodson, J. R.; Klupt, S.; Zhang, C.; Straight, P.; Winkler, W. C. LoaP is a broadly conserved antiterminator protein that regulates antibiotic gene clusters in Bacillus amyloliquefaciens. Nat Microbiol. 2, 17003 (2017). 4. Hoefler, B. C.; Stubbendieck, R. M.; Josyula, N. K.; Moisan, S. M.; Schulze. E. M.; Straight, P. D. A link between linearmycin biosynthesis and extracellular vesicle genesis connects specialized metabolism and bacterial membrane physiology. Cell Chem. Biol. 24, 1238–1249 (2017). 3. Stubbendieck, R. M.; Vargas-Bautista, C.; Straight, P. D. Bacterial communities: Interactions to scale. Front Microbiol. 7, article 1234 (2016). 2. Stubbendieck, R. M.; Straight, P. D. Multifaceted interfaces of bacterial competition. J. Bacteriol. 198, 2145–2155 (2016). Stubbendieck, R. M.; Straight, P. D. Escape from lethal bacterial competition through coupled activation of antibiotic 1. resistance and a mobilized subpopulation. PLoS Genet. 12, e1005722 (2015).

COMPLETED SUPPORT (2015–present) NSF-Career MCB-1243215 Straight, P. (PI) 2013–2020 “Essential functions of secondary metabolic networks for bacterial competition” TAMU-Conacyt 2017-51 Straight, P. (PI) 2017–2019 “Discovery of new antibiotics through EvoMining and fitness typing” TAMU Welch Foundation A-1796 Straight, P. (PI) 2012–2015 “Identification of antibiotic resistance and modifying enzymes from bacterial competitive interactions”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Consultant Lynntech, Inc. 2018–present Ad hoc peer reviewer Various scientific journals 2016–present Reviewer Faculty Tenure and Promotion Review, Claremont McKenna College 2019 Member NSF-BIO SSB – Microbial Systems Grant Review 2017 Member NSF-BIO SSB – Metabolism Grant Review 2015

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Undergraduate Programs Committee BCBP 2020 Reviewer Astronaut Scholars Foundation Program TAMU 2019 Member Outreach Committee – Genetics IDP GENE 2018–2019 Faculty Advisor Secondary Genetics Graduate Student Association GENE 2013–2018 Member PCL Users Committee BCBP 2017

COURSES TAUGHT (2015–present) BICH 440 Biochemistry I 3 cr. 2009–present BICH 489 Molecular Mechanisms of Cell Interactions 3 cr. 2010–present BICH 491/691 Research Variable 2008–present

Sing-Hoi Sze Associate Professor | Departments of Biochemistry and Biophysics, Computer Science and Engineering

EDUCATION Postdoctoral University of California at San Diego 2001–2002 Ph.D. University of Southern California 2000 M.S. Pennsylvania State University 1995 B.Sc. Chinese University of Hong Kong 1990

PROFESSIONAL APPOINTMENTS Associate Professor Biochemistry and Biophysics Texas A&M University 2008–present Computer Science and Engineering Assistant Professor Biochemistry and Biophysics Texas A&M University 2002–2008 Computer Science and Engineering

PEER-REVIEWED PUBLICATIONS (2015–present) 41. Dadaneh, S. Z.; de Figueiredo, P.; Sze, S.-H.; Zhou, M.; Qian, X. Bayesian gamma-negative binomial modeling of single-cell RNA sequencing data. BMC Genomics 21 (Suppl. 9:585) (2020). 40. Liu, Y.-H.; Xu, Y.; Zhang, M.; Cui, Y.; Sze, S.-H.; Smith, C. W.; Xu, S.; Zhang, H.-B. Accurate prediction of a quantitative trait using the genes controlling the trait for gene-based breeding in cotton. Front Plant Sci. 11 (2020). 39. Qiu, C.; Jin, H.; Vvedenskaya, I.; Llenas, J. A.; Zhao, T.; Malik, I.; Visbisky, A. M.; Schwartz, S. L.; Cui, P.; Cabart, P.; Han, K. H.; Lai, W. K. M.; Metz, R. P.; Johnson, C. D.; Sze, S.-H.; Pugh, B. F.; Nickels, B. E.; Kaplan, D. C. Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. Gen. Biol. 21 (2020). 38. Zhang, M.; Cui, Y.; Liu, Y.-H.; Xu, W.; Sze, S.-H.; Xu, S.; Zhang, H.-B. Accurate prediction of maize grain yield using its contributing genes for gene-based breeding. Genomics 112, 225–236 (2020). 37. Fu, S.; Chang, P. L.; Friesen, M. L.; Teakle, N. L.; Tarone, A. M.; Sze, S.-H. Identifying similar transcripts in a related organism from de Bruijn graphs of RNA-Seq data, with applications to the study of salt and waterlogging tolerance in Melilotus. BMC Genomics 20 (Suppl. 5:425) (2019). 36. Pimsler, M. L.; Sze, S.-H.; Saenz, S.; Fu, S.; Tomberlin, J. K.; Tarone, A. M. Gene expression correlates of facultative predation in Chrysomya rufifacies. Ecol. Evol. 9, 8690–8701 (2019). 35. Song, J.-M.; Arif, M.; Zhang, M.; Sze, S.-H.; Zhang, H.-B. Phenotypic and molecular dissection of grain quality using the USDA rice mini-core collection. Food Chem. 284, 312–322 (2019). 34. Zhang, Y.; Pechal, J. L.; Schmidt, C. J.; Jordan, H. R.; Wang, W. W.; Benbow, M. E.; Sze, S.-H.; Tarone, A. M. Machine learning performance in a microbial molecular autopsy context: a cross-sectional postmortem human population study. PLoS One 14, e0213829 (2019). 33. Zhu, Z.; ur Rehman, K.; Yu, Y.; Liu, X.; Wang, H.; Tomberlin, J. K.; Sze, S.-H.; Cai, M.; Zhang, J.; Yu, Z.; Zheng, J.; Zheng, L. De novo transcriptome sequencing and analysis revealed the molecular basis of rapid fat accumulation by black soldier fly (Hermetia illucens, L.) for development of insectival biodiesel. Biotechnol. Biofuels 12 (2019). 32. Pandey, A.; Ding, S. L.; Qin, Q.-M.; Gupta, R.; Gomez, G.; Lin, F.; Feng, X.; Fachini da Costa, L.; Chaki, S. P.; Katepalli, M.; Case, E. D.; van Schaik, E. J.; Sidiq, T.; Khalaf, O.; Arenas, A.; Kobayashi, K. S.; Samuel, J. E.; Rivera, G. M.; Alaniz, R. C.; Sze, S.-H.; Qian, X.; Brown, W. J.; Rice-Ficht, A.; Russell, W. K.; Ficht, T. A.; de Figueiredo, P. Global reprogramming of host kinase signaling in response to fungal infection. Cell Host Microb. 21, 637–649 (2017). 31. Sze, S.-H.; Parrott, J. J.; Tarone, A. M. A divide-and-conquer algorithm for large-scale de novo transcriptome assembly through combining small assemblies from existing algorithms. BMC Genomics 18 (Suppl. 10:895) (2017). 30. Sze, S.-H.; Pimsler, M. L.; Tomberlin, J. K.; Jones, C. D.; Tarone, A. M. A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms. BMC Genomics 18 (Suppl. 4:387) (2017). 29. Yuan, Y.; Zhang, Y.; Fu, S.; Crippen, T. L.; Visi, D. K.; Benbow, M. E.; Allen, M. S.; Tomberlin, J. K.; Sze, S.-H.; Tarone, A. M. Genome sequence of a Providencia stuartii strain isolated from Lucilia sericata salivary glands. Gen. Announc. 5, e00250-17 (2017). 28. Qiu, C.; Erinne, O. C.; Dave, J. M.; Cui, P.; Jin, H.; Muthukrishnan, N.; Tang, L. K.; Babu, S. G.; Lam, K. C.; Vandeventer, P. J.; Strohner, R.; Van den Brulle, J.; Sze, S.-H.; Kaplan, C. D. High-resolution phenotypic landscape of the RNA Polymerase II trigger loop. PLoS Gene. 12, e1006321 (2016). 27. Yuan, Y.; Zhang, Y.; Fu, S.; Crippen, T. L.; Visi, D. K.; Benbow, M. E.; Allen, M. S.; Tomberlin, J. K.; Sze, S.-H.; Tarone, A. M. Genome sequence of a Proteus mirabilis strain isolated from the salivary glands of larval Lucilia sericata. Gen. Announc. 4, e00672-16 (2016). 26. Chen, J.; Fan, J.-H.; Sze, S.-H. Parameterized and approximation algorithms for maximum agreement forest in multifurcating trees. Theor. Comp. Sci. 562, 496–512 (2015). 25. Edman, R. M.; Linger, R. J.; Belikoff, E. J.; Li, F.; Sze, S.-H.; Tarone, A. M.; Scott, M. J. Functional characterization of calliphorid cell death genes and cellularization gene promoters for controlling gene expression and cell viability in early embryos. Insect. Mol. Biol. 24, 58–70 (2015). 24. Fu, S.; Tarone, A. M.; Sze, S.-H. Heuristic pairwise alignment of de Bruijn graphs to facilitate simultaneous transcript discovery in related organisms from RNA-Seq data. BMC Genomics 16 (Suppl. 11:S5) (2015).

CURRENT SUPPORT Texas A&M T3 Miglietta, M. (PI), Hala, D. (co-PI), Sze, S.-H. (co-PI) 2019–2021 “Characterization of toxins in jellyfish species common to the Gulf of Mexico and their toxicological effects in fish” NIH Kaplan, C. (PI), Sze, S.-H. (co-PI) 2017–2021 “Mechanism and regulation of RNA Polymerase II elongation” COMPLETED SUPPORT (2015–present) NIH Kaplan, C. (PI), Nickels, B. (co-PI), Sze, S.-H. (co-PI) 2016–2020 “ Determinants and mechanisms of RNA Polymerase II initiation” National Institute of Justice Taron, A. (PI), Sze, S.-H. (co-PI) 2016–2019 “ Proteomic and microRNA markers of fly development: stable correlates of insect age to improve forensic entomology casework” National Institute of Justice Tarone, A. (PI), Picard, C. (co-PI), Sze, S.-H. (co-PI) 2013–2015 “ Genomic tools to reduce error in PMI estimates derived from entomology evidence”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Panelist NSF Division of Computing and Communication Foundations 2020 Program Committee Member International Conference on Bioinformatics and Biomedical Technology 2017–2020 Program Committee Member International Work-Conference on Bioinformatics and Biomedical 2017–2020 Engineering Program Committee Member IEEE International Conference on Computational Advances in Bio and 2015–2020 Medical Sciences Program Committee Member International Symposium on Bioinformatics Research and Applications 2015–2020 Program Committee Member International Symposium on Network Enabled Health Informatics, 2020 Biomedicine, and Bioinformatics 2015–2018 Program Committee Member International Conference on Bioinformatics and Computational Biology 2020 2015–2016 Program Committee Member IEEE International Conference on Bioinformatics and Biomedicine 2019–2020 2015–2016

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Honors Committee CSCE 2018–2019, 2020 Member Promotion and Tenure Committee CSCE 2015, 2020 Chair Master’s Admissions and Recruiting Committee CSCE 2019–2020 Member Master’s Admissions and Recruiting Committee CSCE 2017–2019 Chair Academic Professional Track Faculty Search Committee CSCE 2017–2019 Member Climate Committee CSCE 2015–2017 Member Graduate Admissions and Recruiting Committee CSCE 2015

