2014 Genetics Academic Program Review - Table of Contents I

2014 Genetics Academic Program Review - Table of Contents I. Executive Summary…………………………………………………..2 II. Introduction………………...…………………………………………..4 A. Welcome……………………………………………………………………….4 1. Mission and Unique Characteristics…………………………………….4 2. Most Recent Academic Program Review………………………………4 3. Current Pressing Issues………………….………………………………4 B. Charge to External Review Committee……………………………………..5 C. Itinerary…………………………………………………………………………6 D. Faculty Liaison and Executive Committee Members…………………….10 III. Background…………………………………………………………………………...11 A. Organizational Structure of the Intercollegiate Faculty…………………..11 B. Interdisciplinary Graduate Degree Program in Genetics………………...11 IV. Current State of the Program……………………………………………………….15 A. 18 Characteristics of a Texas Doctoral Degree Program………………..15 B. Student Retention Rates…………………………………………………….17 C. Student Enrollment…………………………………………………………..17 E. Alignment of Program with Institutional Goals……………………………19 F. Program Curriculum and Duration…………………………………………19 H. Program Finances and Resources………………………………………..22 I. Program Administration…………………………………………………….24 V. Additional Information……………………………………………………………….28 Graduate Student Compensation………………………………………….28 Entrance Requirements…………………………………………………….28 Laboratory Rotations………………………………………………………..28 Seminar Series………………………………………………………………29 Genetics Graduate Student Association………………………………….29 VI. Programmatic Stability………………………………………………………………30 Vision………………………………………………………………………….30 Strengths……………………………………………………………………..30 Weaknesses………………………………………………………………....30 Goals………………………………………………………………………….30 VII. Appendices…………………………………………………………………………..32 Learning Outcomes for the Ph.D. Degree………………………………..33 Learning Outcomes for the M.S. Degree…………………………………41 Faculty of Genetics ByLaws……………………………………………….49 Faculty 2 Page CVs……………………………………………Separate File

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Genetics Academic Program Review Self-Study Report Texas A&M University

I. Executive Summary

Periodic external reviews of all graduate degree-granting units are conducted by Texas A&M University. The last review for the Interdisciplinary Program (IDP) in Genetics occurred in 2007. A number of issues related to the management, reporting structure, resource availability, and support of the Genetics Program were identified in the external evaluators report. Several significant changes have been initiated by Texas A&M University to address several of these issues for all Interdisciplinary Programs since that time.

The oversight and reporting structure of the IDP in Genetics has been streamlined such that administrative issues related to curriculum changes and appointments to the Graduate Faculty are handled directly by the College of Agriculture and Life Sciences, which is now administratively associated with the Genetics Program, such that the program reports directly through the College and has representation on the College Graduate Operating Committee. Further lines of reporting/requests are available through the Dean of Faculties and the Office of Graduate and Professional Studies, with the IDP’s also now having representation on the University Graduate Operating Committee.

A stable and predictable funding line has been established for the IDP’s via a formula- based central distribution of Graduate Enhancement Funds, along with Chair and Staff Support, all of which are transferred to the Genetics Program in a timely manner. This will enable more precise planning of program activities and the setting of longer-term goals.

One of the other primary issues raised during the previous Academic Program Review has had a serious negative impact on the Genetics Program. A faculty member that was teaching one of the Genetics Core Curriculum classes moved to a different institution, leaving the class without an instructor. Since the Genetics Program has no ability to directly negotiate with Departments to release an instructor for the course or to influence hiring decisions, this critical course has not been offered for several years. In addition to this issue, the Faculty of Genetics have identified a need to review the current curriculum to ensure that Genetics students are distinguished from other majors, and that the course offerings provide sufficient breadth to ensure our students are prepared for cutting edge interdisciplinary research.

The IDP in Genetics continues to recruit and train some of the brightest graduate students in the Life Sciences. A vibrant and targeted recruiting program identifies talented prospective graduate students, brings them on campus for a multi-day recruiting experience and has been able to capture 75% of the students to which offers of admission were extended, all of which have high GRE scores and GPAs, previous research experience, and excellent references.

These efforts and the other activities of the IDP in Genetics require a huge time commitment and there is increasing concern that the contributions of the Faculty to

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Genetics Academic Program Review Self-Study Report Texas A&M University

Interdisciplinary activities are not valued during Annual Performance Evaluations and during the Tenure and Promotion process. This is reflected in an increasing difficulty in identifying Faculty volunteers that are willing to serve on the Genetics Executive Committee and several standing committees that are critical to the maintenance and growth of the Graduate Program.

The IDP in Genetics graduates an average of 10 Graduate Students each year and has an important role in enhancing the quality and impact of Texas A&M University on Graduate Education and Training. We look forward to your insights and guidance in further improving our Program.

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Genetics Academic Program Review Self-Study Report Texas A&M University

II. Introduction

A. Welcome to the Interdisciplinary Graduate Degree Program in Genetics

1. Mission and Unique Contributions to the Texas A&M University Graduate Program.

The principal function of the Faculty of Genetics is the administration of the graduate programs leading to the Master of Science and Doctor of Philosophy degrees in Genetics, in conformance with the rules of the Office of Graduate and Professional Studies of Texas A&M University. The Faculty also serves to promote and facilitate communication among geneticists and to foster the development of genetics at Texas A&M University. The Faculty of Genetics arranges for the periodic assembly of geneticists and provides a forum for them and for others with interests in genetics. The organizational and operational characteristics of the Faculty of Genetics are intended to be broad enough to permit consideration of all academic aspects of genetics and all other matters affecting the position and progress of the discipline at Texas A&M University.

The Faculty of Genetics is currently composed of 96 Faculty Members from 5 Academic Colleges and 17 Academic Departments. There are 60 Graduate Students currently studying for their M.S. or Ph.D. graduate degrees in Genetics, distributed across 5 Academic Colleges and 15 Academic Departments. For the 2013 academic year, 12 new Ph.D. students were admitted into the program.

2. Most Recent External Review – May 2007

The last comprehensive external review of the Faculty of Genetics at Texas A&M University occurred in May of 2007. The Faculty self-study can be found here – http://provost.tamu.edu/initiatives/academic-program-review-documents/GENE-Self-Study- 2007.pdf The self-evaluation by the Faculty and the critique generated by that review were in part responsible for a series of specific recommendations that have been implemented for all Interdisciplinary Programs (IDP) within the Texas A&M University. The administrative structure has been streamlined whereby each IDP is associated with a single college (College of Agriculture and Life Sciences for Genetics), thus utilizing the existing processes for the submission of curricula changes, new graduate faculty appointments; and thereby gaining representation on the colleges’ Graduate Operations Committee. The University Gradate Operations Committee also has two faculty members representing the IDP’s. The previous fiscal uncertainty has been resolved through the provision of a predictable and stable annual budget for each IDP; and the chair of the programs now receive a $15,000 stipend that can be 4

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Genetics Academic Program Review Self-Study Report Texas A&M University used as compensation, or for operating costs for their research program. The Genetics Program also continues to benefit from the generosity of the Department of Biochemistry and Biophysics (BCBP), which provides up to 12 Teaching Assistant (TA) positions for first year Genetics Ph.D. students, who then teach in the undergraduate Genetics laboratory courses (GENE 301/302) that are managed by BCBP. These are essential resources for the maintenance of the Genetics Graduate Student Recruiting Program, as well as the partial salary provided by BCBP for staff support. Finally, members of the Faculty of Genetics were heavily involved in the establishment of the Whole Systems Genomics Institute (https://genomics.tamu.edu/), and the IDP in Genetics will continue to be involved by providing needed curricula for WSGI educational initiatives.

However, one of the primary concerns raised by the previous review still exists and has negatively impacted a large number of recent Genetics Graduate Students. A major issue is that the IDP in Genetics does not have any ability to negotiate with Departments to ensure that the most qualified Faculty are available to teach Genetics Core Curriculum Courses, nor does there exist any substantial mechanism to reward the Faculty (or Department) for teaching these courses. As forewarned in the previous self-study; a retirement, or in this case relocation of a key faculty member that was teaching the Population Genetics course (GENE 612) resulted in the course not being offered for several years and will only finally return in the Fall of 2015. Similarly, the Genetics IDP has limited or no involvement in the recruitment of Faculty to ensure the diversity and quality of Genetics course offerings and research programs is maintained.

3. Current Pressing Issues

A substantial period of time has passed since the Faculty of Genetics last modified the curriculum for the Genetics Ph.D. and in preparing for this Academic Program Review, curriculum issues were the most common topic discussed. Several models for modernizing or updating the curriculum were proposed, however given the existing strain on Faculty teaching loads and an inability to negotiate directly with Departments; it seems most prudent to investigate strategies that utilize the existing courses on campus and to add those that are established within existing departmental structures, while continuing the practice of cross- listing courses with a GENE prefix when so desired. We would like to utilize the expertise and experiences of the review team to facilitate this discussion and to provide some recommendations for the Faculty to consider.

Over the past 5-10 years the Faculty of Genetics has lost several long-serving members that were essential to the establishment, growth, and maintenance of the Interdisciplinary Program. In particular, they served important roles in the administration of the program as Chair, Vice-Chair, Executive Committee Members, and Chairs of Standing Committees. With increasing administrative responsibilities, teaching loads, and expectations for accruing external resources, it has become increasingly difficult to recruit Genetics Faculty Members to these positions. It is not clear that performing these roles is valued in the Faculty Annual Performance Review process, or in the Tenure and Promotion Process; and as such, continued difficulties in filling these critical administrative roles are expected.

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Genetics Academic Program Review Self-Study Report Texas A&M University

B. Charge to the Review Committee (Office of Graduate and Professional Studies)

Texas A&M University Academic Program Review (APR) Charge to the External Review Team Department/Program Name

The Academic Program Review (APR) process at Texas A&M University provides the occasion for academic units to plan strategically, assess the quality and efficacy of their programs, and determine the best courses of action for ongoing improvement. The 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 external review team and a brief overview of the department.

External 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 external 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? What improvements (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, please contact Dr. Christine Stanley, Acting Vice Provost, at [email protected] or the APR Program Coordinator, at [email protected]. Thank you.

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Genetics Academic Program Review Self-Study Report Texas A&M University

C. INTINERARY Academic Program Review Interdisciplinary Faculty of Genetics Texas A&M University November 16-19, 2014

Guest accommodations: Rudder Jessup Bed & Breakfast 115 Lee Ave., College Station, TX (979) 693-1749 Itinerary for Doctoral Program Review Team

Sunday, November 16 (Arrival) 5:58pm F. Abel Ponce de Leon arrives at Easterwood Airport on AA Flight #2774 [email protected] 612-419-7870 Craig Coates will escort to Rudder Jessup from Easterwood Airport.

5:58pm Alejandro Aballay arrives at Easterwood Airport on AA Flight #2774 [email protected] 919-403-2020 Craig Coates will escort to Rudder Jessup from Easterwood Airport.

7:30pm Dinner at Bell Ranch Steakhouse for the review team with Craig Coates, Executive Committee members: Hubert Amrein, Terje Raudsepp, Dorothy Shippen, and Hongbin Zhang Hongbin Zhang will escort to Bell Ranch Steakhouse and then to Rudder Jessup.

Monday,, November 17 (Day 1) 7:30 -8:30am Breakfast and entry meeting at Rudder Jessup with: Office of the Provost Administrative Team Hongbin Zhang will pick up review team from Rudder Jessup and escort to Room 501, Agriculute & Life Sciences Building

9:00-10:15am Alan Sams, Executive Associate Dean, College of Agriculture & Life Sciences Ginger Carney, Associate Dean For Undergraduate Research & College Climate, College of Science Robert Burghardt, Associate Dean of Research & Graduate Studies, College of Veterinary Medicine 7

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Genetics Academic Program Review Self-Study Report Texas A&M University

Van Wilson, Associate Dean of Research & Graduate Studies, Texas A&M Health Science Center Hongbin Zhang will escort to the Biochemistry/Biophysics Building.

10:30-:12:00pm Overview of the Faculty of Genetics—Craig Coates & Terje Raudsepp Room 221A, Biochemistry/Biophysics Building Ashley Mattison(grad student) will escort from to Room 203.

12:00-1:30pm Catered lunch by Jason’s Deli with select Graduate Students, Room 203, Biochemistry/Biophysics Building.

1:30 - 2:30pm Genetics Faculty Group Room 203, Biochemistry/Biophysics Building

2:45 - 3:45pm Genetics Faculty Group Room 203, Biochemistry/Biophysics Building

4:00 - 5:00pm Genetics Faculty Group Room 203, Biochemistry/Biophysics Building Hongbin Zhang will pick up review team and escort to the Faculty Social

5:30 - 7:00pm Faculty Social at The University Club Craig Coates will pick up review team and escort to dinner.

7:00-8:30pm Dinner at Cenare’s with former Genetics Executive Committee chairs: Craig Coates, Jim Derr, Jeff Kapler, & Loren Skow. Craig Coates will escort review to Rudder Jessup

Tuesday, November 18 (Day 2) 8:00-9:15 am Breakfast provided by Rudder Jessup Hongbin Zhang will pick up review team from Rudder Jessup and escort to Biochemistry/Biophysics Building

9:30-10:30am Meet with Genetics Recruiting Committee members Room 221A, Biochemistry/Biophysics Building

10:30-12:00pm Meeting with Genetics Leadership: Executive Committee Members and Standing Committee representatives Room 221A, Biochemistry/Biophysics Building Rachel Jordan(grad student) will escort to Room 403, Biochemistry/Biophysics Building

12:00-1:30pm Catered Lunch by Blue Baker with IDP Chairs: Room 403,Biochemistry/Biophysics Building.

1:30- 2:30pm Genetics Faculty Group

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Genetics Academic Program Review Self-Study Report Texas A&M University

Room 403, Biochemistry/Biophysics Building

2:45- 3:45pm Genetics Faculty Group Room 403, Biochemistry/Biophysics Building

4:00 - 5:00pm Genetics Faculty Group Room 403, Biochemistry/Biophysics Building 5:00 pm Hongbin Zhang escort to Rudder Jessup.

5:30-6:30pm Catered Dinner from Epicures to reviewers work room at Rudder Jessup.

6:30-9:30pm Reviewers’ work session, preparation of draft report for exit meeting, faculty debriefing

Wednesday, November, 19 (Day 3) 7:30 -9am Breakfast and exit meeting at Rudder Jessup with: Office of the Provost, Administrative Team and College Deans Hongbin Zhang will escort to the Biochemistry/Biophysics building; will bring team luggage along.

9:30 – 10:30 am Reviewers make final changes to draft report, as necessary, Room 403, Biochemistry/Biophysics building.

10:30-11:00 am Reviewers debrief Genetics Executive Committee Room 403, Biochemistry/Biophysics building. Reed Stubbendieck (grad student) will escort to Room 106A, Biochemistry/Biophysics Building

11:15-11:45 am Reviewers debrief faculty, staff and students on final report, Room106A Biochemistry/Biophysics

12:00-1:00 pm Lunch at Café Eccellwith Dr. Coates, Genetics Executive committee member: Hongbin Zhang

Craig Coates Escort to Easterwood Airport for 2:40pm AA 3386 flights

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Genetics Academic Program Review Self-Study Report Texas A&M University

D. Faculty Liaison and Executive Committee Members

Dr. Craig Coates (At-Large position, 1 year remaining)

Dr. Hubie Amrein (HSC representative, 2 years remaining)

Dr. Hongbin Zhang (At-large position, 1 year remaining)

Dr. Dorothy Shippen (At Large position, term ending)

Dr. Paul Samollow (At-Large position, term ending)

Dr. Terje Raudsepp (CVM representative, term ending)

Dr. Tina Gumienny (At-Large, 1 year remaining)—Need replacement, moving to different institution.

Dr. Tom McKnight (COS representative 2 years remaining)—Need replacement, administrative appointment.

Dr. Jim Wild (COALS representative, 2 years remaining)—Need replacement, retired.

Administrative Associate: Julia Williams, room 109A Bio/Bio, 458-2284

Craig Coates, Chair Office 979-458-1219 Home 979-571-2784 Cell 979-571-2784 [email protected]

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Genetics Academic Program Review Self-Study Report Texas A&M University

III. Background

A. Organizational Structure of the Intercollegiate Faculty

The Faculty of Genetics is an intercollegiate academic unit of The Texas A&M University. It is administratively associated with the College of Agriculture and Life Sciences, and is overseen by the Dean of Faculties and the Office of Graduate and Professional Studies. Genetics Faculty are listed within one or more areas of specialization of genetics, primarily to assist incoming graduate students identify faculty with whom they want to perform research rotations during their first two semesters in the program as they search for their thesis laboratory. The current areas of specialization are as follows.

Bioinformatics and Genomics Conservation and Population Genetics Medical Genetics - Human and Animal Microbial Genetics Molecular, Cellular and Developmental Genetics Plant Genetics

B. The Interdisciplinary Graduate Degree Program in Genetics

The principal function of the Faculty of Genetics is the administration of the Interdisciplinary Graduate Degree Program leading to the Master of Science and Doctor of Philosophy degrees in Genetics. The organization also serves to promote and facilitate communication among geneticists and to foster the development of genetics at Texas A&M University. It arranges for the periodic assembly of geneticists and provides a forum for them and for others with related interests. The organizational and operational characteristics of the Faculty of Genetics are intended to be broad enough to permit consideration of all academic

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Genetics Academic Program Review Self-Study Report Texas A&M University aspects of genetics and all other matters affecting the position and progress of the discipline at Texas A&M University. Admission to the Faculty is determined by the Executive Committee after 1) nomination by the Head of the faculty member’s administrative department, and 2) recommendation by the Membership Committee of the Faculty of Genetics. Full members of the Faculty of Genetics must be full members of the graduate faculty at Texas A&M University and must have significant research, teaching, and service activities in genetics. Members are reviewed every three years, and must maintain active involvement in both academic and service functions of the Faculty of Genetics. Current Genetics Faculty Members are listed in the table below. Intercollegiate Faculty of Genetics Departmental Listing August 2014

College of Agriculture and Life Nutrition (NUTR) Sciences(COALS) ALLRED, Clinton D. CHAPKIN, Robert S. Animal Science (ANSC) STURINO, Joesph GILL, Clare TURNER, Nancy HERRING, Andy ING, Nancy H. RIGGS, Penny K. Plant Pathology (PLPA) DE FIGUERIEDO, Paul RILEY, David DICKMAN, Marty BRYK, Mary EBBOLE, Daniel J. GONZALEZ, Carlos F. Biochemistry & Biophysics (BCBP) KENERLEY, Charles M. HU, James C. MAGILL, Clint W. KUNKEL, Gary R. SHAW, Brian MULLET, John E. WILKINSON, Heather PANIN, Vlad PETERSON, David O. Soil and Crop Science (SCSC) POLYMENIS, Michael KOHEL, Russell J. SHIPPEN, Dorothy E. MURRAY, Seth SMITH, C. Wayne STRAIGHT, Paul STELLY, David M. Entomology (ENTO) COATES, Craig J. YU, John Z. JOHNSTON, J. Spencer ZHANG, Hong-Bin

Forest Science (FRSC) Wildlife and Fishery Science (WFSC) LOOPSTRA, Carol A. GOLD, John HURTADO, Luis Horticulture (HORT) MATEOS, Mariana MILLER, J. Creighton

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Genetics Academic Program Review Self-Study Report Texas A&M University

Health Sciences Center (HSC) RILEY, Bruce ROSENTHAL, Gil Molecular & Cellular Medicine RYAN, Kathyrn LIU, Fei SACHS, Matt BONDOS, Sarah SIEGELE, Deborah AMREIN, Hubert BAYLESS, Kayla J. GUMIENNY, Tina L. College of Veterinary Medicine (CVM)

JI, Junyuan Large Animal Hospital (VLAM) MAXWELL, Steve A. COHEN, Noah SITCHERAN, Raquel KAPLER, Geoffrey M. Veterinary Integrative Biosciences (VIBS) CAI, James Microbial & Molecular Pathogenesis CHOWDHARY, Bhanu ANDREWS- MURPHY, William J. POLYMENIS, Helene PORTER, Westin CIRILLO, Jeffrey RAUDSEPP, Terje LEIBOWITZ, Julian SAMOLLOW, Paul SAMUEL, James E. SKOW, Loren C. SKARE, Jon WELSH, Jane TESH, Vernon Veterinary Pathobiology (VTPB) CRISCITIELLO, College of Science (COS) Michael DERR, James N. Biology (BIOL) DINDOT, Scott ARAMAYO, Rodolfo PAYNE, Susan BELL-PEDERSEN, Deb SEABURY, Christopher BENEDIK, Michael WOMACK, James E. ERICKSON, James GARCIA,L. Rene Veterinary Physiology and Pharmacology GOMER, Richard (VTTP) HALL, Timothy C. LONG, Charles HARDIN, PAUL SAFE, Steve LINTS, Robyn WESTHUSIN, Mark MAGGERT, Keith MCKNIGHT, Thomas College of Education and Human PEPPER, Alan Development (EHD) PERKINS, Brian QIN, Hongmin Health and Kinesiology (HLKN) LIGHTFOOT, Tim

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Genetics Academic Program Review Self-Study Report Texas A&M University

Full members are entitled to: 1) Serve as chair of a thesis or dissertation committee for a Genetics graduate student; 2) Teach graduate GENE courses; 3) Serve on the Faculty of Genetics Executive Committee; 4) Vote on matters requiring a vote of the Faculty of Genetics; 5) Serve on the Faculty of Genetics Membership and Nominating Committee; and 6) Chair standing or ad hoc committees of the Faculty of Genetics.

The responsibilities of members are detailed in the Faculty Bylaws (Appendix).

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Texas A&M University 18 Characteristics of Texas Public Doctoral Programs Programs included only if in existence 3 or more years. Program is defined at the 8-digit CIP code level.

Department Faculty of Genetics

Doctoral Degree Program Genetics Contact Name Julia Williams, Academic Advisor II Contact Phone Number 979-458-2284

Number of Degrees Per Year 2010-2011 8

Average, 2010-2013 2011-2012 2 1 Three-year average of the number of degrees awarded per academic year 2012-2013 8

3 Year Average 6.0

Graduation Rates % Graduating Starting Cohorts: 2001-2003 within 10 Years 97% Three-year average of the percent of first-year doctoral students who graduated within ten years. First- 2 year doctoral students: Those students who have been coded as doctoral students by the institution and have either completed a master’s program or at least 30 SCH towards a graduate degree. Years with Cohort greater than 0 2001,2002,2003

Average Time to Degree Average Years to Students Starting 2001-2003 Degree 5.6 3 Three-year average of the registered time to degree[3] of first-year doctoral students within a ten year period. [3] Registered time to degree: The number of semesters enrolled starting when a student first appears as a doctoral student until she completes a degree, excluding any time taken off during graduate study. The number of years is obtained by dividing the number semsters by three.