COURSES TAUGHT (2015–present) BICH/GENE 419 Computational Techniques for Evolutionary Analysis 2015–present CSCE 222 Discrete Structures for Computing 3 cr. 2016–present CSCE 411 Design and Analysis of Algorithms 3 cr. 2015, 2018–2019 CSCE 629 Analysis of Algorithms 2018 CSCE 628 Computational Biology 2015 David W. Threadgill University Distinguished Professor | Department of Biochemistry and Biophysics Distinguished Professor | Department of Molecular and Cellular Medicine Chair | Interdisciplinary Faculty of Genetics Interim Founding Head | Department of Nutrition Director | Center for Environmental Health Research Founding Director | Genome Society Tom and Jean McMullin Chair of Genetics

EDUCATION Postdoctoral Case Western Reserve University Ph.D. Texas A&M University 1989 B.S. Texas A&M University 1983

PROFESSIONAL APPOINTMENTS Interim Founding Head Nutrition Texas A&M University 2020–present University Distinguished Biochemistry and Biophysics Texas A&M University 2018–present Professor Molecular and Cellular Medicine Chair Interdisciplinary Faculty of Genetics Texas A&M University 2018–present Director Center for Environmental Health Research Texas A&M University 2017–present Founding Director Genome Sciences and Society Texas A&M University 2014–present Tom and Jean McMullin Health Science Center Texas A&M University 2013–present Chair of Genetics Adjunct Professor Biological Sciences North Carolina State University 2013–2019 University Distinguished Veterinary Pathobiology Texas A&M University 2015–2018 Professor Molecular and Cellular Medicine Professor Veterinary Pathobiology Texas A&M University 2013–2015 Molecular and Cellular Medicine Professor and Head Genetics North Carolina State University 2008–2013 Assistant, Associate, Genetics University of North Carolina 2000–2008 Professor Assistant Professor Cell Biology Vanderbilt University 1996–2000

PEER-REVIEWED PUBLICATIONS (2015–present) 166. Eldridge, R.; Osorio, D.; Amstalden, K.; Edwards, C.; Young, C. R.; Cai, J. J.; Konganti, K.; Hillhouse, A.; Threadgill, D. W.; Welsh, C. J.; Brinkmeyer-Langford, C. Antecedent presentation of neurological phenotypes in the Collaborative Cross reveals four classes with complex sex-dependencies. Sci. Rep. 10, 7918 (2020). 165. Garbutt, T. A.; Konganti, K.; Konneker, T.; Hillhouse, A.; Phelps, D.; Jones, A.; Ayler, D.; Threadgill, D. W. Derivation of stable embryonic stem cell-like, but transcriptionally heterogenous, induced pluripotent stem cells from non-permissive mouse strains. Mamm. Genome (2020, in press). 164. Mao, J.-H.; Kim, Y.-H.; Zhou, Y.-X.; Hu, D.; Zhong, C.; Chang, H.; Brislawn, C.; Langley, S.; Wang, Y.; Peisl, B. Y. L.; Celniker, S. E.; Threadgill, D.; Wilmes, P.; Orr, G.; Metz, T. O.; Jansson, J. K.; Snijders, A. Genetic and metabolic links between the murine microbiome and memory. Microbiome 8, 53 (2020). 163. Ma, L.; Li, H.; Hu, J.; Zheng, J.; Zhou, J.; Botchlett, R.; Matthews, D.; Zeng, T.; Chen, L.; Xiao, X.; Athrey, G.; Threadgill, D. W.; Li, Q.; Glaser, S.; Francis, H.; Meng, F.; Li, Q.; Alpini, G.; Wu, C. Indole alleviates diet-induced hepatic steatosis and inflammation in a manner involving myeloid cell PFKFB3. Hepatology (2020, in press). 162. Arora, S.; Li, X.; Hillhouse, A.; Konganti, K.; Little, S.; Lawhon, S.; Threadgill, D. W.; Shelburne, S.; Hook M. The Staphylococcus epidermidis MSCRAMM SesJ is encoded in composite islands. mBio 11, e02911–e02919 (2020). 161. Price, A.; Okumura, A.; Haddock, E.; Feldman, F.; Meade-White, K.; Sharma, P.; Artami, M.; Lipkin, W. I.; Threadgill, D. W.; Feldmann, H.; Rasmuseen, A. L. Transcriptional correlates of tolerance and lethality in mice predict Ebola virus disease patient outcomes. Cell Rep. 30, 1702–1713 (2020). 160. Aminian, M.; Andrews-Polymenis, H.; Gupta, J.; Kirby, M.; Kvinge, H.; Ma, X.; Rosse, P.; Scoggin, K.; Threadgill, D. W. Mathematical methods for visualization and anomaly detection in telemetry datasets. Interface Focus 10, 20190086 (2020). 159. Bissahoyo, A. C.; Xie, Y.; Yang, L.; Pearsall, R. S.; Lee, D. K.; Elliott, R. W.; Demant, P.; McMillan, L.; de Villena, F. P. M.; Angel, J. M.; Threadgill, D. W. A new polygenic model for non-familial colorectal cancer inheritance based on the genetic architecture of the azoxymethane-induced mouse model. Genetics 214, 691–702 (2020). 158. Sudweeks, J.; Hollingsworth, B.; Blondel, D. V.; Campbell, K. J.; Dhole, S.; Eisemann, J. D.; Edwards, O.; Godwin, J.; Howald, G. R.; Oh, K. P.; Piaggio, A. J.; Prowse, T. A. A.; Ross, J. V.; Saah, J. R.; Shiels, A. B.; Thomas, P. Q.; Threadgill, D. W.; Vella, M. R.; Gould, F.; Lloyd, A. L. Locally fixed alleles: a method to localize gene drive to island populations. Sci. Rep. 9, 15821 (2019). 157. Wang, P.; Wang, Y.; Langley, S. A.; Zhou, Y. X.; Jen, K. Y.; Sun, Q.; Brislawn, C.; Rojas, C. M.; Wahl, K. L.; Wang, T.; Fan, X.; Jansson, J. K.; Celniker, S. E.; Zou, X.; Threadgill, D. W.; Snijders, A. M.; Mao, J. H. Diverse tumour susceptibility in Collaborative Cross mice: identification of a new mouse model for human gastric tumourigenesis. Gut 68, 1942–1952 (2019). 156. Perry, A.; Lynch, R. M.; Rusyn, I.; Threadgill, D. W. Long-term combinatorial exposure to trichloroethylene and inorganic arsenic in genetically heterogeneous mice results in renal tubular damage and cancer-associated molecular changes. GGG 9, 1729–1737 (2019). 155. Zhang, K.; Guo, X.; Yan, H.; Wu, Y.; Pan, Q.; Shen, J. Z.; Li, X.; Chen, Y.; Li, L.; Qi, Y.; Xu, Z.; Xie, W.; Zhang, W.; Threadgill, D. W.; He, L.; Villarreal, D.; Sun, Y.; White, M. F.; Zheng, H.; Guo, S. Phosphorylation of forkhead protein FoxO1 at S253 regulates glucose homeostasis in mice. Endocrinology 160, 1333–1347 (2019). 154. Batool, M.; Hillhouse, A. E.; Ionov, Y.; Kochan, K. J.; Mohebbi, F.; Stoica, G.; Threadgill, D. W.; Zelikovsky, A.; Waghela, S. D.; Wiener, D. J.; Rogovskyy, A. S. New Zealand white rabbits effectively clear Borrelia burgdorferi B31 despite the bacterium's functional vlsE antigenic variation system. Infect Immun. 87, e00164-19 (2019). 153. Lewis, L.; Borowa-Mazgaj, B.; de Conti, A.; Chappell, G. A.; Luo, Y. S.; Bodnar, W.; Konganti, K.; Wright, F. A.; Threadgill, D. W.; Chiu, W. A.; Pogribny, I. P.; Rusyn, I. Population-based analysis of DNA damage and epigenetic effects of 1,3-butadiene in the mouse. Chem. Res. Toxicol. 32, 887–898 (2019). 152. Orzabal, M. R.; Lunde-Young, E. R.; Ramirez, J. I.; Naik, V. D.; Hillhouse, A.; Konganti, K.; Threadgill, D. W.; Ramadoss, J. Gestational binge alcohol-induced alterations in maternal uterine artery transcriptome. Reprod. Toxicol. 87, 42–49 (2019). 151. Rogovskyy, A. S.; Threadgill, D. W.; Akimov, I. A.; Nebogatkin, I. V.; Rogovska, Y. V.; Melnyk, M. V.; Rogovskyy, S. P. Borrelia and other zoonotic pathogens in Ixodes ricinus and Dermacentor reticulatus ticks collected from the Chernobyl exclusion zone on the 30th anniversary of the nuclear disaster. Vector Borne Zoonotic Dis. 19, 466–473 (2019). 150. Lunde-Young, R.; Ramirez, J.; Naik, V.; Orzabal, M.; Lee, J.; Konganti, K.; Hillhouse, A.; Threadgill, D. W.; Ramadoss, J. Hippocampal transcriptome reveals novel targets of FASD pathogenesis. Brain Behav. 9, e01334 (2019). 149. Luo, Y. S.; Cickocki, J. A.; Hsieh, N. H.; Lewis, L.; Wright, F. A.; Threadgill, D. W.; Chiu, W. A.; Rusyn, I. Using Collaborative Cross mouse population to fill data gaps in risk assessment: A case study of population-based analysis of toxicokinetics and kidney toxicodynamics of tetrachloroethylene. Environ Health Perspect. 127, 67011 (2019). 148. Orzabal, M. R.; Lunde-Young, E. R.; Ramirez, J. I.; Howe, S. Y. F.; Naik, V. D.; Lee, J.; Heaps, C. L.; Threadgill, D. W.; Ramadoss, J. Chronic exposure to e-cig aerosols during early development causes vascular dysfunction and offspring growth deficits. Transl. Res. 207, 70–82 (2019). 147. Cickocki, J.; Luo, Y.-S.; Furuya, S.; Venkatratnam, A.; Konganti, K.; Chiu, W.; Threadgill, D. W.; Pogribny, I.; Rusyn, I. Modulation of tetrachloroethylene-associated kidney effects by nonalcoholic fatty liver or steatohepatitis in male C57BL/6J mice. Toxicol. Sci. 167, 126–137 (2019). 146. Cuomo, D.; Porreca, I.; Ceccarelli, M.; Threadgill, D. W.; Barrington, W. T.; Petriella, A.; D’Angelo, F.; Cobellis, G.; De Stefano, F.; D’Agostino, M. N.; De Felice, M.; Mallardo, M.; Ambrosino, C. Transcriptional landscape of mouse-aged ovaries reveals a unique set of non-coding RNAs associated with physiological and environmental ovarian dysfunctions. Cell Death Discov. 4, 112 (2018). 145. Dornbos, P.; Warren, M.; Crawford, R. B.; Kaminski, N. E.; Threadgill, D. W.; LaPres, J. J. Characterizing Serpinb2 as a modulator of TCDD-induced suppression of the B cell. Chem. Res. Toxicol. 31, 1248–1259 (2018). 144. Garbutt, T. A.; Konneker, T. I.; Konganti, K.; Hillhouse, A. E.; Swift-Haire, F.; Jones, A.; Phelps, D.; Aylor, D. L.; Threadgill, D. W. Permissiveness to form pluripotent stem cells may be an evolutionarily derived characteristic in Mus musculus. Sci. Rep. 8, 14706 (2018). 143. Konganti, K.; Ehrlich, A.; Rusyn, I.; Threadgill, D. W. gQTL: A web application for QTL analysis using the Collaborative Cross mouse genetic reference population. GGG 8, 2559–2562 (2018). 142. Konganti, K.; Guerrero, F.; Schilkey, F.; Ngam, P.; Jacobi, J.; Umale, P.; de Leon, A. P.; Threadgill, D. W. A whole genome assembly of the horn fly, Haematobia irritans, and prediction of genes with roles in metabolism and sex determination. GGG 8, 1675–1686 (2018). 141. Venkatratnam, A.; House, J. S.; Konganti, K.; McKenney, C.; Threadgill, D. W.; Chiu, W. A.; Aylor, D. L.; Wright, F. A.; Rusyn, I. Population-based dose-response analysis of liver transcriptional response to trichloroethylene in mouse. Mamm. Genome 29, 168–181 (2018). 140. Wells, A.; Barrington, W.; Dearth, S.; Threadgill, D. W.; Campagna, S.; Voy, B. Tissue level diet and sex-by-diet interactions reveal unique metabolite and clustering profiles using untargeted liquid chromatography-mass spectrometry on adipose, skeletal muscle, and liver tissue in C57BL6/J mice. J. Proteome Res. 17, 1077–1090 (2018). 139. Maurizio, P. L.; Ferris, M. T.; Keele, G. R.; Miller, D. R.; Shaw, G. D.; Whitmore, A. C.; West, A.; Morrison, C. R.; Noll, K. E.; Plante, K. S.; Cockrell, A. S.; Threadgill, D. W.; Pardo-Manuel de Villena, F.; Baric, R. S.; Heise, M. T.; Valdar, W. Bayesian diallel analysis reveals Mx1-dependent and Mx1-independent effects on response to influenza A virus in mice. GGG 8, 427–445 (2018). 138. Barrington, W. T.; Wulfridge, P.; Wells, A. E.; Rojaas, C. M.; Howe, S. Y. F.; Perry, A.; Hua, K.; Pellizzon, M. A.; Hansen, K. D.; Voy, B. H.; Bennett, B. J.; Pomp, D.; Feinberg, A. P.; Threadgill, D. W. Improving metabolic health through precision dietetics in mice. GGG 208, 399–417 (2018). 137. Leitschuh, C. M.; Kanavy, D.; Backus, G. A.; Valdez, R. X.; Serr, M.; Pitts, E. A.; Threadgill, D. W.; Godwin, J. Developing gene drive technologies to eradicate invasive rodents from islands. J. Res. Innov. 5, S121–138 (2018). 136. Gao, Y.; Fang, X.; Vincent, D. F.; Threadgill, D. W.; Bartholin, L.; Li, Q. Disruption of postnatal folliculogenesis and development of ovarian tumor in a mouse model with aberrant transforming growth factor beta signaling. Reprod. Biol. Endocrinol. 15, 94 (2017). 135. Brinkmeyer-Langford, C. L.; Rech, R.; Amstalden, K.; Kochan, K. J.; Hillhouse, A. E.; Young, C.; Welsh, C. J.; Threadgill, D. W. Host genetic background influences diverse neurological responses to viral infection in mice. Sci. Rep. 7, 12194 (2017). 134. Cichocki, J. A.; Furuya, S.; Luo, Y. S.; Iwata, Y.; Konganti, K.; Chiu, W. A.; Threadgill, D. W.; Pogribny, I. P.; Rusyn, I. Nonalcoholic fatty liver disease is a susceptibility factor for perchloroethylene-induced liver effects in mice. Toxicol. Sci. 159, 102–113 (2017). 133. Venkatratnam, A.; Furuya, S.; Kosyk, O.; Gold, A.; Bodnar, W.; Koganti, K.; Threadgill, D. W.; Gillespie, K. M.; Aylor, D.; Wright, F. A.; Chiu, W. A.; Rusyn, I. Collaborative Cross mouse population enables refinements to characterization of the variability in toxicokinetics of trichloroethylene and provides genetic evidence for the role of PPAR pathway in its oxidative metabolism. Toxicol. Sci. 158, 48–62 (2017). 132. Cichocki, J. A.; Furuya, S.; Venkatratnam, A.; McDonald, T. J.; Knap, A. H.; Wade, T.; Sweet, S.; Chiu, W. A.; Threadgill, D. W.; Rusyn, I. Characterization of variability in toxicokinetics and toxicodynamics of tetrachloroethylene using the Collaborative Cross mouse population. Environ. Health. Perspec. 125, 057006 (2017). 131. Feng, Y.; Demehri, F. R.; Xiao, W.; Tsai, Y. H.; Jones, J. C.; Brindley, C. D.; Threadgill, D. W.; Holst, J. J.; Hartmann, B.; Barrett, T. A.; Teitelbaum, D. H.; Dempsey, P. J. Interdependency of EGF and GLP-2 signaling in attenuating mucosal atrophy in a mouse model of parenteral nutrition. CMGH Cell Mol. Gastroenterol. 3, 447–468 (2017). 130. Cichocki, J. A.; Furuya, S.; Konganti, K.; Luo, Y. S.; McDonald, T. J.; Iwata, Y.; Chiu, W. A.; Threadgill, D. W.; Pogribny, I. P.; Rusyn, I. Impact of nonalcoholic fatty liver disease on toxicokinetics of tetrachloroethylene in mice. J. Pharmacol. Exp. Ther. 361, 17–28 (2017). 129. Kelly, S. A.; Zhao, L.; Jung, K. C.; Hua, K.; Threadgill, D. W.; Kim, Y.; de Villena, F. P. M.; Pomp, D. Prevention of tumorigenesis in mice by exercise is dependent on strain background and timing relative to carcinogen exposure. Sci. Rep. 7, e43086 (2017). 128. Bautz, D. J.; Sherpa, A. T.; Threadgill, D. W. Prophylactic vaccination targeting ERBB3 decreases polyp burden in a mouse model of human colorectal cancer. OncoImmunology 6, e1255395 (2016). 127. Scheving, L. A.; Zhang, X.; Threadgill, D. W.; Russell, W. E. Hepatocyte ERBB3 and EGFR are required for maximal CCl4-induced liver fibrosis. Am. J. Physiol. Gastrointest. Liver Physiol. 311, G807–816 (2016). 126. Didion, J. P.; Morgan, A. P.; Yadgary, L.; Bell, T. A.; McMullan, R. C.; de Solorzano, L. O.; Britton-Davidian, J.; Bult, C. J.; Campbell, K. J.; Castiglia, R.; Ching, Y. H.; Chunco, A. J.; Crowley, J. J.; Chesler, E. J.; French, J. F.; Gabriel, S. I.; Gatti, D. M.; Garland, T.; Giagia-Athanasopoulous, E. B.; Gimenez, M. D.; Grize, S.; Gunduz, I.; Holmes, A.; Hauffe, H. C.; Herman, J. S.; Holt, J. M.; Hua, K.; Jolley, W. J.; Lindholm, A.; Lopez-Fuster, M. J.; Mitsainas, G.; Mathias, M.; McMillan, L.; Ramalhinho, M. G.; Rehermann, B.; Rosshart, S. R.; Searle, J. B.; Shiao, M. S.; Solano, E.; Svenson, K. L.; Thomas-Laemont, P.; Threadgill, D. W.; Queija, J. A.; Weinstock, G. M.; Pomp, D.; Churchill, G. A.; de Villena, F. P. M. R2d2 drives selfish sweeps in the house mouse. Mol. Biol. Evol. 33, 1381–1395 (2016). 125. Ceddia, R. P.; Lee, D. K.; Maulis, M. F.; Carboneau, B. A.; Threadgill, D. W.; Poffenberger, G.; Milne, G.; Boyd, K. L.; Powers, A. C.; McGuiness, O. P.; Gannon, M.; Breyer, R. M. The PGE2 EP3 receptor regulates diet-induced adiposity in male mice. Endocrinology 157, 220–232 (2016). 124. Scheving, L. A.; Zhang, X.; Stevenson, M. C.; Weintraub, M. A.; Abbasi, A.; Clarke, A. M.; Threadgill, D. W.; Russell, W. E. Loss of hepatocyte ERBB3 but not EGFR impairs hepatocarcinogenesis. Am. J. Physiol. Gastrointest. Liver Physiol. 309, G942–G954 (2015). 123. Gralinski, L. E.; Ferris, M. T.; Aylor, D. L.; Whitmore, A. C.; Green, R.; Frieman, M.; Deming, D.; Menachery, V. D.; Miller, D.; Buus, R. J.; Bell, T. A.; Churchill, G.; Threadgill, D. W.; Katze, M. G.; McMillan, L.; Valdar, W.; Heise, M. T.; de Villena, F. P. M.; Baric, R. S. Genome wide identification of SARS-CoV susceptibility loci using the Collaborative Cross. PLoS Genetics 11, e1005504 (2015). 122. Chen, J. K.; Nagai, K.; Chen, J.; Plieth, D.; Hino, M.; Hu, J.; Sha, F.; Ikizler, A.; Quarles, C. C.; Threadgill, D. W.; Neilson, E. G.; Harris, R. H. Phosphatidylinositol 3-kinass (PI3K) signaling determines kidney size. J. Clin. Investig. 125, 2429–2444 (2015). 121. Song, X.; Fan, P. D.; Bantikassegn, A.; Guha, U.; Threadgill, D. W.; Varmus, H.; Politi, K. ERBB3-independent activation of the PI3K pathway in EGFR-mutant lung adenocarcinomas. Cancer Res. 75, 1035–1045 (2015). 120. Crowley, J. J.; Zhabotynsky, V.; Sun, W.; Huang, S.; Pakatci, I. K.; Kim, Y.; Wang, J. R.; Morgan, A. P.; Calaway, J. D.; Aylor, D. L.; Yun, Z.; Bell, T. A.; Buus, R. J.; Calaway, M. E.; Didion, J. P.; Gooch, T. J.; Hansen, S. D.; Robinson, N. N.; Shaw, G. D.; Spence, J. S.; Quackenbush, C. R.; Barrick, C. J.; Nonneman, R. J.; Kim, K.; Xenakis, J.; Xie, Y.; Valdar, W.; Lenarcic, A. B.; Wang, W.; Welsh, C. E.; Fu, C. P.; Zhang, Z.; Holt, J.; Guo, Z.; Threadgill, D. W.; Tarantino, L. M.; Miller, D. R.; Zou, F.; McMillan, L.; Sullivan, P. F.; Pardo-Manuel de Villena, F. Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. Nat. Genetics 47, 353–360 (2015). 119. Church, R. J.; Gatti, D. M.; Urban, T. J.; Long, N.; Yang, X.; Shi, Q.; Eaddy, J. S.; Mosedale, M.; Ballard, S.; Churchill, G. A.; Navarro, V.; Watkins, P. B.; Threadgill, D. W.; Harrill, A. H. Sensitivity to hepatotoxicity due to epigallocatechin gallate is affected by genetic background in diversity outbred mice. Food Chem. Toxicol. 76, 19–26 (2015). 118. Scheving, L. A.; Zhang, X.; Stevenson, M. C.; Threadgill, D. W.; Russell, W. E. Loss of hepatocyte EGFR has no effect alone but exacerbates carbon tetrachloride-induced liver injury and impairs regeneration in hepatocyte Met-deficient mice. Am. J. Physiol. Gastrointest. Liver Physiol. 308, G364–377 (2015). 117. Didion, J. P.; Morgan, A. P.; Clayshulte, A. M.; Mcmullan, R. C.; Yadgary, L.; Petkov, P. M.; Bell, T. A.; Gatti, D. M.; Crowley, J. J.; Hua, K.; Aylor, D. L. Bai, L.; Calaway, M.; Chesler, E. J.; French, J. E.; Geiger, T. R.; Gooch, T. J.; Garland, T Jr.; Harrill, A. H.; Hunter, K.; McMillan, L.; Hold, M.; Miller, D. R.; O’Brien, D. A.; Paigen, K.; Pan, W.; Rowe, L. B.; Shaw, G. D.; Simecek, P.; Sullivan, P. F.; Svenson, K. L.; Weinstock, G. M.; Threadgill, D. W.; Pomp, D.; Churchill, G. A.; Pardo-Manuel de Villena, F. A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2. PLoS Genetics 11, 31004850 (2015). 116. Campbell, K. J.; Beek, J.; Eason, C. T.; Glen, A. S. Godwin, G.; Gould, F.; Holmes, N. D.; Howald, G. R.; Madden F. M.; Ponder, J. B.; Threadgill, D. W.; Wegmann, A. S.; Baxter, G. S. The next generation of rodent eradications: Innovative technologies and tools to improve species specificity and increase their feasibility on islands. Biol. Conserv. 185, 47–58 (2015).