Employment Profile (In field within one year of graduation). For each of the three most recent years, the number and percent of graduates by year employed, those still seeking employment, and unknown

Employed Still Seeking Employment Unknown 4 Number Percent Number Percent Number Percent

2010-2011 8 89% 1 11% 0 0%

2011-2012 5 83% 1 17% 0 0%

2012-2013 8 82% 2 18% 0 0%

Admissions Criteria Description of admission factors

Prospective students complete a pre-application in which our graduate admission committee reviews. The committee contacts the prospect via email as to whether they would like them to complete a full application. Those students approved through the pre-application process are asked to complete the Texas Comman application through the University graduate admission office on-line. Students are asked to submit a statement of purpose, transcripts, general GRE scores (TOEFL as well for international students), and three recommendation letters. Domestic and foreign national students receive a phone interview from a graduate admission committee member. The domestic and foreign national prospects that submit their application materials by December 20 are elibilbe to receive an ivitation to our Graduate Recruiting Symposium in February. During the symposium,prospective students are given an overview of the of the program, interviewed by faculty members, and interact with current students. The recruiting committee makes their first round of admissions selections from the symposium attendee based on their application 5 material, faculty interviews and graduate student feedback.

Percentage Full-time Students Fall 2011 91.3% FTS/number of students enrolled for the last three fall semesters. 6 Fall 2012 75.0% Fall 2013 88.2%

Average Institutional Financial Support Provided $22,000 7 For those receiving financial support, the average monetary institutional financial support provided per full-time graduate student for the prior year, from assistantships, scholarships, stipends, grants, and fellowships. Does not include tuition or benefits. Percentage Full-Time Students with Institutional Financial Support 100%

8 In the prior year, the number of full-time studentswith at least $1,000 of annual support/the number of full-time students

Number of Core Faculty 91

9 Number of core faculty in the prior year

Student-Core Faculty Ratio 0.6

Three-year average of full-time student equivalent (FTSE) /three-year average of full-time faculty equivalent (FTFE) of core faculty. Core Faculty: 10 Full-time tenured and tenure-track faculty who teach 50 percent or more in the doctoral program or other individuals integral to the doctoral program who can direct dissertation research.

Core Faculty Publications 3.9

Three-year average of the number of discipline-related refereed papers/publications, books/book chapters, juried creative/performance 11 accomplishments, and notices of discoveries filed/patents issued per year per core faculty member.

Core Faculty External Grants Three-year average of the number of core faculty receiving external funds, average external funds per faculty, and total external funds per program per academic year. All external funds received from any source including research grants, training grants, gifts from foundations, etc., reported as expenditures. 12 Average of the Number of Core Faculty receiving 43

Average External Funds per Faculty $242,043 Total External Funds $10,901,603

Faculty Teaching Load 8.5 13 Total number of semester credit hours in organized teaching courses taught per academic year by core faculty divided by the number of core faculty in the prior year

Faculty Diversity Core faculty by ethnicity (White, Black, Hispanic, Other) and gender, updated when changed Male Female

White 55 18 14 Black 1 0

Hispanic 4 1 Other 10 2

Student Diversity Enrollment headcount by ethnicity (White, Black, Hispanic, Other) and gender in program in the prior year Fall 2013

Male Female

15 White 9 15 Black 0 0

Hispanic 2 2 Other 3 3

Date of Last External Review 2006-2007 16 Date of last formal external review, updated when changed

External Program Accreditation Name of body and date of last program accreditation review, if applicable, updated when changed 17

Student Publications/Presentations 6.00 For the three most recent years, the number of discipline-related refereed papers/ publications, juried 18 creative/performance accomplishments, book chapters, books, and external presentations per year by student FTE

B. Student Retention Rates

Genetics Graduate Degrees Awarded

YEAR 08-09 09-10 10-11 11-12 12-13 M.S. 2 3 6 1 7 Ph.D. 6 7 8 2 8 Total 8 10 14 3 15

Over the 5yrs for which the Graduate Degree Award data is available following the previous APR, the Genetics Program has graduated 50 students for an average of 10 graduate degrees per year (3.8 M.S., 6.2 Ph.D.). While the incoming year for those students is not indicated, the average number of admitted students to the program over the last 7 years is 10.5 per year (0.9 M.S., 9.6 Ph.D.). This indicates that the overall student retention rate to a final graduate degree is high. However, just looking at the Ph.D., approximately 2/3rds of the incoming Ph.D. students are graduating with that degree, with the vast majority of the remaining students graduating with a M.S. degree following a change of degree petition. There are a variety of reasons why students change from a Ph.D. to a M.S., including changes in career goals, family/health issues, insufficient research/academic progress, and a lack of available funding. In the vast majority of cases these students are graduating with a M.S. with thesis option; the non-thesis M.S. degree option being the rare exception.

C. Student Enrollment

YEAR DEGREE APPLIED ADMITTED ENROLLED M.S. 6 1 1 2007 Ph.D. 29 13 11 TOTAL 35 14 12 M.S. 6 1 1 2008 Ph.D. 39 10 7 TOTAL 45 11 8 M.S. 7 1 1 2009 Ph.D. 53 13 7 TOTAL 60 14 8 M.S. 12 3 1 2010 Ph.D. 53 17 12 TOTAL 65 20 13

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M.S. 5 1 1 2011 Ph.D. 52 13 9 TOTAL 57 14 10 M.S. 9 1 1 2012 Ph.D. 57 14 12 TOTAL 66 15 13 M.S. 6 0 0 2013 Ph.D. 52 14 12 TOTAL 58 14 12

The average GRE and GPA scores for students admitted to the program has been very consistent for the last 5 years of recruiting cycles. The data for 2 recent cycles is as follows.

2010-2011 For class of 10 + 2 spring transfers: 1199 GRE (500V, 699Q) 3.443 GPA [7 women, 1 “other” (Southwest Asia), 3 International]. 2011-2012 For class of 9: 1208 GRE (524V, 684Q) 3.635 GPA [5 women, 1 African American, 1 Asian American, 1 International].

The total numbers of students applying to the Genetics Graduate Program is misleadingly low due to the process we implemented to streamline our admissions review process, focus on the highest quality students, and improve our “capture rate”, which averages 75% for students that enroll following an offer of admission. All students are encouraged to submit a “pre-application” which mimics the Apply Texas formal application, however the pre-applications are not included in the formal numbers presented above. This allows the Recruiting and Admissions Committee a first pass at reviewing the students, as well as allowing the students to apply with no cost involved. The highest ranked students are contacted and encouraged to submit a full application through the formal process and when received and following review of the complete packets and letters of recommendation, the top students are invited to attend the Genetics Recruiting Weekend, held Thursday-Sunday the 2nd week of February. Typically up to 25 students are invited to attend the recruiting weekend and following interviews with faculty and receiving feedback, the committee admits the highest ranked students who are offered a Teaching Assistantship (TA) to support their first year in the program. It is also made known that the program does not offer direct financial support for M.S. students, hence the low number of applicants for that degree program. However, individual P.I.’s can recruit M.S. students that they fund directly; so long as these students meet the academic standards of the program and are also approved for admission by the recruiting and admissions committee. Similarly, Ph.D. students that are recruited by individual P.I.’s outside of the formal recruiting process must also meet an equivalent academic standard before they are admitted to the program. If there is some doubt regarding a student’s preparation in either of these cases, they may be conditionally admitted under academic probation, or initially into the ______18 Genetics Academic Program Review Self-Study Report Texas A&M University

M.S. degree whereby they can subsequently be removed from probation and/or changed to the Ph.D. degree following suitable academic and research progress.

E. Alignment of Program with stated Institutional Goals

The Interdisciplinary Program in Genetics provides support for the Texas A&M University Vision 2020 goals in several areas. Membership within the Faculty of Genetics is often put forward as a possibility during Faculty Recruiting visits and interviews, with the major benefit being the ability to access the very high quality Ph.D. students that are recruited to the program, in many cases they are superior to students that are recruited to an individual departmental program. By Strengthening Our Graduate Program the Faculty of Genetics and Graduate Students are helping to enhance the reputation of Texas A&M University and to raise the standard of graduate student research on campus in the life sciences. Our Faculty and Students are actively involved in Enhancing the Undergraduate Academic Experience through teaching undergraduate classes, serving as TA’s in undergraduate laboratories, and providing research experiences and mentoring for undergraduate research experiences.

F. Program Curriculum and Duration

The following graduate courses are offered with a GENE prefix. 603. Genetics. (4-0). Credit 4. Development of fundamental concepts related to the structure, function, organization, transmission and distribution of genetic material. Prerequisite: GENE 301. 606. Quantitative Phylogenetics. (2-3). Credit 3. Designed to provide the theory and tools required for inference of phylogenetic (evolutionary) relationships among biological taxa using various types of comparative data including morphological characters, biochemical and molecular characters, and DNA sequences; hands-on analysis of data using contemporary tools. Prerequisite: ENTO 601 or approval of instructor. Cross-listed with ENTO 606 and WFSC 646. 608. Critical Analysis of Genetic Literature. (1-0). Credit 1. An introduction to primary literature in the field of genetics which will give students experience in critically evaluating scientific papers and develop an appreciation of how genetics can be used to address important biological questions. 612. Population Genetics. (3-0). Credit 3. Biological approach to genetic characteristics of populations dealing with genetic equilibrium, allelic variation, determination of genetic variation in populations, effects of mating systems, selection, mutation and drift on population parameters. Prerequisites: GENE 603; STAT 651. 613. Quantitative Genetics I. (3-0). Credit 3. Quantitative genetics concepts particularly dealing with partitioning of phenotypic variance into genetic and environmental components, selection response, effects of systems of mating, genetic covariance and threshold effects. Prerequisites: GENE 612; STAT 652. 614. Maximum Likelihood Estimation of Genetics. (3-0). Credit 3. Theoretical and analytical approaches to the application of maximum likelihood for the estimation of parameters under linear and nonlinear models; single and polygene genetic models including Hardy-Weinberg equilibrium, linkage analysis and quantitative trait loci detection. Prerequisites: GENE 603; STAT 651; STAT 652 or STAT 601. Cross-listed with ANSC 614. 620. Cytogenetics. (3-0). Credit 3. Examination and analysis of variation in chromosome structure, behavior and number; developmental and evolutionary effects of this variation. Prerequisite: GENE 603. 626. Analyses of Gene Expression. (1-3). Credit 2. Proficiency in handling DNA and RNA gained during exercises used routinely in analyses of gene expression; RNA preparation and analysis on Northern blots; in vitro transcription and polyacrylamide gel analysis of nucleic acids; sub- cloning and mRNA quantitation using polymerase chain reaction. Prerequisites: GENE 450 or approval of instructor; radiation safety training. Cross-listed with ANSC 626. Course Descriptions/Genetics 441442 Course Descriptions/Genetics 629. Applied Animal Genomics. (3-0). Credit 3. Theory and application of genomics by livestock industries; consideration of genetic markers, gene mapping methods, genome analysis and emerging technologies such as microarrays, transgenesis, cloning and marker assisted selection; exposure to bio- informatic tools for genomics. Prerequisite: GENE 603 or approval of instructor. Cross-listed with ANSC 629 and POSC 630. 631. Biochemical Genetics. (3-0). Credit 3. Genetic control of cellular metabolism. Mechanism of gene action; gene-enzyme relationships; regulation of gene expression; structure and organization of genomes; biochemical manipulation and characterization of genetic molecules. Prerequisite: GENE 431 or BICH 431; BICH 603. Cross-listed with BICH 631. 633. Conservation Genetics. (3-0). Credit 3. Genetic concepts and techniques relevant to management and conservation of biological

______19 Genetics Academic Program Review Self-Study Report Texas A&M University diversity; research and conservation within a conservation genetics framework. Prerequisites: Introductory courses in genetics and ecology or biological conservation. Cross-listed with WFSC 633. 643. Molecular Quantitative Genetics and Plant Breeding. (3-0). Credit 3. Classical, applied and molecular aspects of quantitative genetics in plant breeding; genetic relationships; genetic diversity; genetic phenomena (linkage, heterosis and epistasis); genotype by environment interaction; mapping quantitative trait loci (QTL); genomic and marker-assisted selection; application of statistical software. Prereq- uisites: STAT 651, SCSC 642 or GENE 613 or approval of instructor. Cross-listed with SCSC 643. 648. Molecular Evolution. (2-2). Credit 3. Theory and tools used in the analysis of molecular evolutionary patterns of DNA and protein sequences; format combines lecture presentations by instructor, discussion of relevant scientific literature, computer exercises, preparation of research proposal or independent research project, and practice in peer review process. Prerequisites: Basic courses in general Genet- ics and in Evolution. Cross-listed with WFSC 648. 654. Analysis of Complex Genomes. (3-0). Credit 3. History and current status of genetic and molecular analysis of higher eukaryotic genomes; coverage of techniques for dissection of genomes into manage- able 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. Prerequisite: GENE 603. Cross-listed with SCSC 654 and MEPS 654. 655. Analysis of Complex Genomes--Lab. (0-7). Credit 3. Laboratory methods in molecular genetic techniques for genetic mapping, physical mapping, and map-based cloning of both qualitative and quantitative phenotypes. Prerequisite: GENE 603 or equivalent or approval of instructor. Cross-listed with SCSC 655 and MEPS 655. 662. Eukaryotic Transcription. (1-0). Credit 1. Intensive short course in molecular mechanisms of eukaryotic transcription and its regulation. Prerequisite: GENE 631 or BICH 631 or approval of instructor. Cross-listed with BICH 662. 673. Gene Expression. (1-0). Credit 1. Oral presentations and discussions related to the biochemistry and molecular biology of gene expression in animal, plant, and microbial systems. Course may be repeated for credit up to 12 times. Prerequisite: Graduate classification in biochemistry or genetics or approval of instructor. Cross-listed with BICH 673. 677. Genes and Diseases. (3-0). Credit 3. Molecular and genetic basis for human disease; structure, function and evolution of chromosomes; epigenetics; gene mapping; complex genetic traits; cancer genetics; neurodegenerative disorders; animal models (yeast, mouse, worms, fruit flies); ethics. Prerequisite: GENE 603, GENE 631, or MSCI 601 or approval of instructor. Cross-listed with MCMD 677. 681. Seminar. (1-0). Credit 1. Reports and discussions of topics of current importance in genetics; reports to be prepared and presented by graduate students enrolled in course. 685. Directed Studies. Credit 1 to 4 each semester. Individual problems or research not pertaining to thesis or dissertation. Prerequisite: Approval of instructor. 689. Special Topics in... Credit 1 to 4. Selected topics in an identified area of genetics. May be repeated for credit. Prerequisite: Approval of instructor. 691. Research. Credit 1 or more each semester. Prerequisite: GENE 603. 697. Teaching Genetics Labs. (1-0). Credit 1. Theory and practical aspects of teaching genetics labs, with emphasis on content, grading, instructional methods and practical aspects of genetics labs. May be repeated for credit. Prerequisites: Graduate classification in genetics; appointment as a TA for genetics labs.

Genetics Ph.D. Students are required to take the following courses to satisfy the minimal degree requirements, with differences for M.S. students as indicated.

GENE 603 – Genetics (4 Cr.) GENE 608 – Critical Analysis of Genetics Literature (1 Cr.) GENE 612 – Population Genetics (3 Cr.) OR GENE 613 3 (Cr.) – Quantitative Genetics (requires graduate level Statistics as a prerequisite) GENE 631 – Biochemical Genetics (3 Cr.) GENE 681 – Seminar (3 x 1 Cr.), or equivalent departmental seminar course (1 only for M.S.) GENE 697 – Teaching Genetics Labs (2 x 1 Cr.), not required for M.S. or Research Assistants. One other 3 Cr. course in Genetics or a closely related topic.

The Genetics Curriculum was designed in a streamlined manner to allow maximum flexibility for students who may need to take additional courses as recommended by their thesis committee. Some students have experienced some specific issues whereby the home department of their P.I. has also required them to take the required curricula classes for the home department major, which at times can be burdensome and at worst tied to departmental funding of that students

______20 Genetics Academic Program Review Self-Study Report Texas A&M University stipend. Taken to its extreme, this has caused some students to change majors, thus reducing the retention rate of the Genetics Program, and causing significant consternation amongst the Faculty given the time and fiscal resources that were utilized to recruit and fund the students. GENE 612 has not been offered for several years as the faculty member that was teaching the class has moved to a different institution and a replacement faculty member on campus could not be identified, or was otherwise unavailable due to existing teaching commitments for their home department. The course will be offered again in the Fall of 2015. Discussions surrounding the Genetics Curriculum were the most prevalent topic in preparations for the APR. One of the concerns that were raised is whether the curriculum allows students to be distinguished as “Genetics” students, compared to comparable curricula offerings that they may receive within another major. Another issue is whether the curriculum currently covers all of the needed academic training in Genetics; for example should coursework in genomics/bioinformatics be required. One of the proposed solutions is to have a suite of courses identified across campus (both GENE and non-GENE prefixes) that fit a variety of fields/areas of genetics, and then require students to take at least one class from each grouping. Our current areas of specialization that are used to organize faculty listings do not appear to be suitable for grouping courses, thus different groupings will be required along with identifying all of the course offerings across the campus that would fit within each area, as well as the minimum number of courses that need to be taken for the degree. The average time (years) to degree is shown in the following table. Year M.S. Ph.D. 06-07 2.50 5.50 07-08 3.58 5.19 08-09 3.75 6.92 09-10 4.17 5.71 10-11 3.83 5.94 11-12 2.50 5.75 12-13 3.29 5.81 Average 3.37 5.83 While the average time to degree for both the M.S. and Ph.D. are higher than desired, it is important to consider that it is not always possible to make the deadlines for the completion of final exams and submission of the thesis to enable the student to graduate that semester, often pushing the actual graduation date to the following semester even though all of the work is completed. Regardless, several of the Genetics Program Learning Outcome measures are tied to reducing the overall time to degree. The M.S. time to degree is also relatively high due to the majority of these degrees being awarded to students that started in the Ph.D. program and then changed to the M.S. program, often after 2-3 years of progress in the Ph.D. program.

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H. Program Finances and Resources

The Office of Graduate and Professional Studies use the following formulas to determine the allocation of resources to the Genetics Program.

Chair Support - $15,000 Staff Support – Total # Students X $300 + # Faculty Chairs/Co-Chairs X $250 Graduate Enhancement – Total Weighted Student Credit Hours X $12 Strategic Support – Total # PhD students X $300 + Total # MS students X $240 + Total PhD Graduates X $500 + Total MS Graduates X $400 Redistribution/Graduate Enhancement Funds – Proportion of unused funds from Colleges

For the past 2 fiscal years these calculations have resulted in the following allocations to the Genetics Program.

FY14 Chair Support - $15,000 (no fringe benefits) Staff Support - $27,236 (includes fringe benefits) Graduate Student Support - $88,750 (no fringe benefits)

FY15 Chair Support - $15,000 (no fringe benefits) Staff Support - $27,236 (includes fringe benefits) Graduate Student Support - $109,897 (no fringe benefits)

The FY14 to FY15 increase was primarily due to an increased allocation of redistributed funds as the other numbers used for the formulas are averaged over 5 years, which smoothes out any variation in those numbers year to year.

It should be noted that the provided Staff Support does not cover the full salary of Mrs. Julia Williams. The Department of Biochemistry and Biophysics generously pays the balance of her salary and fringe benefits, hence she is a part- time employee of both units. The Department of BCBP has also been kind enough to swap resources with the Genetics Program so that we can pay for costs that are not allowable using the restricted state funds that we receive. Finally, BCBP also handles the bookkeeping for the Faculty of Genetics, which includes graduate assistants’ salaries and benefits for first year Genetics graduate students, reimbursements for genetics seminar speakers, and travel costs for prospective graduate students.

The Graduate Student Support funds are utilized for all of the recruiting activities (plane flights, ground transportation, hotels, food, event costs); support of

______22 Genetics Academic Program Review Self-Study Report Texas A&M University visiting seminar speakers and the graduate student run symposium; graduate student stipends to make up any shortfalls in TA support, fellowships or awards; and to provide bridge funding for tuition and fees or stipends - typically for first year students that need to do additional summer rotations, or in rare cases for a later year student that has a financial hardship. There are also several events and activities that are managed by the Genetics Graduate Student Organization (GGSA) that are fully supported by this budget item.

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I. Program Administration The Faculty of Genetics is governed by an Executive Committee, which consists of nine members. Four members serve as college representatives and are elected by the Full Members of the Faculty of Genetics of that academic college. The five other members serve at-large and are elected by all Full Members of the Faculty of Genetics. All terms are for three years. The terms are overlapping, with three members being elected each year. Executive committee members are eligible for re-election. The Executive Committee elects from among its membership a Chair (two-year term) and a Vice-Chair (two-year term). After the first year of leadership by these two members, a Chair–Elect will be chosen. (See the governing bylaws in Appendix) The Chair of the Faculty of Genetics has responsibility for the following: 1) provide leadership for the program and represent the Faculty in College and University meetings; 2) work closely with the Head of the Department of Biochemistry and Biophysics to secure teaching assistantships for students in Genetics; 3) approve degree programs, thesis and dissertation proposals, and theses and dissertations of genetics graduate students; 4) recommend the budget and approve expenditures for teaching functions in Genetics; and 5) ensure that teaching evaluations are completed for Genetics graduate courses. The Vice-Chair replaces the Chair and serves as the chief officer of the Faculty of Genetics in the absence of the chair and assumes the position of the Chair for two years after completion of the first year of service. The Academic Advisor of the Faculty of Genetics, Mrs. Julia Williams, serves as an ad-hoc member of the Executive Committee and is responsible for the preparation and distribution of minutes of the Faculty of Genetics and Executive Committee meetings and maintenance of records of Faculty and Executive Committee activities. The Academic Advisor is also expected to prepare a report for distribution to the Faculty and the Administration near the end of each Spring Semester as well as any other college and university required reports.

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The Executive Committee members implement policy and make decisions to maintain and advance academic quality. In addition, they administer and coordinate the M.S. and Ph.D. graduate programs including admission of prospective graduate students, rotation of new students in faculty laboratories, and advising of all Genetics students. The Executive Committee appoints the chair and other members of Genetics committees.

Most of the work of the Faculty of Genetics is performed by the standing committees (see table below). Committee assignments are made based on indicated preference of all members yearly. Terms are for one year and are renewable. There is at least one member of the Executive Committee on each standing committee and he/she reports to the Executive Committee monthly. The chairs of the standing committees report to the Faculty of Genetics at the annual meetings. In addition, the Executive Committee elects a nominations committee, which is charge to nominate at least two people for each open Executive Committee position. No member of the Executive Committee can serve on the Nominating Committee.

Faculty of Genetics Standing Committees 2013-2014 Recruiting Committee Richard Gomer Membership Committee Paul Straight (Chair) Hubert Amrein (Chair) Clare A. Gill Dorothy Shippen Terje Raudsepp Deborah Bell-Pedersen Raquel Sitcheran Awards Committee Paul Samollow Seminar Committee Marty Dickman Tina Gumienny (Chair) William Murphy Thomas McKnight (Chair) First-Year Advising Committee Paul de Figueiredo (Chair) Graduate Curriculum Paul Hardin Vlad Panin Keith Maggert Clint Magill Hongbin Zhang (Chair)

______

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J. Faculty Qualifications

Two- page NIH-style bio sketches for the Full Members are attached as an Appendix.