CURRENT SUPPORT NIH/NIGMS #T32-GM135748 Threadgill, D. W. (co-PI) 2020–2025 “IMSD at Texas A&M University: Initiative for maximizing student diversity in biomedical sciences” NIH/NIEHS #P30-ES029067 Threadgill, D. W. 2019–2024 “Texas A&M Center for Environmental Health Research” NIH/NIEHS #R01-ES029911 Threadgill, D. W. (co-PI); Rusyn, I. (co-PI); Tretyakova (co-PI); Wright 2019–2024 (co-PI) “Chromatin regions, genes and pathways that confer susceptibility to chemical-induced DNA damage” NIH/NIDDK DP1 DK119129 Threadgill, D. W. (co-I) 2018–2023 “Epigenetic drivers of intrinsic phenotypic variability in metabolic disease” NIH/NIEHS #P42-ES027704 Threadgill, D. W. (co-I) 2017–2022 “Comprehensive tools and models for addressing exposure to mixtures during environmental emergency-related contamination events” NIH/NIHGRI/NIEHS Threadgill, D. W. (co-PI); Feinberg (co-PI) 2016–2021 #RM1-HG008529 “Center for Integration of Genomics and the Environment” DARPA D17AP00004 Threadgill, D. W. 2017–2020 “Tolerance mechanisms through innovative population analysis” COMPLETED SUPPORT (2015–present) NIH/NCI #R25-CA172010 Jackson (PI) 2014–2019 “Workshop on techniques in modeling human cancer in mice” EPA, RD 83580201 Threadgill, D. W. 2015–2019 “Linking in vitro to in vivo toxicity testing using genetically-matched organoids and mice from a novel genetic reference population” NIH/NIEHS #P42-ES004911 Threadgill, D. W. (subcontract PI) 2014–2018 “Environmental microbial and mammalian bimolecular responses to AHR ligands” DARPA Threadgill, D. W. (co-I) 2017–2018 “Restoring ecosystems and biodiversity through development of safe and effective gene drive technologies” NIH/NIEHS #P30-ES023512 Threadgill, D. W. (PI) 2014–2018 “Center for Translational Environmental Health Research” NIH/NCI #U01-CA105417 Threadgill, D. W. (PI) 2004–2016 “Modeling heterogeneity for safe cancer prevention and detection (NCI Mouse Models of Human Cancer Consortium)”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Board of Scientific Counselors NCI – Basic Research 2016–present External Advisory Board Vanderbilt SPOR in CI Cancer 2016–present Steering Committee Member Genetic Biocontrol of Invasive Rodents 2016–present Editorial Board Mammalian Genetics 2011–present Associate Editor G3: Genes, Genomes, and Genetics 2011–present Editorial Board Cancer Prevention Research 2008–present External Advisory Board Peromyscus Genetics Stock Center, University of South Carolina 2015–present Excellence in Mentorship and Genetics Graduate Student Association 2019 Support Award Review Committee Member University of North Texas Health Science Center 2019 Paper of the Year Award Toxicology Sciences 2019 Barbara Bowman Distinguished Texas Genetics Society 2018 Texas Geneticist Award Program Site Reviewer NCI Intramural Genetics Branch 2017 External Review Committee ORNL-UT Governor’s Chair 2017 Associate Editor Genetics 2009–2017 Grant Review Panel NCI Special Emphasis Panel, Cancer Biology 2016 Grant Review Panel NICHD Special Emphasis Panel, Gynecologic Health and Disease 2016 Outstanding Research Leader Award College of Veterinary Medicine and Biomedical Sciences 2015 Grant Review Panel NCI Special Emphasis, Cancer Biology 2015 Grant Review Panel Shriner’s Hospital Research Institute 2015 Ad hoc Grant Reviewer USDA Animal Molecular Genetics and Gene Mapping; USDA Various Sustaining Animal Health and Well-Being; NSF Eukaryotic Genetics; Alberta Innovation and Science; US Department of Energy; Vanderbilt University Discovery Grant Program; NIH Immunological Sciences Study Section; Vanderbilt GI SPORE; Vanderbilt Diabetes Center; Wellcome Trust; Oak Ridge Associated Universities; Bankhead-Coley Cancer Research Program; Pennsylvania Cancer Research Program Performance Review; Research Grants Council of Hong Kong; L’Agence Nationale de la Recherche, France; Medical Research Council Grants Program, UK Ad hoc Peer Reviewer Genomics; Mammalian Genome; Laboratory Animal Science; Cancer Various Research; Journal of Molecular Endocrinology; Cell Growth and Differentiation; Genetics; Molecular and General Genetics; Genome Biology; Genesis; Proceedings of the National Academy of Sciences; BioTechniques; ILAR Journal; Genome Research; Gastroenterology; Molecular and Cellular Biology; Circulation; Cytokine; Clinical Cancer Research; Brain Research; Journal of the American Society for Information Science and Technology; Nature Genetics; Alcoholism: Clinical and Experimental Research; Human Molecular Genetics; Trends in Genetics, Molecular Carcinogenesis; Physiological Genomics; Science; Nature; Nature Medicine; Aging Cell

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member President’s Excellence Fund Advisory Committee TAMU 2018–present Member MD/PhD Program Executive Committee TAMU 2016–present Member Undergraduate Research Organization Council TAMU 2016–present Member Interdisciplinary Faculty of Genetics Executive Committee TAMU 2015–present Member Interdisciplinary Faculty of Toxicology Executive Committee TAMU 2014–present Faculty Supervisor Rodent Phenotyping Core TAMU 2014–present President-elect, President, Council of Principal Investigators TAMU 2017–2020 Past-President Member Distinguished Professor Selection Committee TAMU 2018–2019 Chair College of Medicine Research Advisory Committee TAMU 2018–2019 Member 2014–2019 Co-Chair HSC Associate Vice Chancellor for Research Search Committee TAMU 2017–2019 Member Council of Principal Investigators TAMU 2016–2019 Member Faculty Advisory Task Force for President’s Large Projects TAMU 2017–2018 Initiative Member College of Medicine Faculty Pay Plan Design Committee TAMU 2017–2018 Member Council of Principal Investigators Executive Committee TAMU 2016–2017 Member College of Medicine Dean and VP Search Committee TAMU 2015 Member Department of Veterinary Pathobiology Department Head TAMU 2015 Search Committee Member Research Computing Task Force TAMU 2014–2015

COURSES TAUGHT (2015–present) NFSC 481 Seminar 1 cr. 2020 NFSC 204 Perspectives in Nutrition 1 cr. 2020 BICH 631 Biochemical Genetics (co-taught) 3 cr. 2020 VTPB 212 Genetics in the News 3 cr. 2015–2018 BIMS 489 Introduction to Bioinformatics 3 cr. 2017 GENE 689 Bioinformatics: Command Line Skills 3 cr. 2017 GENE 689 Bioinformatics: Metagenomics Data Analysis 1 cr. 2017 I. J. Cecilia Tommos Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral University of Pennsylvania STINT Fellow 1997–2000 Ph.D. Stockholm University, Stockholm, Sweden 1997 B.S. Stockholm University, Stockholm, Sweden 1992

PROFESSIONAL APPOINTMENTS Professor Biochemistry and Biophysics Texas A&M University 2019–present Research Associate Professor Biochemistry and Biophysics University of Pennsylvania 2015–present Research Assistant Professor Biochemistry and Biophysics University of Pennsylvania 2006–2015 Docent Biochemistry Stockholm University 2006–2007 Swedish Research Council Assistant Biochemistry and Biophysics Stockholm University 2000–2005 Professor

PEER-REVIEWED PUBLICATIONS (2015–present) 28. Nilsen-Moe, A.; Clorice, R. R.; Glover, S. D.; Liang, L.; Hammarström, L.; Tommos, C. Proton-coupled electron transfer from tyrosine in the interior of a de novo protein: Mechanisms and primary proton acceptor. J. Am. Chem. Soc. 142, 11550–11559 (2020). 27. O’Brien, E. S.; Lin, D. W.; Fuglestad, B.; Stetz, M. A.; Gosse, T.; Tommos, C.; Wand, A. J. Improving yields of deuterated, methyl labeled proteins by growing in H2O. J. Biomol. NMR 71, 263–273 (2018). 26. Lee, W.; Kasanmascheff, M.; Huynh, M.; Quartararo, A.; Costentin, C.; Bejenke, I.; Nocera, D. G.; Bennati, M.; Tommos, C.; Stubbe, J. Properties of site-specifically incorporated 3-aminotyrosine in proteins to study redox-active tyrosines: Escherichia coli ribonucleotide reductase as a paradigm. Biochemistry 57, 3402–3415 (2018). 25. Glover, S. D.; Tyburski, R.; Liang, L.; Tommos, C.; Hammarström, L. Pourbaix diagram, proton-coupled electron transfer and decay kinetics of a protein tryptophan radical: Comparing the redox properties of W32• and Y32• generated inside the structurally characterized α3W and α3Y proteins. J. Am. Chem. Soc. 140, 185–192 (2018). 26. Ravichandran, K. R.; Zong, A. B.; Taguchi, A. T.; Nocera, D. G.; Stubbe, J.; Tommos, C. Formal reduction potentials of difluorotyrosine and trifluorotyrosine protein residues: Defining the thermodynamics of multistep radical transfer. J. Am. Chem. Soc. 139, 2994–3004 (2017). 25. Ravichandran, K. R.; Taguchi, A. T.; Wei, Y.; Tommos, C.; Nocera, D. G.; Stubbe, J. A >200 meV uphill thermodynamic landscape for radical transport in Escherichia coli ribonucleotide reductase determined using fluorotyrosine-substituted enzymes. J. Am. Chem. Soc. 138, 13706–13716 (2016). 26. O’Brien, E. S.; Nucci, N. V.; Fuglestad, B.; Tommos, C.; Wand, A. J. Defining the apoptotic trigger: The interaction of cytochrome c and cardiolipin. J. Biol. Chem. 290, 30879–30887 (2015).