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K. Learning Outcomes

The Learning Outcome Reports for both the M.S. and Ph.D. Degree programs are included as an Appendix.

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V. Additional Information

GRADUATE STUDENT COMPENSATION

As we increased our efforts to attract more and higher quality graduate students, it became clear that a significant impediment was the low stipend we had historically offered to incoming graduate students. As a result we have maintained and increased the stipend offered to incoming graduate students that will TA in their first year, with the current stipend set at $24,500. However, the stipend levels and support for subsequent years in the program is determined by the individual P.I. and department and in some cases is significantly lower than the initial stipend, which can cause some issues, especially if not clearly communicated to the student.

Entrance Requirements

Several criteria are taken into consideration in admitting students to the Graduate Program in Genetics. In addition to GRE/GPA scores, essentially all of the students admitted to the program have laboratory research experience. Hence, letters from their research advisors weigh heavily in our decision. We also look for a clear statement of interest in Genetics in the student's narrative. The interviews and student-faculty interactions at the annual Genetics Graduate Student Recruiting Events weigh heavily in the final decision to extend an offer of admission to a prospective student.

Laboratory Rotations

All of the students who enter the Genetics Graduate Program and are supported by a TA Fellowship are required to participate in three, 7 week laboratory rotations. The rotations give students an opportunity to see the breadth of Genetics expertise at TAMU. To provide students with more information about research labs for rotations, we host a Fall Poster Session during the orientation week before classes begin. All graduate students and faculty in the Genetics Program are invited to present a poster to attract rotation students to their laboratories.

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Seminar Program

Due to declining faculty attendance at the formal genetics seminar series and increasing time constraints, the seminar series was cancelled. However, the funding that was available for that series is now used to co-sponsor invited seminar speakers to departmental seminar series when that speaker will be presenting research findings of general or specific interest to the Genetics Faculty and Students. These resources have also been made available to larger symposia with genetics related themes. The Genetics Graduate Student Association have also hosted very well attended symposia once a year in the spring semester; through which they have invited and had nationally and internationally renowned speakers in attendance.

Genetics Graduate Student Association

The Genetics Graduate Student Association (GGSA) is an essential component of the Interdisciplinary Program in Genetics. The GGSA is heavily involved in recruiting and retention efforts for our graduate students and is an important resource for students and faculty alike. A significant portion of the annual budget is made available to the GGSA to support their academic and social programs and every effort is made to support any new initiatives that help to promote and support Genetics graduate students.

The Travel Awards that are given to Genetics Graduate students are in part contingent on the students being active members of the GGSA as an additional incentive to participate in all events. Similarly, the recruitment and orientation events for prospective and new students involve graduate student poster and/or oral presentation competitions that have associated cash awards.

A representative from the GGSA is invited to attend the Genetics Executive Committee meetings as a non-voting participant, during which time they report on GGSA activities, graduate student concerns, and make recommendations for events and funding requests.

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VI. Programmatic Stability Vision

The Interdisciplinary Program in Genetics strives to be recognized as one of the top ten Genetics Graduate Programs at the national level. This goal is in line with The Vision 2020 Plan of Texas A&M University that seeks “to continue the academic evolution of Texas A&M University so that it is generally considered one of the ten best public universities in America by 2020, while maintaining, or even enhancing, the unique features that make Texas A&M University distinctive.”

Strengths

1. Breadth of expertise. The range of expertise represented in the Faculty of Genetics is extensive, covering all critical systems, both eukaryotic and prokaryotic.

2. Faculty dynamism. The members of the Faculty of Genetics are enthusiastic, dynamic, and interact well with each other. This is particularly true of the younger faculty. 3. Excellent infrastructure. The facilities and human and physical infrastructure available to members of the Faculty of Genetics are some of the most comprehensive in the United States.

Weaknesses

1. Lack of interaction and appreciation of common goals with the Heads of the various departments.

2. The volunteer leadership and commitment of the Faculty is inconsistent without support and reward for providing their efforts.

3. Little career support for the involvement of TAMU faculty members in interdisciplinary graduate programs.

4. Minimal financial resources to provide bridging support for genetics graduate students who have lost funding support.

Goals

To expand the impact of the Interdisciplinary Program in Genetics we have identified the following specific goals for the next five years. These include organizational as well as educational goals. ORGANIZATIONAL GOALS. To stabilize and increase the visibility of the Genetics program, we need to: 1. Ensure that the contributions of the faculty to Interdisciplinary Degree Programs are valued and rewarded through Annual Performance Evaluations and during the Tenure and Promotion processes. 2. Have access to a permanent source of funding incentives for Faculty to teach graduate Genetics courses. Continuity of instruction is required to maintain stability in our Core Curriculum. It is essential

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that these mechanisms also assist the Departments that are providing and supporting the Faculty that teach these classes.

EDUCATIONAL AND TRAINING GOALS. To achieve excellence in Genetics education, we aspire to: 1. Provide continuity in our core curriculum by ensuring a long-term vision and availability of appropriate faculty to teach Genetics courses. This goal is inextricably linked to the organizational goals above. 2. Determine an optimal curriculum structure and suite of course offerings that both distinguish Genetics graduate students from other majors, and provide the students with a suitable breadth of Genetics course work to prepare them for cutting edge interdisciplinary research projects.

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VII. Appendices

a) Learning Outcomes for the Ph.D. Degree.

b) Learning Outcomes for the M.S. Degree.

c) 2 Page Faculty CVs.

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Detailed Assessment Report 2014-2015 Genetics, MS As of: 11/10/2014 04:25 AM CENTRAL (Includes those Action Plans with Budget Amounts marked One-Time, Recurring, No Request.)

Mission / Purpose To prepare graduate students for a career in genetics or related fields.

Goals G 1: Goals to fulfill the mission of Genetics M.Sc. Graduate Program To provide comprehensive training in an advanced academic environment, including rigorous classwork, intensive research experience, teaching, developing professional oral and written communication skills, and various service activities.

Student Learning Outcomes/Objectives, with Any Associations and Related Measures, Targets, Findings, and Action Plans SLO 1: Advanced and specialized knowledge of modern genetics Students will demonstrate competency in principles of modern genetics and mastery in a specialized area of genetics related to their chosen career track. Relevant Associations: General Education/Core Curriculum Associations 1 Master the depth of knowledge required for a degree 2 Demonstrate critical thinking 6 Prepare to engage in lifelong learning Strategic Plan Associations Texas A&M University 2 Strengthen our graduate programs. 5 Build on the tradition of the professional education. Related Measures M 1: Degree Plan and Coursework Students will select appropriate coursework to meet the Interdisciplinary program requirements with the guidance of their thesis mentor and advisory committee. Source of Evidence: Academic direct measure of learning - other Target: Students demonstrated competency in their designated field and 80% achieved a GPA of 3.0 or greater at the time of graduation Related Action Plans (by Established cycle, then alpha): For full information, see the Details of Action Plans section of this report. Keep targeted outcomes the same Established in Cycle: 2013-2014 Due to a limited amount of funding, our program generally gives first preference admission into our program to Ph.D. candidates.... M 2: Thesis Proposal 80% of M.Sc. candidates will submit a thesis proposal that conforms to the standards established by the Interdisciplinary Faculty of Genetics and is critically reviewed and approved by their thesis committee, by the end of their 3rd year of study. Source of Evidence: Academic indirect indicator of learning - other Target: 80% of M.Sc. candidates will submit a thesis proposal that conforms to the standards established by the Interdisciplinary Faculty of Genetics and is critically reviewed and approved by their thesis committee, by the end of their 3rd year of study. Related Action Plans (by Established cycle, then alpha): For full information, see the Details of Action Plans section of this report. Keep targeted outcomes the same. Established in Cycle: 2013-2014 Due to a limited amount of funding, our program generally gives first preference admission into our program to Ph.D. candidates.... M 3: Thesis Defense Students will successfully defend thesis, thus demonstrating their proficiency in the broader field of genetics, as well as mastery their area of specialty Source of Evidence: Academic direct measure of learning - other Target: 100% of students will meet or exceed expectations of advanced and specialized knowledge as demonstrated by successful thesis defense upon finishing 4 years of the Program Related Action Plans (by Established cycle, then alpha): For full information, see the Details of Action Plans section of this report. Keep targeted outcomes the same. Established in Cycle: 2013-2014 Due to a limited amount of funding, our program generally gives first preference admission into our program to Ph.D. candidates.... SLO 2: Critical thinking abilities Students will demonstrate the ability to analyze experimental results, to develop and discuss scientific hypothesis and to apply genetic principles to research problems in a specialized area of genetics related to their chosen career track. Relevant Associations: General Education/Core Curriculum Associations 1 Master the depth of knowledge required for a degree 2 Demonstrate critical thinking Strategic Plan Associations Texas A&M University 2 Strengthen our graduate programs. 5 Build on the tradition of the professional education. Related Measures M 2: Thesis Proposal 80% of M.Sc. candidates will submit a thesis proposal that conforms to the standards established by the Interdisciplinary Faculty of Genetics and is critically reviewed and approved by their thesis committee, by the end of their 3rd year of study. Source of Evidence: Academic indirect indicator of learning - other Target: 80% of M.Sc. candidates will submit a thesis proposal that conforms to the standards established by the Interdisciplinary Faculty of Genetics and is critically reviewed and approved by their thesis committee, by the end of their 3rd year of study. M 3: Thesis Defense Students will successfully defend thesis, thus demonstrating their proficiency in the broader field of genetics, as well as mastery their area of specialty Source of Evidence: Academic direct measure of learning - other Target: 100% of students will meet or exceed expectations of demonstrating their critical thinking abilities by successful thesis defense upon finishing 4 years of the Program M 4: Progress Assessment Students' progress towards completing graduate research projects will successfully meet the criteria established by members of their committees Source of Evidence: Senior thesis or culminating major project Target: 70% of students will receive the assessment of their progress as “excellent”, while the progress of 80% of students will be evaluated as at least “satisfactory” by all members of their graduate committees. Related Action Plans (by Established cycle, then alpha): For full information, see the Details of Action Plans section of this report. Keep targeted outcomes the same. Established in Cycle: 2013-2014 Due to a limited amount of funding, our program generally gives first preference admission into our program to Ph.D. candidates.... Keep targeted outcomes the same. Established in Cycle: 2013-2014 Due to a limited amount of funding, our program generally gives first preference admission into our program to Ph.D. candidates.... SLO 3: Professional Competency Students will demonstrate professional competency by mastering their ability to develop and discuss scientific hypotheses, to apply genetic principles to the analyses of experimental results, and to effectively communicate their research to a broader scientific community Relevant Associations: General Education/Core Curriculum Associations 1 Master the depth of knowledge required for a degree 2 Demonstrate critical thinking 3 Communicate effectively 5 Demonstrate social, cultural, and global competence 6 Prepare to engage in lifelong learning 7 Work collaboratively Strategic Plan Associations Texas A&M University 2 Strengthen our graduate programs. 5 Build on the tradition of the professional education. Related Measures M 2: Thesis Proposal 80% of M.Sc. candidates will submit a thesis proposal that conforms to the standards established by the Interdisciplinary Faculty of Genetics and is critically reviewed and approved by their thesis committee, by the end of their 3rd year of study. Source of Evidence: Academic indirect indicator of learning - other Target: 80% of M.Sc. candidates will submit a thesis proposal that conforms to the standards established by the Interdisciplinary Faculty of Genetics and is critically reviewed and approved by their thesis committee, by the end of their 3rd year of study. M 3: Thesis Defense Students will successfully defend thesis, thus demonstrating their proficiency in the broader field of genetics, as well as mastery their area of specialty Source of Evidence: Academic direct measure of learning - other Target: 100% of students will meet or exceed expectations of their professional competency by successful thesis defense upon finishing 4 years of the Program Related Action Plans (by Established cycle, then alpha): For full information, see the Details of Action Plans section of this report. Establish a M.S./Ph.D. decision point Established in Cycle: 2012-2013 The Genetics Executive Committee will determine a decision point timeline whereby students in the Ph.D. program will be assessed... M 5: Research Publications and Presentations Graduate students will demonstrate professional competency by presenting and discussing their original research at student research competitions, scientific meetings and conferences. Students will participate in preparing peer- reviewed research publications Source of Evidence: Academic indirect indicator of learning - other Target: 45% of M.Sc. students will present their original research at a local, regional or national research conference or meeting by the end of their 3rd year. 75% of M.Sc. students will have at least one poster, oral presentation, and a peer-reviewed publication by the time of their thesis defense. Related Action Plans (by Established cycle, then alpha): For full information, see the Details of Action Plans section of this report. Keep targeted outcomes the same. Established in Cycle: 2013-2014 Due to a limited amount of funding, our program generally gives first preference admission into our program to Ph.D. candidates....

Details of Action Plans for This Cycle (by Established cycle, then alpha) Improve data collection and tracking students progress We will improve data collection and tracking students' performance in the program to identify potential problems early and provide timely help. Established in Cycle: 2009-2010 Implementation Status: In-Progress Priority: High Implementation Description: A student worker will be hired to collect and analyze data. Responsible Person/Group: Executive Committees and Graduate Curriculum Additional Resources: A student worker position for data collection and analysis ($8/h, 20h/week) Budget Amount Requested: $8,000.00 (recurring) Database Serach for Peer Review Publications A database search tool will be developed to track our students peer reviewed publications. Established in Cycle: 2011-2012 Implementation Status: Planned Priority: Medium Implementation Description: Different Database search engines will be tested to find one that gives the appropriate results. Projected Completion Date: 07/2013 Responsible Person/Group: GENE executive committee Establish a M.S./Ph.D. decision point The Genetics Executive Committee will determine a decision point timeline whereby students in the Ph.D. program will be assessed for progress and a determination made if they should transfer to the M.S. program to ensure a higher percentage of student completion with 4yrs. This will be assisted by the earlier scheduling of preliminary examinations where possible. Established in Cycle: 2012-2013 Implementation Status: Planned Priority: Low Relationships (Measure | Outcome/Objective): Measure: Thesis Defense | Outcome/Objective: Professional Competency Implementation Description: The language describing this transition and rationale for taking this option will be included in the Genetics Graduation Student Handbook as well as be discussed during new student orientation. Projected Completion Date: 06/2014 Responsible Person/Group: Genetics Executive Committee Additional Resources: None Keep targeted outcomes the same Due to a limited amount of funding, our program generally gives first preference admission into our program to Ph.D. candidates. The M.S. students who we have acquired had already previously found a faculty advisor to support their research or they were initially a Ph.D. candidate who decided to drop down to a M.S. degree. With that in mind, we will keep our M.S. targeted outcomes the same since our M.S. students account for less than 10% of our graduate program. Established in Cycle: 2013-2014 Implementation Status: Planned Priority: High Relationships (Measure | Outcome/Objective): Measure: Degree Plan and Coursework | Outcome/Objective: Advanced and specialized knowledge of modern genetics Keep targeted outcomes the same. Due to a limited amount of funding, our program generally gives first preference admission into our program to Ph.D. candidates. The M.S. students who we have acquired had already previously found a faculty advisor to support their research or they were initially a Ph.D. candidate who decided to drop down to a M.S. degree. With that in mind, we will keep our M.S. targeted outcomes the same since our M.S. students account for less than 10% of our graduate program. Established in Cycle: 2013-2014 Implementation Status: Planned Priority: High Relationships (Measure | Outcome/Objective): Measure: Thesis Proposal | Outcome/Objective: Advanced and specialized knowledge of modern genetics Keep targeted outcomes the same. Due to a limited amount of funding, our program generally gives first preference admission into our program to Ph.D. candidates. The M.S. students who we have acquired had already previously found a faculty advisor to support their research or they were initially a Ph.D. candidate who decided to drop down to a M.S. degree. With that in mind, we will keep our M.S. targeted outcomes the same since our M.S. students account for less than 10% of our graduate program. Established in Cycle: 2013-2014 Implementation Status: Planned Priority: High Relationships (Measure | Outcome/Objective): Measure: Progress Assessment | Outcome/Objective: Critical thinking abilities Keep targeted outcomes the same. Due to a limited amount of funding, our program generally gives first preference admission into our program to Ph.D. candidates. The M.S. students who we have acquired had already previously found a faculty advisor to support their research or they were initially a Ph.D. candidate who decided to drop down to a M.S. degree. With that in mind, we will keep our M.S. targeted outcomes the same since our M.S. students account for less than 10% of our graduate program. Established in Cycle: 2013-2014 Implementation Status: Planned Priority: High Relationships (Measure | Outcome/Objective): Measure: Thesis Defense | Outcome/Objective: Advanced and specialized knowledge of modern genetics Keep targeted outcomes the same. Due to a limited amount of funding, our program generally gives first preference admission into our program to Ph.D. candidates. The M.S. students who we have acquired had already previously found a faculty advisor to support their research or they were initially a Ph.D. candidate who decided to drop down to a M.S. degree. With that in mind, we will keep our M.S. targeted outcomes the same since our M.S. students account for less than 10% of our graduate program. Established in Cycle: 2013-2014 Implementation Status: Planned Priority: High Relationships (Measure | Outcome/Objective): Measure: Progress Assessment | Outcome/Objective: Critical thinking abilities Keep targeted outcomes the same. Due to a limited amount of funding, our program generally gives first preference admission into our program to Ph.D. candidates. The M.S. students who we have acquired had already previously found a faculty advisor to support their research or they were initially a Ph.D. candidate who decided to drop down to a M.S. degree. With that in mind, we will keep our M.S. targeted outcomes the same since our M.S. students account for less than 10% of our graduate program. Established in Cycle: 2013-2014 Implementation Status: Planned Priority: High Relationships (Measure | Outcome/Objective): Measure: Research Publications and Presentations | Outcome/Objective: Professional Competency Non-Thesis M.S. in Genetic Counseling Discussions for improving the value of a non-thesis M.S. in Genetics have focused on preparing students for a career in Genetic Counseling. With the decrease in cost of genome sequencing and typing, an increasing number of people will have access to their genetic data, in many cases with no basis or assistance for understanding the results or implications of this data. Established in Cycle: 2013-2014 Implementation Status: Planned Priority: Medium Implementation Description: Curriculum Committee will discuss and consult with faculty to determine if existing courses are sufficient or if a new course should be added. Projected Completion Date: 08/2015 Responsible Person/Group: Graduate Curriculum Committee

Detailed Assessment Report 2014-2015 Genetics, PhD As of: 11/10/2014 04:25 AM CENTRAL (Includes those Action Plans with Budget Amounts marked One-Time, Recurring, No Request.)

Mission / Purpose To prepare graduate students for a career in genetics or related fields

Goals G 1: Goals to fulfill the mission of the program To provide comprehensive training in an advanced academic environment, including rigorous classwork, intensive research experience, teaching, developing professional oral and written communication skills, and various service activities

Student Learning Outcomes/Objectives, with Any Associations and Related Measures, Targets, Findings, and Action Plans SLO 1: Advanced and specialized knowledge of modern genetics Students will demonstrate competency in principles of modern genetics and mastery in a specialized area of genetics related to their chosen career track. Relevant Associations: General Education/Core Curriculum Associations 1 Master the depth of knowledge required for a degree 6 Prepare to engage in lifelong learning Strategic Plan Associations Texas A&M University 2 Strengthen our graduate programs. 5 Build on the tradition of the professional education. Related Measures M 1: Degree Plan and Coursework Students will select appropriate coursework to meet the Interdisciplinary program requirements with the guidance of their thesis mentor and advisory committee Source of Evidence: Academic direct measure of learning - other Target: 80% of students will achieve a GPA of 3.5 or greater at the time of graduation. M 2: Dissertation Proposal Students will prepare a dissertation proposal demonstrating mastery in their area of expertise Source of Evidence: Academic direct measure of learning - other Target: 90% of Ph.D. candidates will submit a dissertation proposal that conforms to the standards established by the Interdisciplinary Faculty of Genetics and is critically reviewed and approved by their PhD committee, by the end of their 3rd year of study M 3: Preliminary Examination Graduate students will prepare and successfully pass both written and oral parts of preliminary examination, demonstrating in-depth understanding of genetic principles and adequate knowledge of their area of specialty, as well as the ability to critically analyze experimental results and to discuss scientific hypotheses Source of Evidence: Academic direct measure of learning - other Target: 90% of Ph.D. students will pass the preliminary examination administered by their Ph.D. committee within 4 years M 4: Dissertation Defense Students will successfully defend their dissertation, thus demonstrating their proficiency in the broader field of genetics, as well as mastery of their area of specialty Source of Evidence: Senior thesis or culminating major project Target: 90% of students will successfully defend their dissertation within 5 years SLO 2: Critical thinking abilities Students will demonstrate the ability to analyze experimental results, to develop and discuss scientific hypothesis and to apply genetic principles to research problems in a specialized area of genetics related to their chosen career track Relevant Associations: General Education/Core Curriculum Associations 1 Master the depth of knowledge required for a degree 2 Demonstrate critical thinking 3 Communicate effectively 6 Prepare to engage in lifelong learning Strategic Plan Associations Texas A&M University 2 Strengthen our graduate programs. 5 Build on the tradition of the professional education. Related Measures M 2: Dissertation Proposal Students will prepare a dissertation proposal demonstrating mastery in their area of expertise Source of Evidence: Academic direct measure of learning - other Target: 90% of Ph.D. candidates will submit a dissertation proposal that conforms to the standards established by the Interdisciplinary Faculty of Genetics and is critically reviewed and approved by their PhD committee, by the end of their 3rd year of study Related Action Plans (by Established cycle, then alpha): For full information, see the Details of Action Plans section of this report. Improve tracking and reporting of student progress Established in Cycle: 2012-2013 To address the delays in proposal submission and completion of preliminary exams by agreed upon timelines, improved tracking and... M 3: Preliminary Examination Graduate students will prepare and successfully pass both written and oral parts of preliminary examination, demonstrating in-depth understanding of genetic principles and adequate knowledge of their area of specialty, as well as the ability to critically analyze experimental results and to discuss scientific hypotheses Source of Evidence: Academic direct measure of learning - other Target: 90% of Ph.D. students will pass the preliminary examination administered by their Ph.D. committee within 4 years M 4: Dissertation Defense Students will successfully defend their dissertation, thus demonstrating their proficiency in the broader field of genetics, as well as mastery of their area of specialty Source of Evidence: Senior thesis or culminating major project Target: 75% of students will successfully defend their dissertation within 5 years M 5: Progress Assessment Students' progress towards completing graduate research projects will successfully meet the criteria esteblished by members of their PhD committees Source of Evidence: Senior thesis or culminating major project Target: 75% of students will receive the assessment of their progress as “excellent”, while the progress of 90% of students will be evaluated as at least “satisfactory” by all members of their graduate committees. SLO 3: Professional Competency Students will demonstrate professional competency by mastering their ability to develop and discuss scientific hypotheses, to apply genetic principles to the analyses of experimental results, and to effectively communicate their research to a broader scientific community Relevant Associations: General Education/Core Curriculum Associations 1 Master the depth of knowledge required for a degree 2 Demonstrate critical thinking 3 Communicate effectively 6 Prepare to engage in lifelong learning 7 Work collaboratively Strategic Plan Associations Texas A&M University 2 Strengthen our graduate programs. 5 Build on the tradition of the professional education. Related Measures M 2: Dissertation Proposal Students will prepare a dissertation proposal demonstrating mastery in their area of expertise Source of Evidence: Academic direct measure of learning - other Target: 90% of Ph.D. candidates will submit a dissertation proposal that conforms to the standards established by the Interdisciplinary Faculty of Genetics and is critically reviewed and approved by their PhD committee, by the end of their 3rd year of study. M 3: Preliminary Examination Graduate students will prepare and successfully pass both written and oral parts of preliminary examination, demonstrating in-depth understanding of genetic principles and adequate knowledge of their area of specialty, as well as the ability to critically analyze experimental results and to discuss scientific hypotheses Source of Evidence: Academic direct measure of learning - other Target: 90% of Ph.D. students will pass the preliminary examination administered by their Ph.D. committee within 4 years M 4: Dissertation Defense Students will successfully defend their dissertation, thus demonstrating their proficiency in the broader field of genetics, as well as mastery of their area of specialty Source of Evidence: Senior thesis or culminating major project Target: 75% of students will successfully defend their dissertation upon completeing the Program M 6: Research Publications and Presentations Graduate students will demonstrate professional competency by presenting and discussing their original research at student research competitions, scientific meetings and conferences. Students will participate in preparing peer- reviewed research publications Source of Evidence: Academic indirect indicator of learning - other Target: 50% of graduate students will present their original research at a local, regional or national research conference or meeting and will participate in at least one peer-reviewed publication by the end of their 3rd year. 80% of graduate students will have at least one poster or oral presentation at a regional or national research conference and have two peer-reviewed publications by the time of their thesis defense.