COMPLETED SUPPORT (2015–present) NIH #R01-GM079190 Tommos, C. (PI) 2015–2020 “Understanding protein radicals” (*Renewal pending Council meeting in Jan 2021)

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Member NIH study section, MSFA 2020 Ad hoc referee Swiss National Science Foundation 2014–present Ad hoc referee American Chemical Society Petroleum Research Fund 2007–present Ad hoc peer reviewer Journal of the American Chemical Society, Biochemistry, Journal of 2000–present Physical Chemistry, Accounts of Chemical Research, Nature of Chemical Biology, Chemical Science, Inorganic Chemistry, Journal of Inorganic Biochemistry, Proceedings of the National Academy of Sciences USA, Biochimica et Biophysica Acta, Photosynthesis Research, and Protein Engineering, Design & Selection

DEPARTMENT AND SYSTEM SERVICE (2019–present) Member Advisory Committee BCBP 2020–present Member Awards Committee BCBP 2019–present Member Faculty Search Committee BCBP 2019–present Member Graduate Admissions Committee BCBP 2019–2020 COURSES TAUGHT (2015–present) BICH 689 Written Communication 1 cr. 2021 BICH/GENE 491 Research Variable 2019–present BICH 441 Comprehensive Biochemistry II 3 cr. 2020 A. Joshua Wand Professor and Head | Department of Biochemistry and Biophysics Professor | Chemistry, Molecular and Cellular Medicine

EDUCATION Postdoctoral National Research Council of Canada 1985 Ph.D. University of Pennsylvania 1984 M.S. Carleton University 1981 B.S. Carleton University 1979

PROFESSIONAL APPOINTMENTS Head Biochemistry and Biophysics Texas A&M University 2019–present Professor Biochemistry and Biophysics Texas A&M University 2019–present Chemistry Texas A&M University Molecular and Cellular Medicine Texas A&M University Benjamin Rush Professor Biochemistry and Biophysics University of Pennsylvania 2004–2019 Graduate Group Chair Biochemistry and Biophysics University of Pennsylvania 2000–2009 Professor Biochemistry and Biophysics University of Pennsylvania 1998–2019 Director Structural Biology Initiative State University of New York at 1995–1998 Buffalo Professor Biological Sciences, Biophysics State University of New York at 1995–1998 and Chemistry Buffalo Professor Biochemistry, Biophysics, and University of Illinois 1995 Chemistry Associate Professor Biochemistry and Biophysics University of Illinois 1991–1995 Adjunct Assistant Professor Biochemistry and Biophysics University of Pennsylvania School of 1987–1991 Medicine Member Institute for Cancer Research 1990–1991 Associate Member Institute for Cancer Research 1985–1990

PEER-REVIEWED PUBLICATIONS (2015–present) 172. Marques, B.S.; Stetz, M. A.; Jorge, C.; Valentine, K.G.; Wand, A. J.; and Nucci, N.V. Protein conformational entropy is not slaved to water. Sci. Reports (2020). 171. O’Brien, E. S.; Fuglestad, B.; Lessen, H. J.; Stetz, M. A.; Lin, D. W.; Marques, B. S.; Gupta, K.; Fleming, K. G.; Wand, A. J. Membrane proteins have distinct fast internal motion and residual conformational entropy. Angew. Chem. Int. Ed. 59, 2–9 (2020). 170. Fuglestad, B.; Kerstetter, N. E.; Bédard, S.; Wand, A. J. Extending the detection limit in fragment screening of proteins using reverse micelle encapsulation. ACS Chem. Biol. 14, 2224–2232 (2019). 169. Fuglestad, B.; Kerstetter, N. E.; Wand, A. J. Site-resolved and quantitative characterization of very weak protein−ligand interactions. ACS Chem. Biol.14, 1398–1402 (2019). 168. Fuglestad, B.; Gupta, K.; Wand, A.J.; Sharp, K. A. Water loading driven size, shape, and composition of cetyltrimethylammonium /hexanol/pentane reverse micelles. J. Colloid and Interface Sci. 540, 207–217 (2019). 167. O’Brien, E. S.; Lin, D. W.; Fuglestad, B.; Stetz, M. A.; Gosse, T.; Tommos, C.; Wand, A. J. Improving yields of deuterated, methyl labeled protein by growing in H2O. J. Biomol. NMR 71(4), 263–273 (2018). 166. Kumar, G. S.; Clarkson, M. W.; Kunze, M. B. A.; Granata, D.; Wand, A. J.; Lindorff-Larsen, K.; Page, R.; Peti, W. Dynamic activation and regulation of the mitogen-activated protein kinase p38. Proc. Nat. Acad. Sci. 115, 4655–4660 (2018). 165. Caro, J.A.; Harpole, K.W.; Kasinath, V.; Lim, J.; Granja, J.; Valentine, K.G.; Sharp, K.A.; Wand, A.J. Entropy in molecular recognition by proteins. Proc. Natl. Acad. Sci. 114, 6563–6568 (2017). 164. Fuglestad, B.; Stetz, M. A.; Belnavis, Z.; Wand, A. J. Solution NMR investigation of the response of the Lactose repressor core domain dimer to hydrostatic pressure. Biophys. Chem. 231, 39–44 (2017). 163. Stetz, M. A.; Wand, A. J. Accurate determination of rates from non-uniformly sampled relaxation data. J. Biomol. NMR 65, 157–170 (2016). 162. Stetz, M. A.; Wand, A. J. Optimized expression and purification of biophysical quantities of the Lac repressor and Lac repressor regulatory domain. Protein Express. Purif. 123, 75 – 82 (2016). 161. De Picciotto, S.; Dikson, P. M.; Traxlmayr, M. W.; Marques, B. S.; Socher, E.; Zhao, S.; Cheung, S.; Kiefer, J. D.; Wand, A. J.; Griffith, L. G.; Imperiali, B.; Wittrup, K. D. Design principles for SuCESsFul Biosensors: Specific fluorophore/analyte binding and minimization of fluorophore/scaffold interactions. J. Mol. Biol. 428, 4228 – 4241 (2016). 160. O'Brien, E. S.; Wand, A. J.; Sharp, K. A. On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain NMR order parameters. Protein Sci. 25, 1156 – 1160 (2016). 159. Fuglestad, B.; Gupta, K.; Wand, A. J.; Sharp, K. A. Characterization of cetyltrimethylammonium bromide/hexanol reverse micelles by experimentally benchmarked molecular dynamics simulations. Langmuir 32, 1674 – 1684 (2016). 158. Harpole, K. W.; O’Brien, E. S.; Clark, M. A.; McKnight, C. J.; Vugmeyster, L.; Wand, A. J. The unusual internal motion of the Villin Headpiece Subdomain. Protein Sci. 25, 423–432 (2015). 157. O’Brien, E. S.; Nucci, N. V.; Fuglestad, B.; Tommos, C.; Wand, A. J. Defining the apoptotic trigger: the interaction of cytochrome c and cardiolipin. J. Biol. Chem. 290, 30879–30887 (2015). 156. Sharp, K. A.; O’Brien, E.; Kasinath, V.; Wand, A. J. On the relationship between NMR-derived amide order parameters and protein backbone entropy changes. Proteins 83, 922–930 (2015). 155. Kasinath, V.; Sharp, K. A.; Wand, A. J. A sharp thermal transition of fast aromatic ring dynamics in ubiquitin. Angewandte Chimi. Int’l Ed. 54, 102–107 (2015).

CURRENT SUPPORT NIH R01 GM129076 Wand, A. J. (PI) 2020–2024 “The role of the free energy landscape in Parkin’s function and dysfunction in Parkinson’s disease” Mathers Charitable Trust MF-1809-00155 Wand, A. J. (PI) 2018–2021 “Characterization of the role of internal motions and conformational entropy in the function of integral membrane proteins”

COMPLETED SUPPORT (2015–present) NIH 2 T32 GM008275 Wand, A. J. (PI) 2014–2019 “Structural biology & molecular biophysics training program” NIH R21 CA206958 Wand, A. J. (PI) 2016–2018 “Nanoscale Encapsulation for Fragment Based Drug Discovery” Mathers Charitable Trust Wand, A. J.; Englander, W. 2015–2018 “Protein dynamics, folding, function and evolution” NIH R01 GM100910 Wand, A. J.; Peti, W. 2013–2017 “Dynamics & kinetics of p38a kinase regulation by ligands” NIH R01 GM102447 Wand, A. J. (PI) 2012–2017 “Fluctuations and entropy in the energetics and function of protein complexes”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Editorial Board Annual Reviews of Biophysics 2016–present Editorial Board Structure, Folding & Design 2004–present Watkins Lecturer Wichita State University 2018 Keynote Speaker Institute for Bioscience and Biotechnology Research, University of 2018 Maryland Guest Editor Methods in Enzymology 2018 Ad Hoc Member Editorial review, BTRR program, National Institutes of Health 2018 Ad Hoc Member SEP, ZRG1 BCMB-A, National Institutes of Health 2016 Guest Editor PNAS 2015 Fellow American Physical Society 2015

COURSES TAUGHT (2015–present) (*only TAMU courses included) BICH 440 Biochemistry 2020 Ryland F. Young, III University Distinguished Professor | Department of Biochemistry and Biophysics Director | Center for Phage Technology Sadie Hatfield Professor of Agriculture

EDUCATION Postdoctoral Harvard Medical School 1977–1978 Ph.D. University of Texas at Dallas 1975 Massachusetts Institute of Technology 1968–1969 A.B. Rice University 1968 California Institute of Technology 1964–1965

PROFESSIONAL APPOINTMENTS Director Center for Phage Technology Texas A&M University 2010–present Sadie Hatfield Professor Agriculture Texas A&M University 2006–present University Distinguished Professor Biochemistry and Biophysics Texas A&M University 1987–present Associate Professor Biochemistry and Biophysics Texas A&M University 1986–1987 Assistant Professor Medical Biochemistry Texas A&M University 1978–1986