Details of Action Plans for This Cycle (by Established cycle, then alpha) Improve data collection and tracking students' progress We will improve data collection and tracking students' performance in the program to identify potential problems early and provide timely help. Established in Cycle: 2009-2010 Implementation Status: In-Progress Priority: High Implementation Description: A student worker will be hired to collect and analyze data. Responsible Person/Group: Executive and Graduate Curriculum Committees Additional Resources: A student worker position for data collection and analysis ($8/h, 20h/week, shared between MS and PhD programs ) Budget Amount Requested: $8,000.00 (recurring) Establish a peer reviewed publication tracking system A database search script will be written to recover peer review publications from our students in each academic year. Established in Cycle: 2011-2012 Implementation Status: Planned Priority: Medium Implementation Description: This will require testing of database search engines to determine the appropriate search parameters. Projected Completion Date: 07/2013 Responsible Person/Group: GENE executive committee Additional Resources: None Improve tracking and reporting of student progress To address the delays in proposal submission and completion of preliminary exams by agreed upon timelines, improved tracking and reporting of student progress is required. A up to date database will be created and reports generated each semester to ensure adequate student progress. The Genetics Chair will follow up with the thesis committee and student in cases where the timelines are not being met. Established in Cycle: 2012-2013 Implementation Status: Planned Priority: High Relationships (Measure | Outcome/Objective): Measure: Dissertation Proposal | Outcome/Objective: Critical thinking abilities Implementation Description: Student Progress database created and reporting structure designed to easily flag students who are falling behind the desired timelines. Projected Completion Date: 06/2014 Responsible Person/Group: Administrative Assistant and Genetics Chair Additional Resources: None Improve data collection and tracking students' progress Continue to improve data collection and tracking students' progress to improve the program. Established in Cycle: 2013-2014 Implementation Status: Planned Priority: High Projected Completion Date: 09/2014 Responsible Person/Group: Program Executive and graduate curriculum committees Texas A&M University

Detailed Assessment Report 2014-2015 Genetics, MS As of: 11/10/2014 04:28 AM CENTRAL (Includes those Action Plans with Budget Amounts marked One-Time, Recurring, No Request.)

Mission / Purpose To prepare graduate students for a career in genetics or related fields.

Detailed Assessment Report 2014-2015 Genetics, PhD As of: 11/10/2014 04:28 AM CENTRAL (Includes those Action Plans with Budget Amounts marked One-Time, Recurring, No Request.)

Mission / Purpose To prepare graduate students for a career in genetics or related fields

Student Learning Outcomes/Objectives, with Any Associations and Related Measures, Targets, Findings, and Action Plans SLO 1: Advanced and specialized knowledge of modern genetics Students will demonstrate competency in principles of modern genetics and mastery in a specialized area of genetics related to their chosen career track. Relevant Associations: General Education/Core Curriculum Associations 1 Master the depth of knowledge required for a degree 6 Prepare to engage in lifelong learning Strategic Plan Associations Texas A&M University 2 Strengthen our graduate programs. 5 Build on the tradition of the professional education. Related Measures M 1: Degree Plan and Coursework Students will select appropriate coursework to meet the Interdisciplinary program requirements with the guidance of their thesis mentor and advisory committee Source of Evidence: Academic direct measure of learning - other Target: 80% of students will achieve a GPA of 3.5 or greater at the time of graduation. M 2: Dissertation Proposal Students will prepare a dissertation proposal demonstrating mastery in their area of expertise Source of Evidence: Academic direct measure of learning - other Target: 90% of Ph.D. candidates will submit a dissertation proposal that conforms to the standards established by the Interdisciplinary Faculty of Genetics and is critically reviewed and approved by their PhD committee, by the end of their 3rd year of study M 3: Preliminary Examination Graduate students will prepare and successfully pass both written and oral parts of preliminary examination, demonstrating in-depth understanding of genetic principles and adequate knowledge of their area of specialty, as well as the ability to critically analyze experimental results and to discuss scientific hypotheses Source of Evidence: Academic direct measure of learning - other Target: 90% of Ph.D. students will pass the preliminary examination administered by their Ph.D. committee within 4 years M 4: Dissertation Defense Students will successfully defend their dissertation, thus demonstrating their proficiency in the broader field of genetics, as well as mastery of their area of specialty Source of Evidence: Senior thesis or culminating major project Target: 90% of students will successfully defend their dissertation within 5 years SLO 2: Critical thinking abilities Students will demonstrate the ability to analyze experimental results, to develop and discuss scientific hypothesis and to apply genetic principles to research problems in a specialized area of genetics related to their chosen career track Relevant Associations: General Education/Core Curriculum Associations 1 Master the depth of knowledge required for a degree 2 Demonstrate critical thinking 3 Communicate effectively 6 Prepare to engage in lifelong learning Strategic Plan Associations Texas A&M University 2 Strengthen our graduate programs. 5 Build on the tradition of the professional education. Related Measures M 2: Dissertation Proposal Students will prepare a dissertation proposal demonstrating mastery in their area of expertise Source of Evidence: Academic direct measure of learning - other Target: 90% of Ph.D. candidates will submit a dissertation proposal that conforms to the standards established by the Interdisciplinary Faculty of Genetics and is critically reviewed and approved by their PhD committee, by the end of their 3rd year of study Related Action Plans (by Established cycle, then alpha): For full information, see the Details of Action Plans section of this report. Improve tracking and reporting of student progress Established in Cycle: 2012-2013 To address the delays in proposal submission and completion of preliminary exams by agreed upon timelines, improved tracking and... M 3: Preliminary Examination Graduate students will prepare and successfully pass both written and oral parts of preliminary examination, demonstrating in-depth understanding of genetic principles and adequate knowledge of their area of specialty, as well as the ability to critically analyze experimental results and to discuss scientific hypotheses Source of Evidence: Academic direct measure of learning - other Target: 90% of Ph.D. students will pass the preliminary examination administered by their Ph.D. committee within 4 years M 4: Dissertation Defense Students will successfully defend their dissertation, thus demonstrating their proficiency in the broader field of genetics, as well as mastery of their area of specialty Source of Evidence: Senior thesis or culminating major project Target: 75% of students will successfully defend their dissertation within 5 years M 5: Progress Assessment Students' progress towards completing graduate research projects will successfully meet the criteria esteblished by members of their PhD committees Source of Evidence: Senior thesis or culminating major project Target: 75% of students will receive the assessment of their progress as “excellent”, while the progress of 90% of students will be evaluated as at least “satisfactory” by all members of their graduate committees. SLO 3: Professional Competency Students will demonstrate professional competency by mastering their ability to develop and discuss scientific hypotheses, to apply genetic principles to the analyses of experimental results, and to effectively communicate their research to a broader scientific community Relevant Associations: General Education/Core Curriculum Associations 1 Master the depth of knowledge required for a degree 2 Demonstrate critical thinking 3 Communicate effectively 6 Prepare to engage in lifelong learning 7 Work collaboratively Strategic Plan Associations Texas A&M University 2 Strengthen our graduate programs. 5 Build on the tradition of the professional education. Related Measures M 2: Dissertation Proposal Students will prepare a dissertation proposal demonstrating mastery in their area of expertise Source of Evidence: Academic direct measure of learning - other Target: 90% of Ph.D. candidates will submit a dissertation proposal that conforms to the standards established by the Interdisciplinary Faculty of Genetics and is critically reviewed and approved by their PhD committee, by the end of their 3rd year of study. M 3: Preliminary Examination Graduate students will prepare and successfully pass both written and oral parts of preliminary examination, demonstrating in-depth understanding of genetic principles and adequate knowledge of their area of specialty, as well as the ability to critically analyze experimental results and to discuss scientific hypotheses Source of Evidence: Academic direct measure of learning - other Target: 90% of Ph.D. students will pass the preliminary examination administered by their Ph.D. committee within 4 years M 4: Dissertation Defense Students will successfully defend their dissertation, thus demonstrating their proficiency in the broader field of genetics, as well as mastery of their area of specialty Source of Evidence: Senior thesis or culminating major project Target: 75% of students will successfully defend their dissertation upon completeing the Program M 6: Research Publications and Presentations Graduate students will demonstrate professional competency by presenting and discussing their original research at student research competitions, scientific meetings and conferences. Students will participate in preparing peer- reviewed research publications Source of Evidence: Academic indirect indicator of learning - other Target: 50% of graduate students will present their original research at a local, regional or national research conference or meeting and will participate in at least one peer-reviewed publication by the end of their 3rd year. 80% of graduate students will have at least one poster or oral presentation at a regional or national research conference and have two peer-reviewed publications by the time of their thesis defense.

Appendix C Faculty of Genetics Bylaws

Faculty of Genetics Bylaws July 2009

Article I: Description

The Faculty of Genetics of Texas A&M University is an interdisciplinary faculty composed of members from various academic departments in several colleges and the Texas A&M Health Science Center.

Article II: Purpose and Intent

The principal function of the Faculty of Genetics is the administration of the graduate programs leading to the Master of Science and Doctor of Philosophy degrees in Genetics, in conformance with the rules of the Office of Graduate Studies of Texas A&M University – College Station. The organization also serves to promote and facilitate communication among geneticists and to foster the development of genetics at Texas A&M University. The Faculty of Genetics arranges for the periodic assembly of geneticists and provides a forum for them and for others with interests in genetics. The organizational and operational characteristics of the Faculty of Genetics are intended to be broad enough to permit consideration of all academic aspects of genetics and all other matters affecting the position and progress of the discipline at Texas A&M University. The Faculty of Genetics participates in the direction and teaching of the undergraduate program in genetics.

Article III: Membership

1. Admission to membership on the Faculty of Genetics shall be determined by the Executive Committee after nomination by the Head of the faculty member's administrative department and the receipt of a positive recommendation by the Committee on Membership of the Faculty of Genetics.

2. Only full members of the Graduate Faculty of Texas A&M University – College Station with significant academic or service activities in genetics are eligible to be Members of the Faculty of Genetics. Active involvement in academic, service, and recruiting activities of the Faculty of Genetics as described below is required to maintain membership.

3. The activities of each member of the Faculty will be reviewed on a rotating, three-year cycle in order to maintain active status. Each faculty member is expected to support and help to sustain the academic genetics community on campus as indicated below. To remain in good standing, each faculty member must satisfy at least one of the criteria from EACH of the Academic, Service and Recruiting Activities during the three-year review cycle.

A. Academic Activities

1) Teach a lecture, seminar, or laboratory genetics course, or other related courses with a clearly defined and substantive genetics component;

2) Serve as the chair or member of a graduate committee of a genetics student or students;

______C-2 Genetics Academic Program Review Appendix C—Faculty of Genetics Bylaws

3) Function as the sponsor for GENE 285/485 or GENE 685 students involved in specialized studies, research in genetics, or performing a genetics rotation.

B. Service Activities

1) Hosting of a Faculty of Genetics mini-symposium or seminar speaker;

2) Participation in Genetics Faculty standing or ad hoc committees or serving on a College/University committee as a Genetics Faculty representative.

3) PI for a Grant/Award that supports Genetics Program Activities, for example a training grant, conference grant, REU grant.

4) Attendance at the Genetics Faculty Annual Meeting

C. Recruiting Activities

1) Participate in at least one of the recruiting weekend events such as the Welcome Dinner, Interviews, Lunch Function, Research Symposia, Social Event.

2) Participate in independent recruiting activities such as handing out Genetics Program recruiting materials to potential student recruits at conferences or seminar presentations at other academic institutions.

Members of the Faculty of Genetics are eligible to:

a) chair the advisory committee of a Genetics graduate student b) teach graduate GENE courses c) serve on the TAMU Faculty of Genetics Executive Committee d) vote on matters requiring a vote of the Faculty of Genetics e) serve on the Faculty of Genetics Membership and Nominating Committees f) chair standing or ad hoc committees of the Faculty of Genetics

Article IV: Election to the Executive Committee

1. A nominating committee composed of three Members shall be elected by the Executive Committee prior to the annual meeting. No person who is a member of the Executive Committee may be a member of this committee.

2. The Nominating Committee shall recommend at least two candidates for each vacant position on the Executive Committee. Further nominations may be made from the floor at the annual meeting of the Faculty of Genetics.

3. Elections shall be conducted by email ballot to be distributed to Members after the annual Faculty of Genetics meeting. Each Member shall vote for no more candidates than the ______C-3 Genetics Academic Program Review Appendix C—Faculty of Genetics Bylaws

number of positions to be filled. Those persons receiving the most votes will be declared elected. Election results shall be emailed to the members promptly. Elected members shall assume their duties on June 1.

4. Should the terms of the Chair or the Chair-elect be scheduled to end during their administrative cycle, those terms will be automatically extended to the end of their administrative term as Chair. At that time, their position will be filled so as to re-establish the normal re-election cycle.

Article V: Executive Committee

1. The Executive Committee shall consist of nine Members of the Faculty of Genetics.

2. The Executive Committee shall include one designated representative from each of the three academic colleges and the TAM HSC that participate in the Faculty of Genetics and five additional members at large. The designated representatives shall be elected by the Members of the Faculty of Genetics of each given academic college and the TAM HSC. The at large members of the Executive Committee shall be elected at-large by all of the Members of the Faculty of Genetics.

3. Members of the Executive Committee shall serve for three years, and; three members will be elected each year. Their service on the Executive Committee will begin June 1 of the year elected.

4. In June, after the annual election of new members, the Executive Committee shall elect from among its membership a Chair and a Vice-Chair. The chair and the vice-chair shall be elected for two year terms that begin June 1 and continue to May 31. After the first year of the administrative cycle, a chair-elect will be identified to serve for one year in preparation to assuming the Chair. (The Chair-elect may be any member of the Executive Committee excepting the Chair. The Vice-Chair and the Chair-elect may be the same individual or different persons.)

5. The Executive Committee shall fill any vacancies that may occur in its membership or offices between the annual elections by a majority vote of the Executive Committee.

6. The President of the GGSA will be invited to attend meetings of the Executive Committee as a non-voting participant. He/she will be excused from the meeting during any discussions of a sensitive matter concerning personnel.

Article VI: Functions of the Executive Committee

1. The principal functions of the Executive Committee shall be to:

______C-4 Genetics Academic Program Review Appendix C—Faculty of Genetics Bylaws

a. Determine and implement policy for the good of the faculty members and students in the Faculty of Genetics and represent the interests of the Faculty generally to various University authorities and leaders of other agencies.

b. Establish the Faculty of Genetics Standing Committees and ad hoc committees as needed.

c. Develop the budget for graduate-level functions in Genetics.

d. Conduct all additional business deemed necessary for the proper functioning of the Faculty.

2. Technical administrative procedures pertaining to graduate degree programs shall be handled through the appropriate channels of the student's home department (the administrative ad loc department). Other matters shall be administered by the Executive Committee.

Article VII: Functions of the Officers

1. Chair

The chair is the chief officer and representative of the Executive Committee and the Faculty of Genetics. The chair's primary responsibility is the execution of those administrative functions that are delegated to the Faculty of Genetics. The chair shall:

a. Chair the Executive Committee meetings of the Faculty of Genetics.

b. Provide leadership in short- and long-term planning for the program and represent the faculty group in College and University meetings, as appropriate.

d. Work closely with Heads of Departments to secure support for students in the discipline.

c. Approve degree programs, thesis and dissertation proposals, and theses and dissertations of genetics graduate students for the Genetics Faculty.

d. Recommend the budget and approve expenditures for Genetics Programs.

e. Appoint, with approval of the Executive Committee, the chair and other members of standing committees and special committees.

f. Direct graduate student advising.

2. Vice-Chair: The vice-chair shall serve as chief officer of the Faculty of Genetics in the absence of the chair or when designated by the chair.

3. Chair-elect: The Chair-elect shall serve (in “apprenticeship”) for assuming the function of the Chair.

Article VIII: Meetings ______C-5 Genetics Academic Program Review Appendix C—Faculty of Genetics Bylaws

1. The annual meeting of the Faculty of Genetics shall be held during the first two weeks of the month of May each year.

2. Special meetings of the Faculty of Genetics may be held at the call of the chair or by written application to the Executive Committee by five Members of the Faculty of Genetics.

3. A regular meeting of the Executive Committee shall be held each month in the Fall and Spring semesters. Other meetings of the Executive Committee may be held as frequently and for such purposes as are deemed desirable by the Executive Committee.

4. The minutes of each Faculty and Executive Committee meeting shall be distributed to all members of the Faculty of Genetics by email within 10 days after approval by the Executive Committee.

5. At Executive Committee and Faculty of Genetics meetings, Robert's Rules of Order shall be followed in matters of parliamentary procedure.

6. A quorum for Executive Committee meetings shall consist of five members of the Committee. Twenty-five percent of the Members shall constitute a quorum for meetings of the Faculty of Genetics.

7. Voting can also take place outside of the Faculty of Genetics Meetings by email ballots which can be returned by email, fax, campus mail, or in person, within 7 days of receipt of such ballots.

8. Items requiring a faculty vote will pass by a simple majority vote of responding faculty (25% minimum must respond to satisfy the quorum requirement).

9. Changes to the bylaws will pass by a 2/3 majority vote of responding faculty (25% minimum must respond to satisfy the quorum requirement).

Article IX: Standing Committees The members of each standing committee shall be appointed in June of each year and shall serve from July 1 through June 30 of the following year.

1. Committee on Membership

The Committee on Membership shall consist of three Members. It shall screen applications for membership in the Faculty of Genetics and make a recommendation to the Executive Committee as to the acceptability of each applicant. Membership shall be conferred by approval of the Executive Committee. The Committee on Membership shall also review the active status of all members on a three-year basis.

2. Graduate Recruiting Committee

The Graduate Recruiting Committee shall consist of three or more members and will include a non-voting student liaison as nominated by the GGSA. It shall serve as an advisory committee to the Executive Committee by screening and evaluating the applications of ______C-6 Genetics Academic Program Review Appendix C—Faculty of Genetics Bylaws

prospective students for acceptance into the Genetics program and as candidates for Genetics teaching assistantships. The committee shall facilitate the processing of files of acceptable candidates through Faculty review and Office of Graduate Studies notification.

3. The First Year Program Committee

The First Year Program Committee shall consist of three or more members. It shall be responsible for advising and counseling of new students in selecting their academic course work, managing their first year experiences overall, and selecting a research laboratory which will assume their mentoring at the end of the Spring Semester.

4. Graduate Curriculum Committee

The Graduate Curriculum Committee shall consist of three members. The committee will also include an additional student representative as nominated by the GGSA. It shall have responsibility for coordination of the graduate curriculum in genetics. Requests for new courses and course cross-listings will be reviewed by this committee who will then make recommendations to the Executive Committee for approval.

5. Faculty and Student Awards Committee

The Faculty and Student Awards Committee shall consist of 3 members. The committee will also include an additional student representative as nominated by the GGSA. It shall be responsible for the nomination of faculty and students for local and national awards, as well as the judging of any local student competitions and awards.

6. Committee on Seminars

The Committee on Seminars shall consist of three members. It shall coordinate speaker invitations and arrangements for the presentation of seminars and symposia on genetics topics.

Article X: Amendments

Proposed amendments to the Bylaws shall be submitted to the Members of the Faculty of Genetics for approval or disapproval following either (1) approval of a motion to do so by majority vote of the Executive Committee or (2) written petition to the Executive Committee by a minimum of five Members of the Faculty of Genetics. Approval by two-thirds or more of the responding Members voting in an email ballot is required to adopt amendments (25% minimum must respond to satisfy the quorum requirement).

Adopted: May 27 1982 Revised: October 1984 March 1985 August 1986 December 1989 April 1994 September 1998 May 2006 July 2009 ______C-7 Genetics Academic Program Review Appendix C—Faculty of Genetics Bylaws

Program Director/Principal Investigator: ALLRED, Clinton D.

BIOGRAPHICAL SKETCH Provide the following information for the Senior/key personnel and other significant contributors in the order listed on Form Page 2. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Allred, Clinton D. Associate Professor eRA COMMONS USER NAME (credential, e.g., agency login) Associate Department Head CLINTON.ALLRED EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) University of Georgia, Athens B.S.A. 1993-1997 Animal Science University of Illinois, Urbana-Champaign Ph.D. 1997-2002 Nutritional Sciences University of Kentucky College of Medicine, Lexington Postdoctoral 2002-2006 Molecular Endocrinology

A. Personal Statement Dr. Allred is an expert in the area of understanding the role that xenoestrogens play in the development and progression of epithelial derived cancers. He has published ten manuscripts in this area which have significantly impacted the understanding of the physiological role of these compounds. Many of these studies were conducted in vivo utilizing models of tumor development and progression and with emphasis paid to ensure that exposure levels are relevant to those that an individual may be exposed to in their diet. As such, Dr. Allred and his laboratory are well suited to conduct studies in which xenoestrogens are the primary intervention. In addition, Dr. Allred has numerous publications exploring how environmental compounds utilize nuclear receptors to elicit their response. In completion of these studies Dr. Allred developed the molecular techniques to investigate upstream mediators and downstream targets of nuclear receptor function. These approaches will be crucial to completion of the proposed studies. Finally, much of Dr. Allred’s research to date has focused on how endogenous hormones (estradiol) can influence tumor development in the breast and colon. Dr. Allred’s research has been some of the first of its kind in that it demonstrates novel physiological actions of estrogen on non-malignant colonocytes and how they lead to suppressed formation of pre-malignant lesions in the colon. More central to this proposal is that Dr. Allred’s most recent work has been in evaluating how estrogen either suppresses or exacerbates colonic inflammation dependent on the nature of the inflammatory event. Given his research record in xenoestrogens, nuclear receptor signaling, and estrogen action in the colon, Dr. Allred is uniquely suited to complete these studies.

B. Positions and Honors: Positions and Employment 2002-2004 Postdoctoral Fellow, Dept. of Molecular and Biomedical Pharmacology College of Medicine, Univ. of Kentucky. Appointed to a National Institutes of Health Training Grant Fellowship. 2004-2006 Postdoctoral Scholar, Dept. of Molecular and Biomedical Pharmacology, College of Med., Univ. of Kentucky. Awarded and serve as PI on Dept. of Defense 2003 Breast Cancer Research Program Postdoctoral Award. 2006-Present Assistant Professor, Department of Nutrition and Food Science Texas A & M University 2006-Present Intercollegiate Faculty of Nutrition 2006-Present Intercollegiate Faculty of Toxicology 2006-Present Affiliate Member, Institute for Obesity Research and Program Evaluation 2007-Present Intercollegiate Faculty of Genetics 2008-Present Veterinary Integrative Biosciences Adjunct Appointment 2012-Present Associate Professor, Department of Nutrition and Food Science Texas A&M University 2012-Present Associate Department Head of Academic Programs, Dept. of Nutrition & Food Science

PHS 398/2590 (Rev. 06/09) Page Biographical Sketch Format Page Program Director/Principal Investigator: ALLRED, Clinton D. C. Selected peer-reviewed publications: Wang, V.C., Sable, H.J.K., Ju, Y.H., Allred, C.D., Helferich, W.G., Korol, D.L., and Schantz, S.L. Effects of Chronic Estradiol Treatment on Delayed Spatial Alternation and Differential Reinforcement of Low Rates of Responding. Behavioral Neuroscience, 122(4):794-804. 2008. PMCID: None Allred, K.F., Yackley, K., Vanamala, J., and Allred, C.D. Trigonelline is a Novel Phytoestrogen in Coffee Beans. Journal of Nutrition.139(10):1833-1838. 2009. PMCID: None Venditto, V.J., Allred, K., Allred, C.D., and Simanek, E.E. Intercepting the synthesis of triazine dendrimers with nucleophilic pharmacophores: a general strategy toward drug delivery vehicles. Chemical Communication, 5541-5542. 2009. PMCID: None Weige, C.C., Allred, K.F., and Allred, C.D. Estradiol alters cell growth in nonmalignant colonocytes and reduces the formation of preneoplastic lesions in the colon. Cancer Research, 69(23): 9118-9124. 2009. PMCID: None Armstrong, C., Allred, K.F., and Allred, C. D. Dietary fish oil reduces DNA adduct formation while estradiol upregulates apoptosis in response to DNA damage in the rat colon. Digestive Diseases and Sciences, Sep; 56(9):2585-94, 2011. PMCID: None Weige, C.C., Allred, K.F., Armstrong, C.M., and Allred, C.D. P53 mediates estradiol induced activation of apoptosis and DNA repair in non-malignant colonocytes. Journal of Steroid Biochemistry and Molecular Biology, Feb; 128(3-5):113-20, 2012. PMCID: None Yang, L., Allred, K.F., Geera, B., Allred, C.D., and Awika, J.M. Sorghum phenolics demonstrate estrogenic action and induce apoptosis in nonmalignant colonocytes. Nutrition and Cancer, Apr; 64(3):419-27, 2012. PMCID: None Armstrong, C.M., Billimek, A.R., Allred K.F., Sturino, J.M., Weeks, B.R., and Allred, C.D. A Novel Shift in Estrogen Receptor Expression Occurs as Estradiol Suppresses Inflammation-Associated Colon Tumor Formation. Endocrine-Related Cancer ,Jun 27;20(4):515-25, 2013. Menon, R., Watson, S.E., Thomas, L.N., Allred, C.D., Dabney, A., Azcarate-Peril, M.A., and Sturino, J.M. Diet complexity and estrogen receptor β status affect the composition of the murine intestinal microbiota. Applied Environmental Microbiology. Sep;79(18):5763-73, 2013. Billimek, A. Weige, C., Sturino, J., Dabney, A., and Allred, C.D. Estradiol and genistein alter cellular physiology in non-malignant colonocytes. Submitted for publication in The American Journal of Physiology-Gastrointestinal and Liver Physiology.

D. Recent Research Support Active Funding American Cancer Society (Allred) 7/1/11 – 6/30/15 1 cal. month Research Scholar Grant in Basic Research $718,052 Role: Principal Investigator Title: Effects of Estrogens on Sporadic and Inflammation-associated Colon Cancer. Specific Aims: To evaluate the ability of estradiol and diet-derived phytoestrogens to suppress intestinal inflammation and subsequent tumor formation. No scientific or budgetary overlap with the present proposal.

1R25 CA90301 (Carroll) 7/1/11-6/30/16 0.3 cal. month NIH/NCI $499,918/y Role: Co-Investigator Title: Nutrition, Biostatistics, and Bioinformatics Specific Aims: Our goal is to train statistically oriented individuals to function as independent researchers in a multidisciplinary environment focusing on Nutrition and cancer. To achieve this goal we have assembled a team of researchers specializing in Statistics/Biostatistics, Bioinformatics and the biology of Nutrition and cancer. No scientific or budgetary overlap with the present proposal.

National Institutes of Health (Allred) 9/1/12-8/31/15 0.8 cal. month NIH/R21 $394,545 Role: Co-PI Title: The effects of endogenous and dietary estrogens on colonic stem cells

PHS 398/2590 (Rev. 06/09) Page Continuation Format Page Principal Investigator AMREIN, Hubert

BIOGRAPHICAL SKETCH Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Amrein, Hubert Professor & Associate Chair eRA COMMONS USER NAME

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of Zürich, Switzerland B.Sc. 1977-1982 Genetics & Mol. Biology University of Zürich, Switzerland M.Sc. 1983 Zoology University of Zürich, Switzerland Ph.D 1988 Zoology

A. Positions and Honors. Positions and Employment 2011-present Texas A&M University Health Science Center, College Station, TX Associate Department Chair, Molecular and Cellular Medicine, College of Medicine

2009-present Texas A&M University Health Science Center, College Station, TX Professor of Department of Molecular and Cellular Medicine, College of Medicine

2005-2009 Duke University Medical Center, Durham, NC Associate Professor of Molecular Genetics and Microbiology

1998 - 2005 Duke University Medical Center, Durham, NC Assistant Professor of Molecular Genetics and Microbiology

Fellowships and Awards 1993 – 1995 Associate, Howard Hughes Medical Institute Laboratory of Dr. R. Axel, Columbia University, New York, NY

1991 – 1993 Senior Fellow, Swiss National Science Foundation Laboratory of Dr. R. Axel, Columbia University, New York, NY

1989 – 1991 Long Term Fellow, European Molecular Biology Organization Laboratory of Dr. T. Maniatis, Harvard University, Cambridge, MA

1984 Short Term Fellow, European Molecular Biology Organization Laboratory of Dr. V. Pirrotta, EMBL Heidelberg, Germany

B. Selected peer-reviewed publications (in chronological order).

(SINCE 1995, out of 38 total):

Fujii, S., Krishnan, P., Hardin, P. and Amrein, H. (2007): Nocturnal male sex drive in Drosophila. Current Biology 17, 244-251. PMID: 17276917 25) Ebbs, M., and Amrein, H. (2007): Taste and Pheromone Perception in the fruitfly Drosophila melanogaster. Pfluger’s Archive – European Journal of Physiology 454, 735-747. PMID:

PHS 398/2590 (Rev. 09/04) Page 1 Biographical Sketch Format Page Principal Investigator AMREIN, Hubert 17473934

Slone, J., Daniels, J. and Amrein. H. (2007): Sugar Receptors in Drosophila. Current Biology 17, 1809-1816. PMID: 17919910

Thorne, N. and Amrein, H. (2008): Atypical Expression of Drosophila gustatory receptor genes in sensory and central neurons. Journal of Comparative Neurology 506, 548-568. PMID: 18067151

Fujii, S. Toyoma, A., and Amrein H. (2008): male-specific and circadian regulated fatty acid omega-hydroxylase, SXE1, is necessary for efficient male mating in Drosophila melanogaster. Genetics 180, 179-190. PMID: 18716335

Miyamoto, T., and Amrein H. (2008): Courtship Suppression by a Drosophila pheromone receptor. Nature Neuroscience 11 (8), 874-876. PMID: 18641642

Fujii, S. and Amrein, H. (2010) Ventral lateral and DN1 clock neurons mediate distinct properties of male sex drive rhythm in Drosophila. PNAS 107 (21), 10590-105959. PMID: 20498055

Wang, L., Han, X., Mehren, J., Billeter, J.C., Miyamoto, T., Amrein, H., Levine, J.D. and Anderson, D.J. (2011) Hierarchical chemosensory regulation of male-male social interactions in Drosophila. Nature Neuroscience 14 (6), 757-762. PMID: 21516101

Miyamoto, T., Slone J., Song, X. and Amrein, H. (2012) A fructose receptor functions as a nutrient sensor in the Drosophila brain. Cell 151 (5), 1113-1125: PMID: 23178127

Miyamoto T., Chen, Y., Slone J. and Amrein, H. (2013) Identification of a Drosophila Glucose Receptor Using Ca2+ Imaging of Single Chemosensory Neurons. PLoS ONE 8 (2), e56304.

Miyamoto, T., Wright, G., and Amrein, H. (2013). Nutrient Sensors. Current Biology (in press)

Mishra, D., Miyamoto, T., Rezenom, Y.H., Broussard, A., Yavuz, A., Slone, J., Russell D.H. and Amrein, H. (2013) The molecular basis of sugar sensing in Drosophila larvae Current Biology (under revision).

Miyamoto T, and Amrein, H. (2014) Diverse roles for Gr43a in taste perception and nutrient sensing in Drosophila melanogaster Fly 8 (1), 19-25, PMID: 24406333

Chen, Y. and Amrein, H. (2014) Enhancing Perception of Contaminated Food through Acidmediated Modulation of Taste Neuron Responses. Current Biology 24 (17),

Fujii, S., Yavuz, A., Slone J., Jagge C., Song, X., and Amrein, H. (submitted). Drosophila Sugar Receptors: How Flies Perceive Sweet Taste, Revisited. Current Biology

C. Research Support Active: 2014 – 2019 The Regulation of Feeding Behavior by Brain-based Nutrient Sensors NIH-R01DC0113967-01 (PI H. Amrein) Total award sum: $ 1,250,000 (direct costs)

2003 – 2014 Taste Receptor Genes and Sensory Coding NIH-1RO1GMDC05606-01 (PI H. Amrein) Total award sum: $1,250,000 (direct costs) PHS 398/2590 (Rev. 09/04) Page 2 Continuation Format Page Program Director/Principal Investigator:ANDREWS-Polymenis, Helene BIOGRAPHICAL SKETCH Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2. Follow this format for each person. DO NOT EXCEED FOUR PAGES. NAME POSITION TITLE Helene Andrews-Polymenis Associate Professor eRA COMMONS USER NAME ANDREWSH EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing,INSTITUTION and include AND LOCATIONpostdoctoral training.)DEGREE YEAR(s) FIELD OF STUDY Brown University A.B. 1989 Biology Tufts University Ph.D. 1999 Molecular Biology and Microbiology Texas A&M University D.V.M. 2001 Veterinary Medicine A. Personal Statement I have been working in bacterial pathogenesis for 18 years, using bacterial genetics to identify virulence factors and factors important for microbial persistence in cell culture, as well as in model and natural hosts. As a graduate student, I used forward genetic analysis to identify components of the Dot/Icm secretion system in Legionella pneumophila, and participated in the characterization of this system as a type four secretion system (T4SS). This system is essential for intracellular growth and has subsequently been shown to have >150 secreted effectors. As a postdoctoral fellow and junior faculty member I studied a limited set of mutants in Salmonella Typhimurium to identify genes necessary for O-antigen glucosylation, a process that we determined is necessary for persistence of Typhimurium in the intestine of mice and chicks (17). Currently, members of my laboratory are building large-scale targeted deletion libraries for forward genetics and systems biology in Salmonella (1,13), screening these libraries in animal models (mice, chicks, and calves) to identify genes needed for colonization during infection (2,4 and unpublished data), and performing molecular characterization of newly identified novel genes needed during infection (3, 4, 6, 13). We have recently become interested in the functions of a multi-drug efflux systems encoded by macAB that is needed to withstand oxidative stress (3), and a msDNA encoding retron called ST-85 that are critical during infection (4). B. Positions and Honors 2001-2004 Post-Doctoral Research Associate, Texas A&M University HSC (TAMU-HSC) 2004- 2005 Assistant Professor (non-TT), Microbial & Molecular Pathogenesis, TAMU-HSC 2005- 2010 Assistant Professor (TT), Microbial & Molecular Pathogenesis, Texas A&M University HSC 2010-present Associate Professor (T), Microbial Pathogenesis and Immunology, Texas A&M University 2010 Texas A&M Health Science Center Junior Faculty Research Award 2010-present Minireviews Editor, Infection and Immunity C. Selected Publications (of 40 total) 1) Porwollik, S., Santiviago, C.A., Cheng, P. Long, F., Desai, P., Fredlund, J., Srikumar, S., Chu, W., Chen, X., Canals, R., Reynolds, M.M., Bogomolnaya, L., Shields, C. Cui, P., Guo, J., Endicott-Yazdani, T., Yang, H.J., Maple, A., Ragoza, Y., Blondel, C.J., Valenquela, C., Santiviago, C.A., and H. Andrews-Polymenis*, and M. McClelland* (2014) Defined single-gene and multi-gene mutant collections in Salmonella enterica sv. Typhimurium. PLOS One, in press. *Co-corresponding authors 2) Pezoa, D., Blondel, C.J., Silva, C.A., Yang, H.J., Andrews-Polymenis, H.L., Santiviago, C.A., and I. Contreras. (2014) Only one of the two Type VI secretion systems encoded in the Salmonella enterica serotype Dublin genome is involved in colonization of the avian and murine host. Veterinary Research Journal. 45:2. doi:10.1186/1297-9716-45-22) 3)Bogomolnaya, L.M., Andrews, K.D., Talamantes, M., Maple, A., Ragoza, Y. and H. Andrews-Polymenis (2013) An ABC-type efflux pump MacAB is involved in protection of Salmonella enterica serot. Typhimurium against oxidative stress. mBio vol. 4 no. 6 e00630-13. doi: 10.1128/mBio.00630-13. 4) Elfenbein, J.R., Endicott-Yazdani, T., Porwollik, S. Bogomolnaya, L.M., Cheng, P. Guo, J., Zheng, Y., Yang,

H.J., Talamantes, M., Shields, C., Maple, A., Ragoza, Y., DeAtley, K., Tatsch, T., Cui, P., Andrews, K.D., McClelland, M., Lawhon, S., and H. Andrews-Polymenis (2013) Novel determinants of intestinal colonization of Salmonella enterica serotype Typhimurium identified in bovine enteric infection. Infection and Immunity. published ahead of print 9 September 2013 , doi:10.1128/IAI.00874-13. 5) Nagy, T.A., Moreland, S.M., Andrews-Polymenis, H.L., and C. Detweiler (2013) The ferric enterobactin transporter, Fep, is required for persistent Salmonella infection. Infection and Immunity. Published ahead of print 19 August 2013, doi: 10.1128/IAI.00412-13 6) Zheng, Y., Sambou, T., Cirillo, J.D., McClelland, M., and H. Andrews-Polymenis (2013) The EAL-domain containing protein STM2215 (rtn) is a cyclic di-GMP phosphodiesterase that is needed during Salmonella infection. Mol. Microbiology. Online 12 July 2013. DOI: 10.1111/mmi.12284. 7) Pezoa, D., Blondel, C.J., Santiviago, C.A., Andrews-Polymenis, H.L., and I. Contreras (2013) The type VI secretion system encoded in SPI-6 plays a role in gastrointestinal colonization and systemic spread of Salmonella enterica serovar Typhimurium in the chicken. PLoS One 8(5) e63917. PMCID: PMC3653874 8) Kullas, A.L., McClelland, M., Yang, H.J., Torres, A., Porwollik, S., Mena, P., Andrews-Polymenis, H., and A.W.M., van der Velden (2012) Salmonella utilize L-asparaginase II to inhibit the response of mammalian T cells. Cell, Host and Microbe. 12(6), 791-8. doi 10.1016/j.chrom.2012.10.018 9) Winter, S.E., Winter, M. G., Godinez, I. Yang, H.J., Russman, H., Andrews-Polymenis, H.L., and A.J. Baumler (2010) A rapid change in virulence gene expression during the transition from the intestinal lumen into tissue promotes systemic dissemination of Salmonella. PLoS Pathogens, 6(8) e1001060. PMCID: PMC2924370 10) Blondel, C.J. , Yang, H.J., Castro, B., Chiang, S., Toro, C.S., Zaldívar, M., Contreras, I., Andrews- Polymenis, H.L.**, and C.A. Santiviago (2010) Contribution of the Type VI Secretion System Encoded in SPI- 19 to Chicken Colonization by Salmonella enterica Serotypes Gallinarum and Enteritidis. PLoS ONE 5(7): e11724. doi:10.1371, PMCID: PMC2908676 **Co-corresponding for animal studies.

D. Research Support Current 1. NIH 1R01AI083646-01 (Andrews-Polymenis, PI ) 09/24/09- 09/23/2014 (2.4 mo) NIAID $250,000/ yr Title: Identification of Salmonella Genes Important for Systemic Colonization The goal of this work is to identify genes necessary for systemic colonization by Salmonellae in mice.

2. AFRI CSREES 2009-03579 (Andrews-Polymenis, PI) (04/30/10 -06/30/2014) USDA $400,000/4 years Title: Defining Salmonella Genes Important for Colonization and Persistence in Poultry The goal of this work is to identify Salmonella genes necessary for sub-clinical colonization in chicks.

3. NIH/USDA Dual Purpose, Dual Benefit R01 HD072928-01 (Altier, PI), (12/30/2013-12/29/2018) Title: Regulation of Salmonella Virulence by Intestinal Fatty Acids Role: Subcontractor The goal of this work is to understand the role of fatty acids on modulation of virulence during infection.

4. NIH-NCRR T32RR031229 (Keir, PI) (07/10- 07/2015) NCRR $892,704/5 years Title: Comparative Biomedical Research Training for Veterinarians Role: Training Grant Mentor to Johanna Elfenbein (D.V.M., DACVIM) The goal of this work is to train post-graduate veterinarians for research careers.

5. NIH/NIAID HHSN272201000024I (Cirillo, PI) (02/01/10- 1/31/2017) NIAID Contract Title: Small Animal Model Vaccines and Pathogenesis Role: Model Director Program Director/Principal Investigator (Last, First, Middle): ARAMAYO, Rodolfo

BIOGRAPHICAL SKETCH Provide the following information for the Senior/key personnel and other significant contributors. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Aramayo, Rodolfo Associate Professor eRA COMMONS USER NAME (credential, e.g., agency login) raramyo EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable)

University of Brasília BSc 1982 Molecular Biology University of Brasília MSc 1986 Molecular Biology University of Georgia PhD 1992 Genetics University of Wisconsin, Madison Postdoctoral 1996 Genetics Stanford University Postdoctoral 1997 Genetics

A. Personal Statement I am a fungal molecular geneticist. I obtained a Masters degree in Molecular Biology, working on the isolation and purification of peptides produced by Bacillus subtitilis with antifungal activity. I attended the University of Georgia, in Athens, where I obtained a PhD degree in Genetics, working under the supervision of Dr. William E. Timberlake in the genetic and molecular characterization of the asexual sporulation pathway of Aspergillus nidulans. For my Post-doctoral studies, I broaden my knowledge of genetics and fungal biology by studying the sexual developmental pathway of Neurospora crassa working under the supervision of the late Dr. Robert L. Metzenberg. During this time, I discovered an unusual genetic meiotic phenomenon we called Meiotic Silencing. In 1997, I moved from Stanford to Texas A&M University where, funded by the National Institutes of Health, my lab has further the genetic and molecular characterization of Meiotic Silencing. The general aim of this proposal is to speed the rate of discovery of natural products through development of genome and synthetic biology. I am specially qualified to work on this area for several reasons: I am a fungal molecular geneticist that has been trained in both asexual and sexual aspects of fungal development, stages of the life cycle that closely correlate with secondary metabolites production. I am a natural engineer that had to overcome experimental roadblocks by designing and implementing molecular and genetic technologies not existent at the time, to study meiotic silencing, a genetic phenomenon I discovered. I am a geneticist that understanding the need for a global "Systems" view of genetics resurrected a long passion I have with computers and acquired substantial expertise in the areas of Genomics, Bioinformatics and Computational Biology. I started teaching Genomics >12 years ago, well before Genomics textbooks were available, and currently teach Genomics, Computational Genomics and Digital Biology, all at the graduate and undergraduate level. I currently am the Director of the Laboratory for Genome Analysis at Texas A&M, a unit whose objective is to bring Bioinformatics and Computational Biology expertise to the campus community. I coordinate the campus-wide training of scientists in these areas. My understanding of Molecular Biology, Genetics, Genomics and computers has forced me to look at Biology from a highly modular point of view. As a result, I am a strong believer that the combination of genetics, genomics with synthetic biology will revolutionize Biology.

B. Positions and Honors Positions and Employment

ACADEMIC/RESEARCH POSITIONS TITLE INSTITUTION AND LOCATION YEAR(s) Researcher II Department of Genetic Engineering. National Center for Genetic Resources and 1983-1986 Biotechnology (CENARGEN-EMBRAPA). Brasília, D. F., Brazil Assistant Department of Biology. Texas A&M University. College Station, Texas, USA 1997-2004 Program Director/Principal Investigator (Last, First, Middle): ARAMAYO, Rodolfo

Professor Associate Department of Biology. Texas A&M University. College Station, Texas, USA 2004- Professor present C. Selected Peer-reviewed Publications

Most relevant to the current application 1. Aramayo, R. and E.U. Selker, Neurospora crassa, a Model System for Epigenetics Research, in Epigenetics, C.D. Allis, et al., Editors. 2013, Cold Spring Harbor Laboratory Press. 2. Lee, D.W., et al., A cytosine methyltransferase homologue is essential for sexual development in Aspergillus nidulans. PLoS ONE, 2008. 3(6): p. e2531. 3. Hu, J.C., et al., The emerging world of wikis. Science, 2008. 320(5881): p. 1289-90. 4. Borkovich, K.A., et al., Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiology and Molecular Biology Reviews : MMBR, 2004. 68(1): p. 1-108, table of contents. 5. Lee, D.W., J.R. Haag, and R. Aramayo, Construction of strains for rapid homokaryon purification after integration of constructs at the histidine-3 (his-3) locus of Neurospora crassa. Current Genetics, 2003. 43(1): p. 17-23. 6. Haag, J.R., D.W. Lee, and R. Aramayo, A GATEWAY™ destination vector for high-throughput construction of Neurospora crassa histidine-3 gene replacement plasmids. Fungal Genetics Newsletter, 2003. 50: p. 6-8. 7. Haag, J.R. and R. Aramayo, Construction of a his-3 integration vector capable of performing GATEWAY recombinational cloning for high-throughput analysis of Neurospora crassa. Fungal Genetics Newsletter, 2003. 50: p. 6-8. 8. Pratt, R.J. and R. Aramayo, Improving the efficiency of gene replacements in Neurospora crassa: a first step towards a large-scale functional genomics project. Fungal genetics and biology : FG & B, 2002. 37(1): p. 56-71. 9. Aramayo, R. and J.W. Bennet, The importance of fungal genomics. American Society for Microbiology (ASM) News, 1997. 63(4): p. 176-177. 10. Aramayo, R. and R.L. Metzenberg, Gene replacements at the his-3 locus of Neurospora crassa. Fungal Genetics Newsletter, 1996. 43: p. 9-13. 11. Aramayo, R., T.H. Adams, and W.E. Timberlake, A large cluster of highly expressed genes is dispensable for growth and development in Aspergillus nidulans. Genetics, 1989. 122: p. 65-71.