PEER-REVIEWED PUBLICATIONS (2015–present) 166. Krieger, I. V.; Kuznetsov, V.; Chang, J. Y.; Zhang, J.; Moussa, S. H.; Young, R. F.; Sacchettini, J. C. The structural basis of T4 phage lysis control: DNA as the signal for lysis inhibition. Mol. Biol. 432, 4623–4636 (2020). 165. Harb, L.; Chamakura, K.; Khara, P.; Christie, P. J.; Young, R.; Zeng, L. ssRNA phage penetration triggers detachment of the F-pilus. Proc. Natl. Acad. Sci. USA 117, 25751–25758 (2020). 164. Zhang, K.; Young, R.; Zeng, L. Bacteriophage P1 does not show spatial preference when infecting Escherichia coli. Virology 542, 1–7 (2020). 163. Duan, Y.; Llorente, C.; Lang, S.; Brandl, K.; Chu, H.; Jiang, L.; White, R. C.; Clarke, T. H.; Nguyen, K.; Torralba, M.; Shao, Y.; Liu, J.; Hernandez-Morales, A.; Lessor, L.; Rahman, I. R.; Miyamoto, Y.; Ly, M.; Gao, B.; Sun, W.; Kiesel, R.; Hutmacher, F.; Lee, S.; Ventura-Cots, M.; Bosques-Padilla, F.; Verna, E. C.; Abraldes, J. G.; Brown, R. S, Jr.; Vargas, V.; Altamirano, J.; Caballería, J.; Shawcross, D. L.; Ho, S. B,; Louvet, A.; Lucey, M. R.; Mathurin, P.; Garcia- Tsao, G.; Bataller, R.; Tu, X. M.; Eckmann, L.; van der Donk, W. A.; Young, R.; Lawley, T. D.; Stärkel, P.; Pride, D.; Fouts, D. E.; Schnabl, B. Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease. Nature 575, 505– 511 (2019). 162. Chamakura, K.; Young, R. Phage single-gene lysis: Finding the weak spot in the bacterial cell wall. J. Biol. Chem. 294, 3350–3358 (2019). 161. Cahill, J.; Young, R. Phage lysis: Multiple genes for multiple barriers. Adv. Virus Res. 103, 33–70 (2019). 160. Kongari, R.; Snowden, J.; Berry, J. D.; Young, R. Localization and regulation of the T1 unimolecular spanin. J. Virol. 92, e00380-18 (2018). 159. Kongari, R.; Rajaure, M.; Cahill, J.; Rasche, E.; Mijalis, E.; Berry, J.; Young, R. Phage spanins: Diversity, topological dynamics and gene convergence. BMC Bioinform. 19, 326 (2018). 158. Trinh, J. T.; Alkahtani, M. H.; Rampersaud, I.; Rampersaud, A.; Scully, M.; Young, R. F.; Hemmer, P.; Zeng, L. Fluorescent nanodiamond-bacteriophage conjugates maintain host specificity. Biotechnol. Bioeng. 115, 1427–1436 (2018). 157. Hernandez-Morales, A. C.; Lessor, L. L.; Wood, T. L.; Migl, D.; Mijalis, E. M.; Cahill, J.; Russell, W. K.; Young, R. F.; Gill, J. J. Genomic and biochemical characterization of acinetobacter podophage petty reveals a novel lysis mechanism and tail-associated depolymerase activity. J. Virol. 92, e01064-17 (2018). 156. Gill, J.; Wang, B.; Young, R.; Chu, K. H. Characterization of a novel tectivirus phage toil and its potential as an agent for biolipid extraction. Sci. Rep. 18, 1062 (2018). 155. Chamakura, K. R.; Sham, L. T.; Davis, R. M.; Min, L.; Cho, H.; Ruiz, N.; Bernhardt, T. G.; Young, R. A viral protein antibiotic inhibits lipid II flippase activity. Nat. Microbiol. 2, 1480–1484 (2017). 154. Cui, Z.; Gorzelnik, K. V.; Chang, J. Y.; Langlais, C.; Jakana, J.; Young, R.; Zhang, J. Structures of Qβ virions, virus- like particles, and the Qβ-MurA complex reveal internal coat proteins and the mechanism of host lysis. Proc. Natl. Acad. Sci. USA 114, 11697–11702 (2017). 153. Piya, D.; Vara, L.; Russell, W. K.; Young, R.; Gill, J. J. The multi-component antirestriction system of phage P1 is linked to capsid morphogenesis. Mol. Microbiol. 105, 399–412 (2017). 152. Schooley, R. T.; Biswas, B.; Gill, J. J.; Hernandez-Morales, A.; Lancaster, J.; Lessor, L.; Barr, J. J.; Reed, S. L.; Rohwer, F.; Benler, S.; Segall, A. M.; Taplitz, R.; Smith, D. M.; Kerr, K.; Kumaraswamy, M.; Nizet, V.; Lin, L.; McCauley, M. D.; Strathdee, S. A.; Benson, C. A.; Pope, R. K.; Leroux, B. M.; Picel, A. C.; Mateczun, A. J.; Cilwa, K. E.; Regeimbal, J. M.; Estrella, L. A.; Wolfe, D. M.; Henry, M. S.; Quinones, J.; Salka, S.; Bishop-Lilly, K. A.; Young, R.; Hamilton, T. Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection. Antimicrob. Agents Chemother. 61, e00954–17 (2017). 151. Cahill, J.; Rajaure, M.; Holt, A.; Moreland, R.; O’Leary, C.; Kulkarni, A.; Sloan, J.; Young, R. Suppressor analysis of the fusogenic lambda spanins. J. Virology 91, e00413-17 (2017). 150. Chamakura, K. R.; Edwards, G. B.; Young, R. Mutational analysis of the MS2 lysis protein L. Microbiology 163, 961– 969 (2017). 149. Yao, G. W.; Duarte, I.; Le, T. T.; Carmody, L.; LiPuma, J. J.; Young, R.; Gonzalez, C. F. A broad host range tailocin from Burkholderia cenocepacia. Appl. Environ. Microbiol. 83, e03414-16 (2017). 148. Chamakura, K. R.; Tran, J. S.; Young, R. MS2 lysis of Escherichia coli depends on host chaperone DnaJ. J. Bacteriol. 199, e00058-17 (2017). 147. Cahill, J.; Rajaure, M.; O’Leary, C.; Sloan, J.; Marrufo, A.; Holt, A.; Kulkarni, A.; Hernandez, O.; Young, R. Genetic analysis of the lambda spanins Rz and Rz1: Identification of functional domains. G3 Genes 7, 2741–753 (2017). 146. Fan, X.; Duan, X.; Tong, Y.; Huang, Q.; Zhou, M.; Wang, H.; Zeng, L.; Young, R.; Xie, J. The global reciprocal reprogramming between mycobacteriophage SWU1 and mycobacterium reveals the molecular strategy of subversion and promotion of phage infection. Front. Microbiol. 7, 41 (2016). 145. Gorzelnik, K. V.; Cui, Z.; Reed, C. A.; Jakana, J.; Young, R.; Zhang, J. Asymmetric cryo-EM structure of the canonical allolevivirus Qβ reveals a single maturation protein and the genomic ssRNA in situ. Proc. Natl. Acad. Sci. USA 113, 11519–11524 (2016). 144. Chen, Y.; Young, R. The last r locus unveiled: T4 RIII is a cytoplasmic antiholin. J. Bacteriol. 198, 2448–2457 (2016). 143. Young, R.; Gill, J. J. Phage therapy redux – What is to be done? Science 350, 1163–1164 (2015). 142. Das, M.; Bhowmick, T. S.; Ahern, S. J.; Young, R.; Gonzalez, C. F. Control of Pierce's Disease by phage. PLoS One 10, e0128902 (2015). 141. Liu, M.; Bischoff, K. M.; Gill, J. J.; Mire-Criscione, M. D.; Berry, J. D.; Young, R.; Summer, E. J. Bacteriophage application restores ethanol fermentation characteristics disrupted by Lactobacillus fermentum. Biotechnol. Biofuels 8, 132 (2015). 140. Liu, M.; Gill, J. J.; Young, R.; Summer, E. J. Bacteriophages of wastewater foaming-associated filamentous Gordonia reduce host levels in raw activated sludge. Sci. Rep. 5, 13754 (2015). 139. Rajaure, M.; Berry, J.; Kongari, R.; Cahill, J.; Young, R. Membrane fusion during phage lysis. Proc. Natl. Acad. Sci. USA 112, 5497–5502 (2015). 138. Fan, X.; Yan, J.; Zeng, L.; Young, R. F. III; Xie, J. Genomic and proteomic features of mycobacteriphage SWU1 isolated from China soil. Gene 561, 45–53 (2015).

CURRENT SUPPORT NIH #R35-GM136396-01 Young, R. (PI) 2020–2025 “Phage lysis” DARPA/Signature Science (subcontract) Young, R. (PI); Gill, J. (co-PI); Herman, J. (co-PI) 2019–2020 “Spore-Phage Amplified Detection (SPADe) for Subterranean Chemical Threats” NSF #M1602394 Young, R. (PI); Gill, J. (co-PI); Hu, J. (co-PI) 2016–2020 “Implementing Galaxy for community-based phage genomics”

COMPLETED SUPPORT (2015–present) Giner, Inc. Young, R. (PI); Gill, J. (co-PI) 2015–2020 “Pathogen-specific antimicrobial coating”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Scientific Advisory Board GangaGen Corporation 2002–present Associate Editor Emerging Topics in Life Sciences, Portland Press 2016 Regents Professor Award Texas A&M University 2016 Dean’s Outstanding Achievement College of Agriculture and Life Sciences 2015 Award for Excellence in Faculty Mentoring Faculty Recognition Award TAMU Biochemistry Graduate Association 2015

DEPARTMENT AND SYSTEM SERVICE (2015–present) Chair, Vice-Chair TAMU Intellectual Property Constituents Committee TAMU 2012–2016 Member Department Head Search Committee BCBP 2016

COURSES TAUGHT (2015–present) BICH 676 Phage and Bacterial Cell Biology (Journal Club) 1 cr. 2012–present BICH 608 Critical Analysis of the Biochemical Literature 2 cr. 2009–present BICH 464 Phage Genomics 3 cr. 2009–present BICH 491/691 Research Variable 1987–present Lanying Zeng Associate Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral University of Illinois at Urbana-Champaign with I. Golding 2007–2011 Ph.D. University of Illinois at Urbana-Champaign with S. Balachandar 2007 M.E. Beijing University of Aeronautics and Astronautics with S. Wu 2001 B. E. Beijing University of Aeronautics and Astronautics with H. Zhang 1998

PROFESSIONAL APPOINTMENTS Associate Professor Biochemistry and Biophysics Texas A&M University 2018–present Assistant Professor Biochemistry and Biophysics Texas A&M University 2012–2018

PEER-REVIEWED PUBLICATIONS (2015–present) 24. Harb, L.; Chamakura, K.; Khara, P.; Christie, P. J.; Young, R.; Zeng, L. ssRNA phage penetration triggers detachment of the F-pilus. PNAS 117, 25751–25758 (2020). 23. Trinh, J. T.; Zeng, L. Structure regulates phage lysis-lysogeny decisions. Trends Microbiol. 27, 3–4 (2019). 22. Guan, J.; Ibarra, D.; Zeng, L. The role of side tail fibers during the infection cycle of phage lambda. Virology 527, 57–63 (2019). 21. Gordeeva, J.; Morozova, N.; Sierro, N.; Isaev, A.; Tsvetkova, K.; Matlashov, M.; Ivanov, N.; Zeng, L.; Severinov, K. BREX system of Escherichia coli distinguishes self from non-self by methylation of a specific DNA site. Nuc. Acids Res. 47, 253–265 (2019). 20. Shao, Q.; Trinh, J. T.; Zeng, L. High-resolution studies of lysis-lysogeny decision making in bacteriophage lambda. J. Biol. Chem. 294, 3343–3349 (2019). 19. Shao, Q.; Cortes, M.; Trinh, J. T.; Guan, J.; Balázsi, G.; Zeng, L. Coupling of DNA replication and negative feedback controls gene expression for cell-fate decisions. iScience 6, 1–12 (2018). 18. Wang, X.; Park, S.; Zeng, L.; Jain, A.; Ha, T. Towards single-cell single-molecule pull-down. Biophys. J. 115, 283–288 (2018). 17. Trinh, J. T.; Alkahtani, M. A.; Rampersaud, I.; Rampersaud, A.; Scully, M.; Young, R. F.; Hemmer, P.; Zeng, L. Fluorescent nanodiamond-bacteriophage conjugates maintain host specificity. Biotechnol. Bioeng. 115, 1427–1436 (2018). 16. Cortes, M.; Trinh, J. T.; Zeng, L.; Balázsi, G. Late-arriving signals contribute less to cell fate decisions. Biophys. J. 113, 2110–2120 (2017). 15. Trinh, J. T.; Zeng, L. Virus interactions: Competition or cooperation? Future Microbiol. 12, 561–564 (2017). 14. Guan, J.; Shi, X.; Burgos, R.; Zeng, L. Visualization of phage DNA degradation by a Type I CRISPR-Cas system at the single-cell level. Quant. Biol. 5, 67–75 (2017). 13. Trinh, J. T.; Székely, T.; Shao, Q.; Balázsi, G.; Zeng, L. Cell fate decisions emerge as phages cooperate or compete inside their host. Nat. Commun. 8, article 14341 (2017). 12. Shao, Q.; Trinh, J. T.; McIntosh, C. S.; Christenson, B.; Balázsi, G.; Zeng, L. Lysis-lysogeny coexistence: Prophage integration during lytic development. Microbiologyopen. 6, e00395 (2016). 11. Fan, X.; Duan, X.; Huang Q.; Zhou, M.; Wang, H.; Zeng, L.; Young, R.; Xie, J. The global reciprocal reprogramming between mycobacteriophage SWU1 and mycobacterium reveals the molecular strategy of subversion and promotion of phage infection. Front. Microbiol. 7, article 41 (2016). 10. Shao, Q.; Hawkins, A.; Zeng, L. Phage DNA dynamics in cells with different fates. Biophys. J. 108, 2048–2060 (2015). 9. Fan, X.; Yan, J.; Zeng, L.; Young, R. F. III; Xie, J. Genomic and proteomic features of mycobacteriphage SWU1 isolated from China soil. Gene 561, 45–53 (2015).