D. Research Support Ongoing Research Support

SOURCE: College of Science/Department of Biology TITLE: Implementation of a Galaxy Server to Enhance and expand Computational Genomics at Texas A&M University PRINCIPAL INVESTIGATOR: Dr. Rodolfo Aramayo, Dr. Tom McKnight, Dr. Alan Pepper

SOURCE: Tier One Program (TOP)/Activity 2 grant TITLE: Comparative genomics of endosymbiotic bacteria (genus Spiroplasma) associated with Drosophila flies PRINCIPAL INVESTIGATOR: Dr. Mariana Mateos, Dr. Rodolfo Aramayo

Completed Research Support

SOURCE: National Institutes of Health TITLE: Genetics and Molecular Study of Meiotic Trans-sensing and Meiotic Silencing PRINCIPAL INVESTIGATOR: Dr. Rodolfo Aramayo NUMBER: R01-GM58770 PERIOD: 01/01/1999 to 12/31/2011

Program Director/Principal Investigator: BANKAITIS, Vytas A.

BIOGRAPHICAL SKETCH Provide the following information for the Senior/key personnel and other significant contributors. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Bankaitis, Vytas A. E.L. Wehner-Welch Foundation Chair in Chemistry eRA COMMONS USER NAME (credential, e.g., agency login) VYTAS_BANKAITIS EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) Edinboro University, Edinboro, PA B.S. 1978 Biology Clemson University , Clemson, SC M.S. 1980 Microbiology University of North Carolina, Chapel Hill, NC Ph.D. 1984 Microbiology California Institute of Technology, Pasadena, CA Postdoctoral 1986 Cell Biology

A. Positions and Honors. Professional Experience: 1978-1980 Graduate Student, Department of Microbiology, Clemson University, Clemson, South Carolina. Advisor: Dr. Ellis L. Kline. 1980-1984 Predoctoral Fellow of the Humphrey Foundation, Department of Microbiology and Immunology, The University of North Carolina School of Medicine. Advisor: Dr. Philip J. Bassford, Jr. 1984-1986 Postdoctoral Fellow of the Helen Hay Whitney Foundation, Division of Biology, The California Institute of Technology, Pasadena, CA. 1986-1992 Assistant Professor, Department of Microbiology, University of Illinois, Urbana, IL. Head: Dr. Charles G. Miller. 1992-2001 Associate Professor then Professor, Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL. Head: Dr. Richard B. Marchase. 2001-2011 Professor and Chair, Department of Cell & Developmental Biology, The University of North Carolina School of Medicine, Chapel Hill, NC. 2011-2012 Professor, Department of Cell & Developmental Biology, The University of North Carolina School of Medicine, Chapel Hill, NC. 2012 – E.L. Wehner-Welch Foundation Chair in Chemistry, Texas A&M Health Science Center.

Honors: Recipient of an NCAA Postgraduate Fellowship - A national award presented to 6 outstanding student- athletes, 1978. Recipient of the President’s Award for the outstanding student research presentation; regional meeting for the Southeastern and South Carolina branches of the American Society for Microbiology, November, 1979. Recipient of a Predoctoral Fellowship of the Humphrey Foundation - awarded to outstanding incoming graduate students at the University of North Carolina, August, 1980. Recipient of a Postdoctoral Fellowship of the Helen Hay Whitney Foundation, January, 1984. Designated an Arnold Beckman Scholar, University of Illinois, 1986. Member, Cell Biology Advisory Panel, National Science Foundation, 1988-1992. Member CDF-2 IRG, NIH, 2001-2004. Chairman CDF-2 and MMBP Initial Review Group, NIH, 2004-2006. Member, Faculty of 1000, Membrane Trafficking and Sorting Section Vice-Chair -- Gordon Research Conferences -- Signal Transduction Within the Nucleus 2009 Chair -- Gordon Research Conferences -- Signal Transduction Within the Nucleus 2011 Member, Program Planning Committee, American Society for Biochemistry and Molecular Biology Annual Meeting, 2011. E.L. Wehner-Welch Foundation Chair in Chemistry, Texas A&M Health Science Center, September 2012 – Program Director/Principal Investigator: BANKAITIS, Vytas A. present.

B. Selected Peer-reviewed Publications (Selected from 140 peer-reviewed publications) 1. Alb, J.G. Jr., Cortese, J.D., Phillips, S.E., Albin, R.L., Nagy, T.R., Hamilton, B.A., and Bankaitis, V.A. 2003. Mice lacking phosphatidylinositol transfer protein alpha exhibit spinocerebellar degeneration, intestinal and hepatic steatosis, and hypoglycemia. J. Biol. Chem. 278: 33501-33518. PMID: 12788952 2. Alb, J.G. Jr., Phillips, S.E., Wilfley, L.R., Philpot, B.D., and Bankaitis, V.A. 2007. The pathologies associated with functional titration of phosphatidylinositol transfer protein α activity in mice. J. Lipid Res. 48: 1857-1872. (Cover Article) PMID: 17525475 3. Ile, K.E., Kassen, S., Cao, C., Vihtehlic, T., Shah, S.D., Huijbregts, R.P.H., Alb, J.G., Jr., Stearns, G.W., Brockerhoff, S.E., Hyde,D.R., and Bankaitis, V.A. 2010. The zebrafish class 1 phosphatidylinositol transfer protein family: PITPβ isoforms and double cone cell outer segment integrity in retina. Traffic 11: 1151-1167. PMID: 20545905 4. Nile, A.H., Tripathi, A., Yuan, P., Mousley, C.J.., Suresh, S., Wallace, I.M., Shah, S.D., Teotico Pohlhaus, D., Temple, B., Nislow, C., Giaever,, G., Tropsha, A., Davis, R.W., StOnge, R.P., and Bankaitis, V.A. 2014. A sterol binding protein integrates endosomal lipid metabolism with TOR signaling and nitrogen sensing. Nature Chemical Biology 10: 76-84. (Cover Article) PMCID: 4059020. 5. Lee, A.Y. et al. 2014. Mapping the cellular response to small molecules using chemogenomic fitness signatures. Science 344: 208-211. PMID:24723613 6. Bankaitis, V. A., J. F. Aitken, A. E. Cleves, and W. Dowhan. 1990. An essential role for a phospholipid transfer protein in yeast Golgi function. Nature 347: 561-562. (News and Views). PMID: 2215682 7. Cleves, A. E., T. P. McGee, E. A. Whitters, K. Champion, J. R. Aitken, W. Dowhan, M. Goebl, and V. A. Bankaitis. 1991. Mutations in the CDP-choline pathway for phospholipid biosynthesis bypass the requirement for an essential phospholipid transfer protein. Cell 64: 789-800. PMID: 1997207 8. Kearns, B.G., McGee T.P., Mayinger, P., Gedvilaite, A., Phillips, S.E., Kagiwada, S., and Bankaitis, V.A. 1997. Essential role for diacylglycerol in protein transport from the yeast Golgi complex. Nature 387: 101-105. (News and Views). PMID: 9139830 9. Sha, B., Phillips, S.E., Bankaitis, V.A.** and Luo, M.** 1998. Crystal structure of the Saccharomyces cerevisiae phosphatidylinositol transfer protein Sec14p. Nature 391: 506-510. ** -- Denotes co-corresponding authorship. PMID: 9461221 10. Vincent, P., Chua, M., Nogue, F., Fairbrother, A., Mekheel, H., Xu, Y., Allen, N., Bibikova, T.N., Gilroy, S., and Bankaitis, V.A. 2005. A Sec14p-nodulin domain phosphatidylinositol transfer protein polarizes membrane growth of Arabidopsis root hairs. Journal of Cell Biology 168: 801- 812. Faculty of 1000 (Must Read – 6.4) PMID: 15728190 11. Slessareva, J.E., Routt. S.M., Temple, B., Bankaitis, V.A., and Dohlman, H.G. 2006. G protein activation of a PtdIns 3-kinase at the endosome. Cell 126: 191-203. Faculty of 1000 (Exceptional– 10.0) PMID: 16839886 12. Ryan, M.M., Temple, B.R.S., Phillips, S.E., and Bankaitis, V.A. 2007. Conformational dynamics of the major yeast phosphatidylinositol transfer protein Sec14p: Insights into the mechanisms of phospholipid exchange and diseases of Sec14p-like protein deficiencies. Mol. Biol. Cell 18: 1928-1942. (InCytes Article. Cover Article). PMID: 17344474 13. Liu, Y., Boukhelifa, M., Tribble, E., Morin-Kensicki, E., Uetrecht, A., Bear, J.E., and Bankaitis, V.A. 2008. The Sac1 phosphoinositide phosphatase regulates Golgi membrane morphology and mitotic spindle organization in mammals. Mol. Biol. Cell 19: 3080-3096. (InCytes Article). PMID: 18480408 14. Schaaf, G., Ortlund, E.A., Tyeryar, K.R., Mousley, C.J., Ile, K.E., Woolls, M.J., Garrett, T.A., Raetz, C.R.H., Redinbo, M.R., and Bankaitis, V.A. 2008. The functional anatomy of phospholipid binding and regulation of phosphoinositide homeostasis by proteins of the Sec14-superfamily. Molecular Cell 29: 191- 206. Faculty of 1000 (Must Read – 6.0) PMID: 18243114 15. Mousley, C., Yuan, P., Gaur, N.A., Trettin, K.D., Nile, A.H., Deminoff, S., Dewar, B.J., Wolpert, M., Macdonald, J.M., Herman, P.K., Hinnebusch, A.G., and Bankaitis, V.A. 2012. A sterol binding protein integrates endosomal lipid metabolism with TOR signaling and nitrogen sensing. Cell 148: 702-715. Faculty of 1000 (Must Read – 6.0) PMID: 22341443.

Program Director/Principal Investigator: BAYLESS, Kayla J.

BIOGRAPHICAL SKETCH Provide the following information for the Senior/key personnel and other significant contributors. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Bayless, Kayla J. eRA COMMONS USER NAME (credential, e.g., agency login) Associate Professor BAYLESSK EDUCATION/TRAINING DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable)

Texas Lutheran University, Seguin, TX B.S. 1994 Molecular Biology

Texas A&M University Ph.D. 1999 Medical Physiology

Texas A&M Health Science Center post-doctoral 1999-2004 Pathology

POSITIONS AND HONORS Positions and Employment:

2002-2004 NIH Postdoctoral Fellow, Department of Pathology and Laboratory Medicine, Texas A&M Health Science Center, College Station, TX. 2004-2006 Research Assistant Professor, Department of Pathology and Laboratory Medicine, Texas A&M Health Science Center, College Station, TX. 2006-present Assistant and Associate Professor, Department of Molecular & Cellular Medicine, Texas A&M Health Science Center, College Station, TX.

Honors:

1990-1994 Pacesetter Award 1999,2001,2004 American Society for Cell Biology Travel Award 2002-2004 NIH Postdoctoral Fellow 2011 Herbert Tabor Young Investigator Award, Journal of Biological Chemistry 2012 Excellence in Research Award, Junior Investigator, College of Medicine, Texas A&M HSC

Panel Member for Study Sections: 2012-2014 American Heart Association, Vascular Wall Biology: Angiogenesis, Atherosclerosis, General Inflammation Basic Sciences 2013-2017 National Institutes of Health, Atherosclerosis, Inflammation, and Cardiovascular Sciences (AICS)

Ad hoc Reviewer for Study Sections: 2007 American Heart Association, Western Peer Review Committee 2010 Independent Reviewer, Post-Doctoral Application; The Lalor Foundation, Inc. 2012 National Institutes of Health; Atherosclerosis and Inflammation of the Cardiovascular System (February, October) 2012 National Science Foundation, CAREER award reviewer

SELECT PEER-REVIEWED PUBLICATIONS from post-docs and graduate students mentored at Texas A&M (47 total)

1. Su SC, EA Mendoza, HI Kwak, and KJ Bayless. (2008) Molecular profile of endothelial invasion of three- dimensional collagen matrices: insights into angiogenic sprout induction in wound healing. American Journal of Physiology - Cell Physiology. 295, C1215-C1229.

2. Kang H, KJ Bayless, R Kaunas. (2008) Fluid shear stress modulates endothelial cell invasion into three- dimensional collagen matrices. American Journal of Physiology - Heart & Circulatory Physiology. 295, H2087-H2097.

Program Director/Principal Investigator: BAYLESS, Kayla J. 3. Kwak HI, EA Mendoza, and KJ Bayless. (2009) ADAM17 Co-purifies with TIMP-3 and Modulates Endothelial Invasion Responses in Three-Dimensional Collagen Matrices. Matrix Biology. 28:470-479.

4. Lee PF, AT Yeh, KJ Bayless. (2009) Nonlinear optical microscopy reveals invading endothelial cells anisotropically alter three-dimensional collagen matrices. Exp. Cell Res. 315, 396-410.

5. Bayless KJ, HI Kwak, SC Su. (2009) Investigating endothelial invasion and sprouting behavior in three- dimensional collagen matrices. Nature Protocols 4, 1888-1898.

7. Larson AM, A Lee, PF Lee, KJ Bayless, AT Yeh. (2009) Ultrashort Pulse Multispectral Nonlinear Optical Microscopy. J. Innov. Opt. Health Sci. 2, 27-35.

8. Erikson DW, RC Burghardt, KJ Bayless, and GA Johnson. (2009) Secreted phosphoprotein 1 (SPP1, osteopontin) binds to integrin alpha v beta 6 on porcine trophectoderm cells and integrin alpha v beta 3 on uterine luminal epithelial cells, and promotes trophectoderm cell adhesion and migration. Biol. Reprod. 81, 814-825.

9. Dunlap KA, HI Kwak, RC Burghardt, FW Bazer, RR Magness, GA Johnson, and KJ Bayless. (2010) The sphingosine 1-phosphate (S1P) signaling pathway is regulated during pregnancy in sheep. Biol. Reproduction. 82, 876-887.

10. Su SC, SA Maxwell, and KJ Bayless. (2010) Annexin 2 regulates endothelial morphogenesis by controlling AKT activation and junctional integrity. Journal of Biological Chemistry. 285, 40624-40634. PMCID: PMC3003361

11. Kang H, HI Kwak, RR Kaunas, and KJ Bayless. (2011) Fluid Shear Stress and Sphingosine 1-Phosphate Activate Calpain to Promote MT1-MMP Membrane Translocation and Endothelial Invasion in Collagen Matrices. Journal of Biological Chemistry. 286, 42017-42026. PMCID: PMC3234924

12. Kwak HI, H Kang, JM Dave, EA Mendoza, SC Su, SA Maxwell, KJ Bayless. (2012) Calpain-mediated vimentin cleavage occurs upstream of MT1-MMP membrane translocation to facilitate endothelial sprout initiation. Angiogenesis. 15, 287-303. PMCID: PMC3338915

13. Su SC, Bayless KJ. (2012) Utilizing sphingosine-1-phosphate to stimulate sprouting angiogenesis. Methods Mol Biol. 874:201-13. PMID: 22528450

14. Lee DW, D Ramakrishnan, J Valenta, IF Parney, KJ Bayless, R Sitcheran. (2013) The NF-κB RelB protein is an oncogenic driver of mesenchymal glioma. PLoS One. 8(2):e57489. PMID: 23451236

15. Lee PF, Bai Y, Smith RL, Bayless KJ, Yeh AT. (2013) Angiogenic responses are enhanced in mechanically and microscopically characterized, microbial transglutaminase crosslinked collagen matrices with increased stiffness. Acta Biomater. 9(7):7178-90. PMID: 23571003

16. Dave JM, Kang H, Abbey CA, Maxwell SA, Bayless KJ. (2013) Proteomic profiling of endothelial invasion revealed receptor for activated C kinase 1 (RACK1) complexed with vimentin to regulate focal adhesion kinase (FAK). J Biol Chem. 288, 30720-33. PMID: 24005669

17. Gao Y, Bayless KJ, Li Q. TGFBR1 Is Required for Mouse Myometrial Development. (2014) Mol Endocrinol. 28:380-94. PMID: 24506537

18. Dave JM, Bayless KJ. (2014) Vimentin as an integral regulator of cell adhesion and endothelial sprouting. Microcirculation. 21(4):333-44 PMID: 24387004

19. Bai Y, Lee PF, Gibbs HC, Bayless KJ, Yeh AT. (2014) Dynamic multicomponent engineered tissue reorganization and matrix deposition measured with an integrated nonlinear optical microscopy-optical coherence microscopy system. J Biomed Opt. 19(3):36014. PMID: 24647972 Program Director/Principal Investigator: BELL-PEDERSEN, Deborah BIOGRAPHICAL SKETCH Provide the following information for the Senior/key personnel and other significant contributors in the order listed on Form Page 2. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Bell-Pedersen, Deborah Professor of Biology eRA COMMONS USER NAME (credential, e.g., agency login) EDUCATION/TRAININGdbpedersen (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION (if MM/YY FIELD OF STUDY applicable) State University of New York at Morrisville A. A. S. 1977-1979 Natural Res. Cons. State University of New York at Albany B.S. 1980-1982 Biology State University of New York at Albany M.S. 1984-1987 Molecular Biology State University of New York at Albany Ph. D. 1987-1991 Molecular Biology

A. Positions and Honors

Positions and Employment 1984 - 1991 Graduate Research Assistant, New York State Health Department 1991 - 1997 Postdoctoral Research Fellow, Biochemistry, Dartmouth Medical School 1997 - 2002 Assistant Professor of Biology, TAMU 1997 - present Member of the Interdisciplinary Genetics Faculty, TAMU 1997 - present Member of the Program for the Biology of Filamentous Fungi, TAMU 2003 - 2007 Associate Professor of Biology, TAMU 2003 - present Member of the Center for Biological Clocks Executive Committee, TAMU 2007 - present Member of the Chemical Biology and Undergraduate Biology and Math Training Programs 2007 - present Professor of Biology, TAMU 2014 - present Associate Department Head, Biology Dept. TAMU

Other Experience and Professional Memberships 1993 - present Member, Society for Research on Biological Rhythms (SRBR) 2002 - 2004 Elected Chair of the Neurospora Policy Committee 2004 - present Associate Editor, Fungal Genetics and Biology 2008 - present Editorial Board, Eukaryotic Cell 2010 - 2014 NIH Cellular Signaling and Regulatory Systems Study Section Panel Member 2010 - 2012 Society for Research on Biological Rhythms Program Chair 2012 - present Associate Editor, Fungal Genetics and Biology 2014 - present Society for Research on Biological Rhythms, Executive Board Member 2014 - present Associate Editor Journal of Biological Rhythms

Honors and Awards 2005 Jo Ann Treat Award for Excellence in Research, TAMU 2006 Distinguished Achievement Award in Teaching, TAMU 2009 Texas A&M Distinguished Lecturer 2010 Ethel Ashworth-Tsutsui Memorial Lecture and Award, TAMU 2011 Davidson Award Lecture, Baylor College 2013 Eminent Scholar Award, Women’s Former Student Association, TAMU 2014 Fellow, American Academy of Microbiology Program Director/Principal Investigator: BELL-PEDERSEN, Deborah B. SELECTED PEER-REVIEWED PUBLICATIONS (Postdocs and Graduate Students as shown) 1. Correa, A, Lewis, ZA, Greene, AV, March IJ, Gomer, R, and Bell-Pedersen, D. (2003) Microarray profiling reveals multiple oscillators regulate circadian gene expression in Neurospora. Proc. Natl. Acad. Sci. USA. 100: 13597-602. PMC263859 2. Galagan, J., Calvo, S.E., Borkovich, K.. Selker, E., Read, N., FitzHugh W., Ma, L-M., Smirnov S., Purcell, S., Rehman, B, Elkins,T. Engels,R., Wang, S., Nielsen, C.B., Roy, A., Ianakiev, P., Davis, R., Nelson, MA, Werner-Washburne, M., Mewes, W., Kinsey, J., Braun, E., Zelter, A., Shulte U., Kothe, G., Jedd, G., Bell- Pedersen, D., Staben, C., Marcotte, E., Greenberg, D., Selitrennikoff, C.P., Foley, K., Naylor, J., Stange- Thomann, N., Barrett, R., Butler, J., Gnerre, S., Jaffe, D., Qui, D., Kamvysselis, M., Kamal, M., Metzenberg, R., Perkins, D., Dunlap, J., Glass, L., Yarden, O., Plamann, M., Seiler, S., Radford, A., Orbach, M., Berglund, J.A., Voelker,, R., Mannhaupt, G., Natvig, D., Aramayo, R., Ebbole, D., Freitag, M., Paulsen, I., Sachs, M., Lander, E.S., Nusbaum, C., and Birren, B. (2003) The genome sequence of the filamentous fungus Neurospora crassa Nature 422: 859-869. 3. Vitalini, M, Morgan, L, March, IJ, and Bell-Pedersen, D (2004) A genetic selection for circadian output pathway (cop) mutations in Neurospora crassa. Genetics. 167: 119-29. PMC1470853 4. Bell-Pedersen, D, Cassone, VM, Earnest, DJ, Golden SS, Hardin, PE, Thomas TL, Zoran, MJ (2005) Circadian rhythms from multiple oscillators: lessons from diverse organisms. Nat Rev Genet. 6:544-556. PMC2735866 5. Galagan, JE, Calvo SE, Cuomo C, Ma L-J, Wortman, J, Batzoglou S, Lee S-I, Baştürkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farmam, M, Butler, J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D’Enfert C, Bouchier, C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker, EU, Archer, DB, Peñalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paolett, M, Fischer, R, Miller, B, Dyer, P, Sachs MS, Osmani SA, & Birren, B. (2005) Sequencing of Aspergillus nidulans and Comparative Analysis with A. fumigatus and A. oryzae Nature 438: 1105-1115 6. Pregueiro AM, Price-Lloyd, N, Bell-Pedersen, D, Heintzen, C, Loros, JL, Dunlap, JC (2005) Assignment of an essential role for the Neurospora frequency gene in circadian entrainment to temperature cycles. Proc. Natl. Acad. Sci. USA 102: 2210-2215 PMC548525 7. Vitalini, M, dePaula, RM, Goldsmith, C, Jones, C, Borkovich, K, and Bell-Pedersen, D (2007) Circadian rhythmicity mediated by temporal regulation of the activity of a p38 MAPK. Proc. Natl. Acad. Sci USA 104(46):18223-8. PMC2084324 8. dePaula, RM, Vitalini, MW, Gomer, RH, and Bell-Pedersen, D (2007) Complexity of the Neurospora crassa circadian clock system: Multiple loops and oscillators. Cold Spring Harbor Symposia on Quantitative Biology: Clocks and Rhythms, Volume 72:345-51. Review 9. dePaula, RM, Lamb, TM, Bennett, L, and Bell-Pedersen, D (2008) A connection between MAPK pathways and circadian clocks. Cell Cycle 7:2630-4. PMC2577295 10. Smith, KM, Sancar, G, Dekhang, R, Sullivan, CM, Li, S, Bredeweg, EL, Priest, H, McCormick, RF, Tag, A, Thomas, T, Sancar, C, Carrington, JC, Bell-Pedersen, D, Brunner, M, Stajich, JE, Freitag, M. (2010) Light signaling networks in Neurospora crassa revealed by genome-wide mapping of direct targets for WHITE COLLAR-2. Euk Cell 9: 1549-1556. PMC2950426 11. Lamb TM, Goldsmith CS, Bennett L, Finch KE, Bell-Pedersen D. (2011) Direct Transcriptional Control of a p38 MAPK Pathway by the Circadian Clock in Neurospora crassa. PLoS One. 6(11):e27149. PMC3210137 12. Lamb, TM, Finch, KE, and Bell-Pedersen, D (2012) The Neurospora crassa OS MAPK Pathway-Activated Transcription Factor ASL-1 Functions To Generate Circadian Rhythms In Pathway Responsive Clock- Controlled Genes. Fungal Genetics and Biology 49(2):180-8 . PMC3278502 13. Bennett, LD, Beremand, P, Thomas TL, and Bell-Pedersen, D (2013) Circadian Activation of the Mitogen- Activated Protein Kinase MAK-1 Facilitates Rhythms in Clock-Controlled Genes in Neurospora crassa. Euk Cell 12:59-69. PMC3535850 14. Lamb, TM, and Bell-Pedersen, D. (2013) Regulation of gene expression in Neurospora crassa with a copper responsive promoter. Genes Genomes Genetics. (PMC Journal - in progress). 15. Goldsmith CS, and Bell-Pedersen, D. (2013) Diverse roles for MAPK signaling in circadian clocks. Adv. Genet. 84: 1-39 PMID 24262095