CURRENT SUPPORT NSF MCB-2013762 Zeng, L. (PI) 2020–2025 “Role of Spatial Structure in Decision Making” NSF MCB-1902392 Zhang, J. (PI), Zeng, L. (co-PI), Hu, J. (co-PI) 2019–2022 “Molecular Mechanism for Genomic RNA Delivery in ssRNA Phages” TAMU X-Grant Zhang, X. (PI), Zhang, J. (co-PI), Ji, J. (co-PI), Cai, J. (co-PI), Cruz- 2019–2022 Reyes, J. (co-PI), Sczepanski, J. (co-PI), Patrick, K. (co-PI), Zeng, L. (co-PI) “Biology Hidden in RNA Structures and Epi-modifications” Texas A&M AgriLife Research Zeng, L. (PI) 2018–2022 TAMU Presidential Zeng, L. (PI) 2020–2021 Transformational Teaching Grant “Integrating Mathematical Modeling and Research Components into Biophysics Teaching” TAMU Triads for Transformation Zeng, L. (PI), Jiang (co-PI), Liu (co-PI) 2020–2021 “Visualizing Protein Delivery” TAMU Neuhaus-Shepardson Zeng, L. (PI) 2020–2021 Faculty Development Grant

COMPLETED SUPPORT (2015–present) NIH #R01-GM107597 Zeng, L. (PI), Balazsi (MPI) 2015–2020 “Integration of Diverse Inputs Determines Developmental Outcomes” TAMU Neuhaus-Shepardson Zeng, L. (PI) 2017–2018 Faculty Development Grant TAMU-NSFC Young, R. (PI), Zeng, L. (co-PI), Xie (PI) 2014–2015 “Characterizing the Key Deteminants of the Mycophage Infection Cycle using Quantitative Live-cell Imaging”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Academic Editor PLoS One 2018–present Grant Reviewer NSF QLCI Pre-A Panel 2020 Grant Reviewer National Science Center, Poland 2020 Grant Reviewer UK Research and Innovation-BBSRC 2020 Guest Editor JoVE, Methods Collections 2020 Poster Judge ASM Texas Branch Meeting 2017

DEPARTMENT AND SYSTEM SERVICE (2015–present) Chair Advisory Committee BCBP 2020–present Member Undergraduate Biophysics Degree Committee BCBP 2020–present Member Graduate Admissions Committee BCBP 2019–present Member Awards Committee BCBP 2019–present Member Post-Tenure Review Committee BCBP 2020 Member IT Oversight Committee BCBP 2019–2020 Member Faculty Search Committee BCBP 2016–2019 Member Graduate Recruitment and Admissions Committee BCBP 2014–2019

COURSES TAUGHT (2015–present) BICH 403 Cellular Biophysics 3 cr. 2018–present BICH 404 Biochemical Calculations 2 cr. 2017–present BICH 491/691 Research Variable 2012–present BICH 676 Phage and Bacterial Cell Biology (Journal Club) 1 cr. 2012–present BICH 489 Introductory Biophysics and Systems Biology/Physical Biology of the 0–4 cr. 2013–2017 Cell BICH 605 Methods of Biochemical Analysis 3 cr. 2014 Junjie Zhang Associate Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Stanford University with M. Levitt 2009–2013 Ph.D. Baylor College of Medicine with W. Chiu 2009 B.S. Fudan University with J.-Y. Chen 2004

PROFESSIONAL APPOINTMENTS Associate Professor Biochemistry and Biophysics Texas A&M University 2020–present Assistant Professor Biochemistry and Biophysics Texas A&M University 2014–2020

PEER-REVIEWED PUBLICATIONS (2015–present) 27. Chang, J. Y.; Yang, K.; Cui, X.; Huang, J.; Minary, P.; Zhang, J. Natural move Monte Carlo refines large RNA structures into Cryo-EM densities. Epub 26, 1755–1766 (2020). 26. Krieger, I.; Kuznetsov, V.; Chang, J.; Zhang, J.; Moussa, S.; Young, R.; Sacchettini, J. The structural basis of T4 lysis control: DNA as the signal for lysis inhibition. J. Mol. Biol. 432, 4623–4363 (2020). 25. Peng, Z.; Simeon, R.; Mitchell, S. B.; Zhang, J.; Feng, H.; Chen, Z. Designed Ankyrin Repeat Protein (DARPin) neutralizers of TcdB from Clostridium difficile ribotype 027. mSphere 4, e00596–e00519 (2019). 24. Wang, B.; Zhang, J.; Wu, Y. A multiscale model for the self-assembly of coat proteins in bacteriophage MS2. J. Chem. Info. Mod. (2019). 23. Meng, R.; Jiang, M.; Cui, Z.; Chang, J. Y.; Yang, K.; Jakana, J.; Yu, X.; Wang, Z.; Hu, B.; Zhang, J. Structural basis for the adsorption of a single-stranded RNA bacteriophage. Nat. Commun. 10, 3130 (2019). 22. Simeon, R.; Jiang, M.; Chamon, A. M.; Yu, H.; Zhang, Y.; Meng, R.; Peng, Z.; Jakana, J.; Zhang, J.; Feng, H.; Chen, Z. Selection and characterization of ultra-high potency designed ankyrin repeat protein inhibitors of C. difficile toxin B. PLoS Biol. 17, e3000311 (2019). 21. Brock, D. J.; Kustigian, L.; Jiang, M.; Graham, K.; Wang, T. Y.; Erazo-Oliveras, A.; Najjar, K.; Zhang, J.; Rye, H.; Pellois, J.-P. Efficient cell delivery mediated by lipid-specific endosomal escape of supercharged branched peptides. Traffic (2018). 20. Cui, Z.; Gorzelnik, K. V.; Chang, J.; Langlais, C.; Jakana, J.; Young, R.; Zhang, J. Structures of Qβ virions, virus-like particles, and the Qβ-MurA complex reveal internal coat proteins and the mechanism of host lysis. Proc. Natl. Acad. Sci. USA 114, 11697–11702 (2017). 19. Yang, K.; Chang, J.; Cui, Z.; Li, X.; Meng, R.; Duan, L. Thongchol, J.; Jakana, J.; Huwe, C. M.; Sacchettini, J. C.; Zhang, J. Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis. Nucl. Acid Res. 45, 10884–10894 (2017). 18. Weaver, J.; Jiang, M.; Roth, A.; Puchalla, J; Zhang, J.; Rye, H. GroEL actively stimulates folding of the endogenous substrate protein PepQ. Nat. Commun. 8, 15934 (2017). 17. Gorzelnik, K. V.; Cui, Z.; Reed, C. A.; Jakana, J.; Young, R.; Zhang, J. Asymmetric cryo-EM structure of the canonical Allolevivirus Qβ reveals a single maturation protein and the genomic ssRNA in situ. Proc. Natl. Acad. Sci. (2016). 16. Lee, J. R.; Xie, X.; Yang, K.; Zhang, J.; Lee, S. Y.; Shippen, D. E. Dynamic interactions of Arabidopsis TEN1: Stabilizing telomeres in response to heat stress. Plant Cell (2016). 15. Yang, K.; Ren, Z.; Raushel, F. M.; Zhang, J. Structures of the carbon-phosphorus lyase complex reveal the binding mode of the NBD-like PhnK. Structure 24, 37–42 (2016). 14. Li, X.; Sun, Q.; Jiang, C.; Yang, K.; Hung, L. W.; Zhang, J.; Sacchettini, J. C. Structure of ribosomal silencing factor bound to Mycobacterium tuberculosis ribosome. Structure 23, 1858–1865 (2015).

CURRENT SUPPORT NIH R01 AI145287 Li, P. (PI), Zhang, J. (co-PI) 2019–2024 “Molecular basis of viral DNA sensing through the cGAS-STING pathway” Welch A1863 Zhang, J. (PI) 2020–2023 “Ribosomal structures in drug-resistant Mycobacterium tuberculosis” NIH P01 AI095208 Sacchettini, J. C. (PI). Zhang, J. (co-PI) 2018–2023 “Structure-based discovery of critical vulnerabilities of Mycobacteria” NIH R21 AI156846 Zeng, L. (PI), Zhang, J. (co-PI) 2020–2022 “Reducing virulence through the suppression of retractile pili” NSF Zhang, J. (PI) 2019–2022 “Molecular mechanism for genomic RNA delivery in ssRNA phages” TAMU X-Grant Program Zhang, J. (co-PI) 2019–2022 “Biology hidden in RNA structure and epi-modifications” NIH R21 AI137696 Zhang, J. (PI) 2018–2021 “Characterize essential regions in C. difficile toxin B for its neutralization” NIH U24 GM116787 Chui (PI), Zhang, J. (co-PI) 2016–2021 “CryoEM data collection facility consortium at NCMI”

COMPLETED SUPPORT (2015–present) TAMU T3 Program Zhang, J. (PI) 2018–2020 “Characterize functional motions of macromolecules by cryo-EM, statistical, and computational modeling” Welch Foundation A1863 Zhang, J. (PI) 2017–2020 “Functions of unique structures in Mycobacterium tuberculosis translation” TAMU College of Science Strategic Sczepanski, J. (PI), Zhang, J. (co-PI) 2017–2020 Transformative Research Program “RNAplex: A genetically encoded electron microscopy reporter for RNA” CST*R Pilot Grant Chen (PI), Zhang, J. (co-PI) 2017–2018 “Engineering novel protein therapeutics against Shing Toxin 1” Welch Foundation A1863 Zhang, J. (PI) 2014–2017 “The structural basis of ribosomal silencing in tuberculosis” NIH P01AI095208 Sacchettini, J. C. (PI), Zhang, J. (co-PI) 2014–2017 “Structure-based discovery of critical vulnerabilities of Mycobacteria”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Reviewer Molecular Foundry/NCEM proposal panel, LBNL 2013–present Reviewer NIH study section, MSFC 2020 Peer reviewer Nature, Nature Structure and Molecular Biology, Nature Various Communications, Structure, Journal of Virology, Biochemistry, Advanced Structural and Chemical Imaging, Biomedical and Environmental Sciences, Molecules, ACS Synthetic Biology, Molecular Microbiology