NAME POSITION TITLE Michael Benedik Regents Professor eRA COMMONS USER NAME (credential, e.g., agency login) mbenedik EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable)

Stanford University, Stanford CA PhD 1982 Biology University of Chicago, Chicago, Ill BA 1976 Biology

Positions and Honors • Regents Professor, Texas A&M University, 2012 • SEC Academic Leadership Development Fellow 2012-13 • American Society for Microbiology – International Professor for Africa, 2010 • First scholar selected for the Great Program, Capitol Normal University, Beijing China, 2009 • Regional Vice-President – Texas Branch AAUP (2012-present)

• Editorial Board, Bioengineered Bugs (now Bioengineered) (2010-present) • Editorial Board, Journal of Microbial and Biochemical Technology (2010-present )

• Dean of Faculties and Associate Provost (1/13-present) • Faculty Ombuds Officer, Texas A&M University (2010-2013) • Professor, Department of Biology and Faculty of Genetics, Texas A&M (2004-present) • Assistant, Associate and Professor of Biology and Biochemistry, University of Houston (1991-2004) • Assistant Professor of Biology, Texas A&M University (1985-89) Associate Director, Laboratory for Cloning and Gene Transfer, Department of Medical Biochemistry and Genetics,Texas A&M College of Medicine (1984-85) • Staff Scientist, DNAX Research Institute of Molecular & Cellular Biology, (1982-1984) Palo Alto, CA

Current and Recent Funding • Engineering Improved Microbial Nitrilases Robert A. Welch Foundation $150,000 (2008-11) • Cyanide Remediation: Evolving Improved Enzymes. Texas Hazardous Waste Research Center. $25,000 (9/2012-8/2013) • Cyanide Remediation: Evolving Improved Enzymes. Texas Hazardous Waste Research Center. $40,000 (9/2013-8/2015)

Graduate and Postgraduate Students Supervised: • 10 Ph.D. Students • 11 M.S. Students • 7 Postdoctoral Fellows • 3 Visiting Professors

PHS 398/2590 (Rev. 06/09) Page 1 Biographical Sketch Format Page Recent Peer-reviewed Publications (>90) 1. Kwan BW, Osbourne DO, Hu Y, Benedik MJ, Wood TK. (2014) Phosphodiesterase DosP increases persistence by reducing cAMP which reduces the signal indole. Biotechnol Bioeng. doi: 10.1002/bit.25456. [Epub ahead of print]. 2. Hu Y, BW Kwan, DO Osbourne, MJ Benedik and TK Wood. (2014) Toxin YafQ increases persister cell formation by reducing indole signaling. Environ Microbiol. 2014 Jul 15. doi: 10.1111/1462-2920.12567. [Epub ahead of print] 3. Vilo C, Benedik MJ, Ilori M, Dong Q. (2014) Draft genome sequence of Cupriavidus sp. strain SK-3, a 4- chlorobiphenyl- and 4-chlorobenzoic acid-degrading bacterium. Genome Announc. 2014 Jul 3;2(4). pii: e00664- 14. doi: 10.1128/genomeA.00664-14. 4. Vilo C, Benedik MJ, Ilori M, Dong Q. (2014) Draft genome sequence of Cupriavidus sp. strain SK-4, a di-ortho- substituted biphenyl-utilizing bacterium isolated from polychlorinated biphenyl-contaminated sludge. Genome Announc. 2014 May 22;2(3). pii: e00474-14. doi: 10.1128/genomeA.00474-14. 5. Guo Y, C Quiroga, Q. Chen, MJ McAnulty, MJ Benedik, TK Wood, and X Wang. (2014) RalR (a DNase) and RalA (a small RNA) form a type I toxin-antitoxin system in Escherichia coli. Nucl Acids Res. 42:6448-62. 6. Cheng HY, VWC Soo, S Islam, MJ McAnulty, MJ Benedik, and TK Wood. (2013) Toxin GhoT of the GhoT/GhoS TA system damages the cell membrane to reduce ATP and to reduce growth under stress. Environ Microbio. 16:1741-54. 7. Martinez, AK, E Gordon, A Sengupta, NH Shirole, D Klepacki, B Martinez-Garriga, L Brown, MJ Benedik, C Yanofsky, A Mankin, N Vázquez-Laslop, MS Sachs, and LR Cruz-Vera (2013) Interactions of the TnaC nascent peptide with rRNA in the exit tunnel enable the ribosome to respond to free tryptophan. Nucleic Acids Res. 42:1245-56. 8. Ilori, M., F Picardal, R Aramayo, SA Adebusoye, OS Obayori, and MJ Benedik. (2013) Catabolic plasmid specifying polychlorinated biphenyl degradation in Cupriavidus sp. strain SK-4: mobilization and expression in a pseudomonad. J. Basic Microbiol. doi: 10.1002/jobm.201200807. 9. Kwan, BW, JA Valenta, MJ Benedik, and TK Wood. (2013) Arrested protein synthesis increases persister-like cell formation. Antimicrob. Agents Chemother. 57:1468-73. 10. Wang X, DM Lord, SH Hong, W Peti, MJ Benedik, R Page, and TK Wood. (2013) Type II toxin/antitoxin MqsR/MqsA controls type V toxin/antitoxin GhoT/GhoS. Environ Microbiol. 15:1734-44. 11. Vilo, CA, MJ Benedik, DA Kunz, Q Dong (2012) Draft genome sequence of the cyanide-utilizing bacterium Pseudomonas fluorescens strain NCIMB 11764. J. Bacteriol. 194:6618-19. 12. Wang, X, DM Lord, H-Y Cheng, DO Osbourne, SH Hong, V Sanchez-Torres, C Quiroga, K Zheng, T Herrmann, W Peti, MJ Benedik, R Page, and TK Wood (2012) A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS. Nature Chemical Biology 8:855-61. 13. Hong, SH, X Wang, HF O’Connor, MJ Benedik and TK Wood (2012) Bacterial persistence increases as environmental fitness decreases. Microbial Biotechnology 5:509-22. 14. Martinez, AK, NH Shirole, S Murakami, MJ Benedik, MS Sachs, LR Cruz-Vera. (2012) Crucial elements that maintain the interactions between the regulatory TnaC peptide and the ribosome exit tunnel responsible for Trp inhibition of ribosome function. Nucleic Acids Res. 40:2247-57. 15. Hu, Y, MJ Benedik and TK Wood. (2012) Antitoxin DinJ influences the general stress response through transcript stabilizer CspE. Environ. Microbio 14:669-79. 16. Wang L, JM Watermeyer, AE Mulelu, BT Sewell, and MJ Benedik (2012) Engineering pH tolerant mutants of a cyanide dihydratase. Applied Microbiology and Biotechnology 94:131-140. 17. Wang, X, Y Kim, SH Hong, Q Ma, BL Brown, M Pu, AM Tarone MJ. Benedik, W Peti, R Page, and TK Wood. (2011) Antitoxin MqsA helps mediate the bacterial general stress response. Nature Chemical Biology 7:359-366. 18. Abou-Nader, M and MJ Benedik. (2010) Rapid generation of random mutant libraries. Bioengineered Bugs 1:337-340. 19. Dvoracek, C.M., G. Sukhonosova, M.J. Benedik, and J.C. Grunlan. (2009) Antimicrobial behavior of polyelectrolyte- surfactant thin film assemblies. Langmuir 25:10322-8 20. Ju J, Qi J, Xu S, Ohnishi K, Benedik MJ, Xue Y, Ma Y. (2009) Crystallization and preliminary X-ray study of alkaline alanine racemase from Bacillus pseudofirmus OF4. Acta Crystallogr Sect F Struct Biol Cryst Commun. 65:166-8.

PHS 398/2590 (Rev. 06/09) Page 2 Biographical Sketch Format Page BIOGRAPHICAL SKETCH

NAME POSITION TITLE SARAH BONDOS, PH.D. Assistant Professor EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable)

University of North Carolina at Chapel Hill B.S. with 05/1993 Chemistry honors

University of Illinois at Urbana-Champaign Ph.D. 08/1998 Biochemistry

Rice University, Houston, TX Postdoctoral 1998-2004 Postdoctoral Research Res. Fellow

A. Positions and Honors Positions and Employment 1993-1994 University Fellow (Graduate student), University of Illinois at Champaign-Urbana, laboratories of Dr. Stephen G. Sligar and Dr. Jiri Jonas. 1994-1997 NSF Predoctoral Fellow, University of Illinois at Champaign-Urbana, laboratories of Dr. Stephen G. Sligar and Dr. Jiri Jonas. 1997-1998 Graduate Research Assistant, University of Illinois at Champaign-Urbana, laboratories of Dr. Stephen G. Sligar and Dr. Jiri Jonas. 1998-2001 Postdoctoral Research Associate, Rice University, laboratory of Dr. Kathleen S. Matthews. 2001-2003 Robert A. Welch Postdoctoral Fellow, Rice University, laboratory of Dr. Kathleen S. Matthews. 2003-2004 Research Scientist, Rice University, laboratory of Dr. Kathleen S. Matthews. 2004-2008 Faculty Fellow (non-tenure track research faculty), Rice University. 2008-2014 Adjunct Assistant Professor, Department of Biochemistry and Cell Biology, Rice University. 2008-2014 Assistant Professor, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine. 2014-present Adjunct Associate Professor, Department of Biochemistry and Cell Biology, Rice University. 2014-present Associate Professor, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine.

Honors NSF CAREER Award (2012-2017) American Heart Association Beginning Grant-In-Aid (2008-2010) Robert A. Welch Foundation Postdoctoral Fellowship (2001-2003) National Science Foundation Predoctoral Fellowship (1994-1997) University of Illinois, University Fellowship (1993-1994) Participant, NIH Cell and Molecular Biology Training Grant (1993-1996) Graduation with honors and distinction, University of North Carolina (1993) Martin Marietta Corporation Foundation Scholarship (1989-1993) Tennessee Honors Program Scholarship (1989) National and Select Regional Activities Editorial Board, Intrinsically Disordered Proteins (2013-present) Councilor, Intrinsically Disordered Proteins Subgroup (2011-2014) Review panel for the Division of Materials Research, NSF (2013, 2014) Review panel for Scientific Meeting Applications, NIH (2014) Member, Program and Organizing Committee, Texas Protein Folders Meeting (2010-present, chair in 2011)

B. Selected original research publications.

1. Tsai, S.P., Howell, D.W., Huang, Z., Hsiao, H.C., Lu, Y., Matthews, K.S., Lou, J., Bondos, S.E. (2014), The effect of protein fusions on the production and mechanical properties of protein-based materials. Adv. Funct. Mater., submitted. 2. Patterson, J., Abbey, C.A., Bayless, K.J., Bondos, S.E. (2014) Materials composed of the Drosophila melanogaster protein Ultrabithorax are cytocompatible. J. Biomed. Mat. Res. A. 102A, 97-104. 3. Patterson, J., Arenas, A., Wang, T.Y., Hsiao, H.C., Pellois, J.P., Rice-Ficht, A., Bondos, S.E. (2014) Materials composed of the Drosophila Hox protein Ultrabithorax are biocompatible and non- immunogenic. J. Biomed. Mater. A., in press. 4. Majithia, R., Patterson, J., Bondos, S.E., Meissner, K.E. (2011) On the design of composite protein – quantum dot composite biomaterials via self-assembly. Biomacromolecules 12, 3629-3637. 5. Huang, Z., Salim, T., Brawley, A., Patterson, J., Matthews, K.S., Bondos, S.E. (2011) Functionalization and patterning of protein-based materials using active Ultrabithorax chimeras. Advanced Functional Materials 21, 2633-2640. 6. Huang, Z., Lu, Y., Majitha, R., Shah, J., Meissner, K., Matthews, K.S., Bondos, S.E., Lou, J. (2010) Size dictates mechanical properties for fibers self-assembled by the Drosophila Hox transcription factor Ultrabithorax. Biomacromolecules 11, 3644-3651. 7. Self –assembly of protein-based biomaterials with multiple morphologies” U.S. application (Serial No. 12/618,518), PCT application (Serial No. PCT/US09/64449). 8. Greer, A., Huang, Z., Oriakhi, A., Lu, Y., Lou, J., Matthews, K.S., Bondos, S.E. (2009) The Drosophila transcription factor Ultrabithorax self-assembles into protein-based biomaterials with multiple morphologies. Biomacromolecules 10, 829-837. 9. Bondos, S.E., Bicknell, A.A. (2003) Prediction and prevention of protein aggregation before, during, and after purification. Anal. Biochem. 316, 223-231. Fourth-most downloaded article for Analytical Biochemistry in 2003. Chosen for Proteomics Selects Virtual Journal, Issue 9, 23 April 2003.

Program Director/Principal Investigator (Last, First, Middle): Bryk, Mary Elizabeth

NAME POSITION TITLE Bryk, Mary E. Associate Professor eRA COMMONS USER NAME (credential, e.g., agency login) brykma EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Cornell University, Ithaca, NY B.S. 1985 Animal Science Albany Medical College, Albany, NY M.S. 1991 Micro./Mole. Biology Albany Medical College, Albany, NY Ph.D. 1994 Micro./Mole. Biology

A. Position and Honors Positions and Employment: 1995-97 Postdoctoral Fellow. Advisor: Dr. M. Joan Curcio. Wadsworth Center, New York State Department of Health. 1997-02 Postdoctoral Fellow. Advisor: Dr. Fred Winston. Department of Genetics, Harvard Medical School. 2002-07 Assistant Professor, Department of Biochemistry and Biophysics and Member, Interdisciplinary Faculty of Genetics, Texas A&M University 2008-present Associate Professor, Department of Biochemistry and Biophysics and Member, Interdisciplinary Faculty of Genetics, Texas A&M University 2012-14 ADVANCE Administrative Faculty Fellow, Texas A&M University Honors and Awards: 1990 Dean’s Certificate and Prize for Excellence in Research, Albany Medical College 1990 Graduate Research Award, Eastern New York Branch of the American Society for Microbiology 1992 Frank C. Ferguson Prize for Excellence in Academic Studies, Albany Medical College 1993 Leonard Procita Prize for Outstanding Research Presentation, Albany Medical College 1993 Dean’s Certificate and Prize for Excellence in Research, Albany Medical College 1994 Graduation Address, Graduate Studies Program, Albany Medical College 1995-98 American Cancer Society Postdoctoral Fellowship 1998-01 Leukemia Society of America Senior Postdoctoral Fellowship

B. Selected Peer-reviewed Publication 19. Williamson, K., Schneider, V., Jordan, R.A., Mueller, J.E., Henderson Pozzi, M. and Bryk, M. (2013) The catalytic and functional roles of conserved amino acids in the SET domain of the S. cerevisiae lysine methyltransferase Set1. PLoS One 8(3): e57974. 18. Smith Jr., D.L., Li, C., Matecic, M., Maqani, N., Bryk, M. and Smith, J.S. (2009) Differential calorie restriction effects on silencing and recombination at the yeast rDNA. Aging Cell 8: 633-642. 17. Blank, H., Li, C., Mueller, J.E., Bogomolnaya, L.M., Bryk, M. and Polymenis, M. (2008) Mitochondria actively promote nuclear DNA replication in yeast. PLoS Genetics 4: e1000047.

16. Li, C., Mueller, J.E., Elffine, M. and Bryk, M. (2008) Linker histone H1 represses recombination at the ribosomal DNA locus in the budding yeast Saccharomyces cerevisiae. Molecular Microbiology 67: 906- 919. 15. Mueller, J. E., Li, C. and Bryk, M. (2007) Isw2 regulates gene silencing at the ribosomal DNA locus in S. cerevisiae. Biochemical and Biophysical Research Communications 361: 1017-1021. 14. Mueller, J.E. and Bryk, M. (2007) Isw1 acts independently of Isw1a and Isw1b complexes in regulating transcriptional silencing at the ribosomal DNA locus in Saccharomyces cerevisiae. Journal of Molecular Biology 371: 1-10. 13. Li, C. Mueller, J.E. and Bryk, M. (2006) Sir2 represses endogenous Pol II transcription units in the ribosomal DNA non-transcribed spacer. Molecular Biology of the Cell 17: 3848-3859. 12. Mueller, J.E., Canze, M. and Bryk, M. (2006) The requirements for COMPASS and Paf1 in transcriptional silencing and methylation of histone H3 in Saccharomyces cerevisiae. Genetics 173: 557- 567. 11. Briggs, S.D., Bryk, M., Strahl, B.D., Cheung, W.L., Davie, J.K., Dent, S. Y. R., Winston, F., and Allis, C.D. (2001) 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. 10. Bryk, M., Briggs, S.D., Strahl, B.D., Curcio, M.J., Allis, C.D. and Winston, F. (2002) Evidence that Set1, a factor required for methylation of histone H3 at multiple loci, regulates rDNA silencing in Saccharomyces cerevisiae by a Sir2-independent mechanism. Current Biology 12: 165-170.

C. CURRENT SUPPORT: Federal or International NSF Grant # DBI-0851611: Kunkel, G. (PI); Bryk, M. (co-PI); "REU Site: Summer Undergraduate Research Program in Biochemistry" (2009-2014) NSF Grant # DBI-1358941: Kunkel, G. (PI); Bryk, M. (co-PI); "REU Site: Summer Undergraduate Research Program in Biochemistry" (2014-2019) State or Local None

Program Director/Principal Investigator: BYRAM, Thomas D

NAME POSITION TITLE Byram, Thomas, D. Assistant Professor eRA COMMONS USER NAME

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Hendrix College, Conway, AR B.A. 1971-1975 Biology Texas A&M University, College Station, TX M.S. 1975-1978 Forestry Molecular and Texas A&M University, College Station, TX Ph.D. 1992-200 Environmental Plant Sciences

A. Positions and Honors Employment

1976-1978 Research Assistant, Department of Forest Science, Texas A&M University, College Station, TX. 1978-2001 Assistant Geneticist, Texas Forest Service. 2001-Present Geneticist, Texas Forest Service. Responsible for the direction of the Texas Forest Service Pine and Hardwood Tree Improvement Programs, Western Gulf Forest Tree Improvement Program – Pine, Western Gulf Forest Tree Improvement Program – Hardwood, and Urban Tree Improvement Program. 2001-Present Assistant Professor, Department of Ecosystem Science and Management (formerly Forest Science). Research problems addresses operational tree improvement problems for both pine and hardwood species.

Other Experience and Professional Memberships

Society of American Foresters SAF Genetics and Tree Improvement Working Group Seed Orchard Pest Management Subcommittee of the Southern Forest Tree Improvement Committee (Current Chair) Texas Forestry Association Tree Genes Initiative Consortium Graduate College Faculty appointments to the Departments of Ecosystem Science and Management, Genetics, and Molecular and Environmental Plant Sciences

Honors

1995 & 1999 Tony Squillace Award for the best presentation at SFTIC 2011 USDA Secretary of Agriculture Honor Award for Excellence - Conifer Translational Genomics Team

B. Selected peer-reviewed publications (Postdocs and Graduate Students as shown)

Chhatre, V., T. D. Byram, D. B. Neale, J. L. Wegrzyn and K. V. Krutovsky. 2013. Genetic structure and association mapping of adaptive and selective traits in the East Texas loblolly pine (Pinus taeda L.) breeding populations. Tree Genetics and Genomes. 9:1161-1178. PHS 398/2590 (Rev. 09/04) Page 1 Biographical Sketch Format Page Program Director/Principal Investigator: BYRAM, Thomas D McKeand, S.E., E.J. Jokela, D.A. Huber, T.D. Byram, H. L. Allen, B. Li, T.J. Mullin. 2006. Performance of improved genotypes of loblolly pine across different soils, climates, and silvicultural inputs. Forest Ecology and Management 227:178-184.

Byram, T.D., J.H. Myszewski, D.P. Gwaze and W.J. Lowe. 2005. Improving wood quality in the Western Gulf Forest Tree Improvement Program: The problem of multiple breeding objectives. Tree Genetics and Genomes 1(3): 1-8.

Byram, T. D., T.J. Mullin, T. L. White, and J.P. van Buijtenen. 2005. Tree Improvement: Alternative visions for the next decade. Southern Journal of Applied Forestry 29(2): 88-95.

Bridgwater, F. E., T. Kubisiak, T.D. Byram, and S. E. McKeand. 2005. Risks management with current deployment strategies for genetically improved loblolly and slash pines. Southern Journal of Applied Forestry 29(2): 80-87.