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Graduate Admissions Committee BCBP 2021–present Member Graduate Outreach and Recruitment Committee BCBP 2019–present Member Cyro-EM Faculty Hiring Committee BCBP 2019–present Member High-Performance Research Computing Center Hiring Committee TAMU On-going Member Microscopy and Imaging Center (MIC) Capabilities Review Committee TAMU On-going Member Graduate Program Committee BCBP 2014–2019

COURSES TAUGHT (2015–present) BICH 689 Cryo-EM of Molecular Machines 1 cr. 2018–present BICH 685 Directed Studies 1 cr. 2020 BICH 404 Biochemical Calculations 2 cr. 2020 BICH 303 Elements of Biological Chemistry 3 cr. 2015–present BICH/GENE 101 Perspectives in Biochemistry and Genetics 1 cr. 2020–present BICH 624 Enzymes, Proteins and Nucleic Acids 3 cr. 2015, 2017 Xiuren Zhang Professor | Department of Biochemistry and Biophysics

EDUCATION Postdoctoral Rockefeller University 2003–2008 Ph.D. Cornell University 2003 M.S. Auburn University 1999 M.S. China Agricultural University 1994 B.S. Wannan Agricultural College 1989

PROFESSIONAL APPOINTMENTS Professor Plant Genomics and Biotechnology, Texas A&M University 2018–present Biochemistry and Biophysics Associate Professor Plant Genomics and Biotechnology, Texas A&M University 2014–2018 Biochemistry and Biophysics Assistant Professor Plant Genomics and Biotechnology, Texas A&M University 2008–2014 Biochemistry and Biophysics Assistant to Director Beijing Academy of Agriculture and China 1994–1997 Forestry

PEER-REVIEWED PUBLICATIONS (2015–present) 36. Zhu, J.; Peng, X.; Zhang, X. Architecture of RNA influences plant biology. J. Exp. Biol. (2020, under review). 35. Li. Y.; Sun, D.; Ma, Z.; Yamaguchi, K.; Wang, L.; Zhong, S.; Yan, X.; Shang, B.; Nagashima, Y.; Koiwa, H.; Han, J.; Xie, Q.; Zhou, M.; Wang, Z.; Zhang, X. Degradation of serrate via ubiquitin-independent 20S proteasome to survey RNA metabolism. Nat. Plants 6, 970–982 (2020). 34. Kumar, V.; Ivens, A.; Goodall, Z.; Meehan, J.; Doharey, P. K.; Hillhouse, A.; Hurtado, D. O.; Cai, J. J.; Zhang, X.; Schnaufer, A.; Cruz-Reyes, J. Site-specific and mRNA-specific control of accurate mRNA editing by a helicase complex in trypanosomes. RNA 076513.120 (2020). 33. Sun, D.; Ma, Z.; Zhu, J.; Zhang, X. Identification and quantification of small non-coding RNAs. Arabidopsis Book (2020, in press). 32. Nagashima, Y.; Ma, Z.; Zhang, X.; von Schaewen, A.; Koiwa, H. Lack of endoplasmic reticulum quality control (ERQC) promotes tonoplast (TP) targeting of KORRIGAN 1 (KOR1). Plant Signal Behav. 20, 1744348 (2020). 31. Nagashima, Y.; Ma, Z.; Liu, X.; Qian, X.; Zhang, X.; von Schaewen, A.; Koiwa H. Multiple quality control mechanisms in the ER and TGN determine subcellular dynamics and salt-stress tolerance function of KORRIGAN1. Plant Cell 32, 470–485 (2020). 30. Hu, T.; Huang, C.; He, Y.; Castillo-González, C.; Gui, X.; Wang, Y.; Zhang, X.; Zhou, X. βC1 protein encoded in geminivirus satellite concertedly targets MKK2 and MPK4 to counter host defense. PLoS Pathog. 115, e1007728 (2019). 29. Wang, Z.; Wang, Y.; Wang, T.; Zhang, Y.; Zhang, X. Genome-wide probing RNA structure with the modified DMS- MaPseq in Arabidopsis. Methods 155, 30–40 (2019). 28. Castillo-Gonzalez, C.; Zhang, X. The Trojan horse of the plant kingdom. Cell Host & Microbe 24, 1–3 (2018). 27. Ma, Z.; Castillo-González, C.; Wang, Z.; Sun, D.; Hu, X.; Shen, X.; Potok, M. E.; Zhang, X. Arabidopsis serrate coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression. Dev. Cell 45, 769–784 (2018). 26. Ma, Z.; Zhang, X. Actions of plant Argonautes: predictable or unpredictable? Curr. Opin. Plant Biol. 45, 59–67 (2018). 25. Wang, Z.; Ma, Z.; Castillo-González, C.; Sun, D.; Li, Y.; Yu, B.; Zhao, B.; Li, P.; Zhang, X. SWI/SNF subunit CHR2 remodels pri-miRNAs via SE to inhibit miRNA production. Nature 557, 516–521 (2018). 24. Castillo-Gonzalez, C.; Zhang, X. Transactivator: The new face of Arabidopsis AGO1. Dev. Cell 44, 277–279 (2018). 23. Njaci, I.; Williams, B.; Castillo-González, C.; Dickman, M.; Zhang, X.; Mundree, S. Genome-wide investigation of the role of microRNAs in desiccation tolerance in the resurrection grass Tripogon loliiformis. Plants 7, 68 (2018). 22. Mei, Y.; Yang, X.; Huang, C.; Zhang, X.; Zhou, X. Tomato leaf curl Yunnan virus-encoded C4 induces cell division through enhancing stability of Cyclin D 1.1 via impairing NbSKη -mediated phosphorylation in Nicotiana benthamiana. PLoS Pathog. 14, e1006789 (2018). 21. Zhang, X. Tough GC beats transgene silencing. Nat. Plants 3, 850–851 (2017). 20. Fukudome, A.; Sun, D.; Zhang, X.; Koiwa, H. Salt-stress and CTD phosphatase-like 4 mediate transcriptional switching of snRNA to mRNA in Arabidopsis thaliana. Plant Cell 29, 3214–3233 (2017). 19. Zhang, Z.; Hu F.; Sung, M. W.; Shu, C.; Castillo, C.; Koiwa, H.; Dickman, M.; Li, P.; Zhang, X. RISC-interacting clearing 3'-5' exoribonucleases (RICEs) degrade uridylated cleavage fragments to maintain functional RISC in Arabidopsis. eLife 6, e24466 (2017). 18. Zhang, Z.; Guo, X.; Ge, C.; Ma, Z.; Jiang, M.; Li, T.; Koiwa H.; Yang, S. K.; Zhang, X. KETCH1 (Karyopherin Enabling the Transport of the Cytoplasmic HYL1) imports HYL1 to nucleus for miRNA biogenesis in Arabidopsis. PNAS 114, 4011–4016 (2017). 17. Li, S.; Castillo-Gonzalez, C.; Yu, B.; Zhang, X. The functions of plant small RNAs in development and in stress responses. Plant J. 90, 654–670 (2017). 16. Guo, X.; Ma, Z.; Zhang, Z.; Cheng, L.; Zhang, X.; Li, T. Small RNA-sequencing links physiological changes and RdDM process to vegetative-to-floral transition in apple. Front. Plant Sci. 8, 873 (2017). 15. Zhang, Z.; Liu, X.; Guo, X.; Wang, X.-J.; Zhang, X. Arabidopsis AGO3 predominantly recruits 24-nt small RNAs to regulate epigenetic silencing. Nat. Plants 2,16049 (2016). 14. Zhou, Y.; Honda, M.; Zhu, H.; Zhang, Z.; Guo, X.; Li, T.; Li, Z.; Peng, X.; Nakajima, K.; Duan, L; Zhang, X. Spatiotemporal sequestration of miR165/166 by Arabidopsis Argonaute10 promotes shoot apical meristem maintenance. Cell Rep. 10, 1819–27 (2015). 13. Wang, T.; Castillo-González, C.; You, L.; Li, R.; Wen, L.; Zhu, H.; Zhang, X. In vitro reconstitution assay of miRNA biogenesis by Arabidopsis DCL1. Bio-protocol 5, e1454 (2015). 12. Castillo-González, C.; Liu, X.; Huang, C.; Zhao, C.; Hu, T.; Sun, F.; Ma, Z.; Zhou, Y.; Zhou, X.; Wang, X.; Zhang, X. Geminivirus-encoded TrAP suppressor inhibits the histone methyltransferase SUVH4/KYP to counter host defense. eLife 4, e06671 (2015). 11. Williams, B.; Njaci, I.; Moghaddam, L.; Long, H.; Dickman, M.; Zhang, X.; Mundree, S. Trehalose Accumulation triggers autophagy during plant desiccation. PLoS Genet. 11, e1005705 (2015).

CURRENT SUPPORT NIH #R01-1R01GM132401 Zhang, X. (PI) 2019–2023 “Roles of SWI/SNF complexes in posttranscriptional processing of RNA” NIH #1R01-GM127742-01 Zhang, X. (PI) 2018–2023 “Suppression mechanism of Geminivirus-encoded TrAP protein” TAMU X-Grant Zhang, X. (PI); Cai, J. (co-PI); Ji, J-Y (co-PI); Patrick, K. (co-PI); Cruz-Reyes, J. 2019–2022 (co-PI); Sczepanski, J. (co-PI); Zhang, J. (co-PI); Zeng, L. (co-PI) “Biology hidden in RNA secondary structures and modifications” NIH PO Admin. Equipment Zhang, X. (PI) 2020–2021 Supplement “Roles of SWI/SNF complexes in posttranscriptional processing of RNA” Welch Foundation #A- Zhang, X. (PI) 2018–2021 1973-20180324 “Biochemical basis of SWI2/SNF2 ATPase in remodeling RNA complexes” NSF MCB-1716243 Zhang, X. (PI) 2017–2021 “Roles of the SERRATE protein in regulation of miRNA biogenesis and transposable element silencing in Arabidopsis thaliana” Texas A&M AgriLife Zhang, X. (PI) 2018–2020 “Manipulating rice traits through CRISPR/Cas9-guided insertion of a synthetic and RNA-silencing resistant genes”

COMPLETED SUPPORT (2015–present) NSF (MCB-1253369) Zhang, X. (PI) 2013–2019 “CAREER: Arabidopsis Argonaute10-protein interactome” CPRIT #RP160822 Zhang, X. (PI); Wu, C. (co-PI) 2016–2018 “Exploring Geminivirus-Encoded Suppressor of Histone Methyltransferases as an Anti-Cancer Drug”

AWARDS, HONORS, & EDITORIAL, REVIEW, AND ADVISORY BOARD APPOINTMENTS (2015–present) Chancellor EDGES Fellow Texas A&M University 2019 Faculty Fellow AgriLife Research 2019 NIH Panel Member Special emphasis 2019 Norman Borlaug Outstanding Faculty Texas A&M University 2016 NSF Panel Member Genetics, Genomics, and Proteomics; MCB; ISO; DEV1 Various

DEPARTMENT AND SYSTEM SERVICE (2015–present) Member Seminar Committee BCBP 2020–present Member Promotion and Tenure Committee BCBP 2018–present Executive Committee Member MEPS Program AgriLife 2017–present Member Grant study section BCBP 2020

COURSES TAUGHT (2015–present) BICH 456/656 RNA World 3 cr. 2008–present GENE 302 Principles of Genetics 4 cr. 2008–present BICH 491/691 Research Variable 2008–present