Myszewski, J.H., F.E. Bridgwater, W. J. Lowe, T.D. Byram. R. A. Megraw. 2004. Genetic variation in the microfibril angle of loblolly pine from two test sites. Southern Journal of Applied Forestry 28(4):196-204.

Myszewski, J. H., F. E. Bridgwater, and T. D. Byram 2003. Determination of the minimum number of stool bed ortets required to capture a desirable genotype from full-sib family crosses. Southern Journal of Applied Forestry 27(3): 160-206.

McKeand, S., T. Mullin, T Byram, and T White. 2003. Deployment of genetically improved loblolly and slash pine in the south. J. For. 101(3): 32-37.

Gwaze, D.P., F.E. Bridgwater, T.D. Byram and W.J. Lowe. 2001. Genetic parameter estimates for growth and wood density in loblolly pine (Pinus taeda L,). Forest Genetics 8: 44-57.

Williams, C.G. and T.D. Byram. 2001 Forestry’s third revolution: Integrating biotechnology into Pinus taeda L. breeding programs. Southern Journal of Applied Forestry. 25(3): 116-121.

Gwaze, D.P., F.E. Bridgwater, T.D. Byram, J.A. Woolliams and C.G. Williams. 2000. Predicting age-age genetic correlations: a case study with Pinus taeda L. Theoretical and Applied Genetics 100:199-206.

Byram, T.D., W. J. Lowe, and G.D. Gooding. 2000. Western Gulf Forest Tree Improvement Program gene conservation plan for loblolly pine. Forest Genetic Resources 27:55-59.

Lowe, W.J., T.D. Byram and F.E. Bridgwater. 1999. Selecting loblolly pine parents for seed orchards to minimize the cost of producing pulp. Forest Science 45(2): 213-216.

Byram, T.D., J.W. Richardson, and W.J. Lowe. 1999. Predicting seed yields from loblolly pine seed orchards: A simulation approach using TImpSim. Southern Journal of Applied Forestry 23(2): 117-123.

Bridgwater, F.E., D.L. Bramlett, T.D. Byram, and W.J. Lowe. 1998. Controlled mass-pollination in loblolly pine to increase genetic gains. The Forestry Chronicle. 74(2):185-189.

Byram, T.D. and W.J. Lowe. 1988. Specific gravity variation in a loblolly pine seed source study in the Western Gulf Region. Forest Sci. 34(3):798-803.

PHS 398/2590 (Rev. 09/04) Page 2 Continuation Format Page Program Director/Principal Investigator: CAI, James J.

NAME POSITION TITLE Cai, James Jing Assistant Professor eRA COMMONS USER NAME (credential, e.g., agency login) Texas A&M Univ. JAMESCAI DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) Henan Medical Univ., China B.S. 08/96 General Medicine Univ. of New South Wales, Australia M.S. 05/02 Biotechnology Univ. of Hong Kong, Hong Kong Ph.D. 08/06 Fungal Genomics Stanford Univ., USA Post-Doc 08/10 Population Genomics

A. Positions and Honors

Positions and Employment 1996-1998 Research Scientist, Institute of Biological Research, Henan Academy of Sciences, China 1999-2002 System Analyst & Programmer, Viper Communications Group Ltd. Co., Sydney, Australia 2002-2002 Research Associate, HKU-Pasteur Research Institute, Hong Kong 2005-2006 Cheung Kong Research Fellow, Australian National Univ., Canberra, Australia 2006-2010 Postdoctoral Fellow, Department of Biology, Stanford Univ., Stanford, CA 2010-Present Assistant Professor, Dept. of Veterinary Integrative Biosciences, Texas A&M Univ., TX

Other Experience and Professional Memberships 2004-Present Member, Society for Molecular Biology and Evolution (SMBE) 2011-Present Associate Editor, Frontiers in Genetics (ISSN 1664-8021) 2011-Present Editorial Board, Genomics, Proteomics & Bioinformatics (ISSN 1672-0229)

B. Selected Peer-reviewed Publications (Selected from 33 publications, *Corresponding author) 1. Wang G, Yang E, Smith KJ, Zeng Y, Ji G, Connon R, Fangue NA, Cai JJ* (2014) Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension. Frontiers in Genetics, 5:312 doi: 10.3389/fgene.2014.00312 2. Yang E, Chow WN, Wang G, Woo PCY, Lau SKP, Yuen KY, Lin X, Cai JJ* (2014) Signature gene expression reveals novel clues to the molecular mechanisms of dimorphic transition in Penicillium marneffei. PLoS Genetics, doi:10.1371/journal.pgen.1004662 3. Wang G, Yang E, Brinkmeyer-Langford CL, Cai JJ* (2014) Additive, epistatic, and environmental effects through the lens of expression variability QTLs in a twin cohort. Genetics, 196:413-25 4. Wang G, Yang E, Mandhan I, Brinkmeyer-Langford CL, Cai JJ* (2014) Population-level expression variability of mitochondrial DNA-encoded genes in humans. European Journal of Human Genetics, 1-7 5. Konganti K, Wang G, Yang E, Cai JJ* (2013) SBEToolbox: a Matlab toolbox for biological network analysis. Evolutionary Bioinformatics, 9:1-8 6. Hulse AM, Cai JJ* (2013) Genetic variants contribute to gene expression variability in humans. Genetics, 193(1):95-108 7. Cai JJ* (2011) Evolutionary bioinformatics with a scientific computing environment. Systems and Computational Biology - Bioinformatics and Computational Modeling Ning-Sun Yang (Ed.), 51-74, ISBN 978-953-307-875-5, InTech. 8. Chang CL, Cai JJ, Park JI, Lo C, Amigo J, Cheng PJ, Chueh HY, Hsu SYT (2011) Adaptive selection of an incretin gene in Eurasian populations. Genome Research, 21(1):21-32 9. Cai JJ*, Borenstein E, Petrov DA (2010) Broker genes in human disease. Genome Biology and Evolution, 2:815-25 10. Cai JJ, Macpherson M, Sella G, Petrov DA (2009) Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genetics, 5(1):e1000336 Principal Investigator/Program Director (Last, First, Middle): CASOLA, Claudio

NAME POSITION TITLE Casola, Claudio Assistant Professor eRA COMMONS USER NAME ccasola EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of Pisa, Italy M.S. 1992-2001 Biology University of Pisa, Italy Ph.D. 2002-2006 Molecular Biotechnology Postdoctoral University of Texas Arlington, TX 2006-2007 Evolutionary Genomics Training Postdoctoral Indiana University, Bloomington , IN 2007-2012 Evolutionary Genomics Training

A. Positions and Honors

Employment

2006-2007 Postdoctoral Research Associate, University of Texas Arlington, TX 2007-2012 Postdoctoral Research Associate, Indiana University, Bloomington , IN 2012-2013 Assistant Professor, Saint Louis University, St. Louis, MO 2014-present Assistant Professor, Texas A&M University Member, Faculty of Genetics Member, Faculty of Molecular & Environmental Plant Sciences Member, Faculty of Ecology and Evolutionary Biology

Other Experience and Professional Memberships

The Society for Molecular Biology & Evolution (SMBE)

B. Selected peer-reviewed publications

Carbone L, 99 more authors [Casola C, contributing author] (2014) “Gibbon genome and the fast karyotype evolution of small apes”. Nature 513:195-201.

Worley K, 110 more authors [Casola C, contributing author] (2014) “The Common Marmoset Genome Provides Insight into Primate Biology and Evolution”. Nat Genet 46:850-7.

Casola C, Conant GC, Hahn MW (2012) “Very low rate of gene conversion in the yeast genome”. Mol Biol Evol 29:3817-26.

Casola C, Zekonyte U, Phillips AD, Cooper DN, Hahn MW (2012) “Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease”. Genome Res 22:429-35.

Emera D, Casola C, Lynch VJ, Wildman D, Agnew D, Wagner GP (2012) “Independent origin of alternative promoters for uterine PRL expression in the human and elephant lineage: the role of lineage specific transposable elements”. Mol Biol Evol 29:239-47. PHS 398/2590 (Rev. 09/04) Page 1 Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle): CASOLA, Claudio

Colbourne JK, 66 more authors [Casola C, contributing author] (2011) “The expansive genome of Daphnia pulex with environment-dependent gene regulation”. Science 331:555-61.

Locke DP, 104 more authors [Casola C, contributing author] (2011) “Comparative and demographic analysis of orangutan genomes”. Nature 469:529-533.

Casola C, Ganote CL, Hahn MW (2010) “Non-allelic gene conversion in the genus Drosophila”. Genetics 185:95-103.

Casola C, Hahn MW (2009) “Gene conversion among paralogs results in moderate false detection of positive selection using likelihood methods”. J Mol Evol 68:679-87.

Han MV, Demuth JP, McGrath CL, Casola C, Hahn MW (2009) “Adaptive evolution of young gene duplicates in mammals”. Genome Res 19:859-67.

McGrath CL, Casola C, Hahn MW (2009) “Minimal effect of ectopic gene conversion in four mammalian genomes”. Genetics 182:615-22.

Casola C, Hucks D, Feschotte C (2008) “Convergent domestication of pogo-like transposases into centromere-binding proteins in fission yeast and mammals”. Mol Biol Evol 25:29-41.

Lin R, Ding L, Casola C, Ripoll DR, Feschotte C, Wang H (2007) “Transposase-derived transcription factors regulate light signaling in Arabidopsis”. Science 318:1302-5.

Casola C, Lawing AM, Betrán E, Feschotte C (2007) “PIF-like transposons are common in Drosophila and have been repeatedly domesticated to generate new host genes”. Mol Biol Evol 24:1872-88.

Bai Y, Casola C, Feschotte C and Betrán E (2007) “Constant rate of origination and convergent acquisition of functional retrogenes in Drosophila”. Genome Biol 8:R11.

PHS 398/2590 (Rev. 09/04) Page 2 Continuation Format Page Program Director/Principal Investigator: CHAPKIN, Robert S.

BIOGRAPHICAL SKETCH

NAME POSITION TITLE Chapkin, Robert S Distinguished Professor, Regents Professor and University Faculty Fellow eRA COMMONS USER NAME Robert_S_Chapkin

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of Guelph, Ontario, Canada B.Sc. 1981 Nutrition & Biochemistry University of Guelph, Ontario, Canada M.Sc. 1983 Nutrition University of California - Davis Ph.D. 1986 Nutr. & Physiol. Chemistry University of California - Davis Post-doc 1986-88 Cell Biology

A. Personal Statement: Dr. Chapkin is an expert in environmental modulators related to chemoprevention of colon cancer and chronic inflammatory diseases, e.g., inflammatory bowel disease. He has been continuously funded by NIH for the past 25 years and has made highly significant contributions in cancer chemoprevention and T cell/inflammation biology with specific emphasis in: (i) elucidation of signal transduction processes in intestinal stem cells, (ii) membrane biology and nutritional modulation of epithelia/immune cell membrane structure and function, (iii) investigation of the role of inflammation as a critical factor in cancer development, and its modulation by environmental agents, (iv) establishment of models for chronic inflammation and cancer prevention studies, and (v) development of novel noninvasive Systems Biology-based methodologies to assess crosstalk between the gut microbiome and the host transcriptome and its application to translational research. These activities, together with a history of basic and translational (biomarkers) research using cutting-edge genomics and computational biology methodologies, demonstrate that Dr. Chapkin has the scientific credentials necessary to contribute to this proposal. Dr. Chapkin serves as the Deputy Director of the – the P30 NIEHS sponsored Texas A&M Center for Translational Environmental Health Research (CTEHR).

B. Positions and Honors: 1986-1988: Postdoctoral Fellow, Immunology-Tumor Biology Laboratory, Department of Cell Biology and Human Anatomy, School of Medicine, University of California-Davis. 1988-1993: Assistant Professor, Human Nutrition, Center for Environmental and Rural Health, Texas A&M University. 1991-1992: Pew National Nutrition Program Faculty Scholar. 1996: American Society for Nutrition (ASN) Bio Serv Award in Experimental Animal Nutrition. 1994-1999: Associate Professor, Department of Veterinary Integrated Biosciences and Faculty of Nutrition. 1999-Present: American Institute for Cancer Research Grant Review Panel 1999-Present: Professor, Nutrition, Center for Environmental and Rural Health (CERH), Texas A&M University. 2000: Texas A&M Faculty Fellow Award 2001-2006: Texas A&M University Faculty Fellow Scholar 2002-2005: Chair, Intercollegiate Faculty of Nutrition, Texas A&M University 2002-2004: Editorial Board, Journal of Nutrition 2002-2005: NIH Charter Member: Metabolic Pathology/Chemo-Dietary prevention (CDP) Study Sections 2004-2010: Member, Division Hematol./Oncology, Scott & White Hospital, Texas A&M Health Sci. Center. Co-Director, Genomics and Systems Biology Facility Core, Texas A&M University. 2005-Present: Editorial Board, Chemistry & Physics of Lipids 2005-2010: Director of the P30 NIEHS CERH Genomics & Bioinformatics Core, Texas A&M University 2006: Sigma Xi Distinguished Scientist Award, Texas A&M University Chapter 2007: Texas A&M Senior Faculty Fellow Award 2010-Present: Regents Professor, Texas A&M University System 2010-Present: Editorial Board, British Journal of Nutrition 2011: Distinguished Achievement Award – Association of Former Students, Texas A&M University 2011-2013: Review Editor – Frontiers in Nutrigenomics

2012-Present: Deputy Director – Center for Translational Environmental Health Research, Texas A&M University and Baylor College of Medicine 2012-Present: co-Director – Quantitative Biology Core - Center for Translational Environmental Health Research, Texas A&M University and Baylor College of Medicine 2013: American Society for Nutrition (ASN) Osborne and Mendel Award 2014-Present: Distinguished Professor, Texas A&M University System

C. SELECTED (15) PEER REVIEWED PUBLICATIONS FROM A TOTAL OF 229:

Most relevant to the current application: C. Zhao, I. Ivanov, E.R. Dougherty, T.J. Hartman, E. Lanza, N.H. Colburn, J.R. Lupton, L.A. Davidson, R.S. Chapkin. Non-invasive detection of candidate molecular biomarkers in subjects with a history of insulin resistance and colorectal adenomas. Cancer Prevent Res 2:590-597, 2009. PMCID: PMC2745241 L.A. Davidson, N. Wang, I. Ivanov, J. Goldsby, J.R. Lupton, R.S. Chapkin. Identification of actively translated mRNA transcripts in a rat model of early stage colon carcinogenesis. Cancer Prevent Res 2:984-994, 2009. PMCID: PMC2783859 L.A. Davidson, N. Wang, M.S. Shah, I. Ivanov, J.R. Lupton, R.S. Chapkin. n-3 polyunsaturated fatty acids modulate carcinogen-directed non-coding microRNA signatures in rat colon. Carcinogenesis 30:2077-2084, 2009. PMCID: PMC2792315 R.S. Chapkin, C. Zhao, I. Ivanov, L.A. Davidson, J.S. Goldsby, J.R. Lupton, R.A. Mathai, M.H Monaco, D. Rai, M. Russell, S.M. Donovan, E.R. Dougherty. Non-invasive stool-based detection of infant gastrointestinal development using gene expression profiles from exfoliated epithelial cells. Am J Physiol 298:G582-G589, 2010. PMCID: PMC2867429 M. Shah, S.L. Schwartz, C. Zhao, L.A. Davidson, B. Zhou, J.R. Lupton, I. Ivanov, R.S. Chapkin. Integrated microRNA and mRNA expression profiling in a rat colon carcinogenesis model: Effect of a chemoprotective diet. Physiol Genomics 43:640-654, 2011. PMID:21406606 J.M. Monk, W. Kim, E. Callaway, W. He, B. Weeks, R.C. Alaniz, D.N. McMurray, R.S. Chapkin. Immunomodulatory action of dietary fish oil and targeted deletion of intestinal epithelial cell PPARδ in inflammation-induced colon carcinogenesis. Am J Physiol 302:G153-G167, 2012. PMID:21940900 L.A. Davidson, J.S. Goldsby, E.S. Callaway, N. Barker, R.S. Chapkin. Alteration of colonic stem cell signatures during the regenerative response to injury. Biochmicia et Biophysica Acta-Molec Basis Dis 1822:1600-1607, 2012. PMID: 22750333 H.F. Turk, R. Barhoumi, R.S. Chapkin. Alteration of EGFR spatiotemporal dynamics suppresses signal transduction. PLoS One 7(6):e39682 PMCID: PMC3384615 J.M. Monk, T.Y. Hou, H.F. Turk, B. Weeks, C. Wu, D.N. McMurray, R.S. Chapkin.. Dietary n-3 polyunsaturated fatty acids (PUFA) decrease obesity-associated Th17 cell-mediated inflammation during colitis. PLoS One 7(11)e49739, PMCID:PMC3500317 S. Schwartz, I. Friedberg, I.V. Ivanov, L.A. Davidson, J.S. Goldsby, D.B. Dahl, D. Herman, M. Wang, S.M. Donovan, R.S. Chapkin. A Metagenomic study of diet-dependent interaction between gut microflora and host in infants reveals differences in developmental and immune responses. Genome Biology 13:R32 doi:10.1186/gb-2012-13-4-r32. PMID: 22546241 K. Triff, K. Konganti, S. Gaddis, B. Zhou, I. Ivanov and R.S. Chapkin. Genome wide analysis of the rat colon reveals site- specific differences in histone modifications and proto-oncogene expression. Physiological Genomics 45:1229-1243, 2013. PMID:24151245 Y.Y. Fan, L.A. Davidson, E.S. Callaway, J.S. Goldsby and R.S. Chapkin. Differential effects of 2 and 3-series prostaglandins on in vitro expansion of Lgr5+ intestinal stem cells. Carcinogenesis 35:606-612, 2014. PMID:24336194 U.H. Jin, S.O. Lee, G. Sridharan, K. Lee, L.A. Davidson, A. Jayaraman, R.S. Chapkin, R. Alaniz and S. Safe. Microbiome-derived tryptophan metabolites and their aryl hydrocarbon receptor-dependent agonist and antagonist activities. Molecular Pharmacology 85:777-788, 2014. PMID:24563545. J.M. Knight, L.A. Davidson, D. Herman, C.R. Martin, J.S. Goldsby, I.V. Ivanov, S.M. Donovan and R.S. Chapkin. Non- invasive analysis of intestinal development in premature and full term infants using RNA-Sequencing. Scientific Reports Nature 4:5453; DOI:10.1038/srep05453 (2014). PMID:24965658 S.M. Donovan, M. Wang, M.H. Monaco, C.R. Martin, L.A. Davidson, I. Ivanov and R.S. Chapkin. Noninvasive molecular fingerprinting of host microbiome interaction in neonates. FEBS Letters (In Press). PMID:25042036.

Principal Investigator/Program Director (Last, First, Middle):CIRILLO, Jeffrey D.

NAME POSITION TITLE Cirillo, Jeffrey D. Professor of Microbial Pathogenesis & Immunology eRA COMMONS USER NAME jcirillo EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Pitzer College, Claremont, CA B.A. 1986 Biology/Chemistry Albert Einstein College of Medicine M.S. 1989 Biological Sciences Albert Einstein College of Medicine Ph.D. 1992 Microbiol. & Immunol. Stanford University School of Medicine Postdoc 1992-95 Microbiol. & Immunol. (Mentors - Stanley Falkow and Lucy Tompkins) A. Positions and Honors Positions and Employment 1992 - 95 Postdoctoral Fellow, Dept. Micro. & Immuno., Stanford University, Stanford, CA 1995 - 97 Assistant Professor, Dept. Microbiology, University of Hawaii, Honolulu, HI 1998 - 2001 Assistant Professor, Dept. Vet. & Biomedical Sci., University of Nebraska, Lincoln, NE 2001 - 05 Associate Professor, Dept. Vet. & Biomedical Sci., University of Nebraska, Lincoln, NE 2005 - 09 Associate Professor, Micro. & Mol. Path., Texas A&M Coll. Med., Coll. Station, TX 2007 - present Director, Center for Airborne Pathogens Res. & Tuberculosis Imaging Resources. 2009 - present Professor, Micro. & Mol. Path. Texas A&M Coll. Med., Coll. Station, TX 2010 - present Director, Small Animal Model Vaccines and Pathogenesis (SAMVAP), Texas A&M University System, College Station, TX. Selected Other Experience and Professional Memberships 2009 NIH/NIAID Panel Member, Special Emphasis Panel, ZRG1 IMM-E 58 R 2010 NIH/NHLBI Panel Member, Special Emphasis Panel RFA-HL-10-015, HL-10-022 2011 – present Editorial Board, The Journal of Infectious Diseases 2011 – present Editorial Board, Applied and Environmental Microbiology 2011 NIH/NIAID Panel Member, Study Section, “Host Interactions with Bacterial Pathogens” 2012 DOD/DMRDP Panel Member, Review Panel, “AR-Military Infectious Diseases” Honors 1999 Junior Faculty Recognition for Excellence in Research 2000 Dinsdale Family Faculty Award for Excellence in Research 2010 Excellence in Innovation Award, Texas A&M University System 2010 Technology Innovation (TIEP) Award, Qatar Science & Technol. 2011 Senior Faculty Recognition for Excellence in Research 2011 Outstanding Service Online Mentor, ASM Minority Program 2014 Frost & Sullivan, Global Imp. Healthcare Access Visionary Innovation Leadership Award B. Selected 15 Most Relevant Publications (out of >90 papers; 5 book chapters and 40+ abstracts) 1. R.G. Barletta, S.B. Snapper, J.D. Cirillo, N.D. Connell, D.D. Kim, W.R. Jacobs, Jr., and B.R. Bloom (1990). Recombinant BCG as a Candidate Oral Vaccine Vector. Res. Microbiol. (Institut Pasteur) 141:931-939. 2. J.D. Cirillo, C.K. Stover, B.R. Bloom, W.R. Jacobs, Jr., R.G. Barletta (1995). Recombinant Bacterial Vaccines and Bacille Calmette-Guerin (BCG). Clin. Infect. Dis. 20:1001-1009. PMID: 7795044 3. L. Danelishvili, M. Wu, B. Stang, M. Harriff, S.L.G. Cirillo, J.D. Cirillo, R. Bildfell, B. Arbogast, L.E. Bermudez 2007. Identification of Mycobacterium avium pathogenicity island important for macrophage and amoeba infection. PNAS 104:11038-11043. PMCID: PMC1904132. 4. C. Attila, A. Ueda, S.L.G. Cirillo, J.D. Cirillo, W. Chen and T.K. Wood (2008). Pseudomonas aeruginosa PA01 virulence factors and poplar tree response in the rhizosphere. Microb. Biotech. 1:17- 29. PHS 398/2590 (Rev. 06/09) Page Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle):CIRILLO, Jeffrey D. 5. S.L.G. Cirillo, S. Subbian, B. Chen, T.R. Weisbrod, W.R. Jacobs, Jr., J.D. Cirillo 2009. Protection of Mycobacterium tuberculosis from reactive oxygen species conferred by the mel2 locus impacts persistence and dissemination. Infect. Immun. 77:2557-2567. PMCID: PMC2687327. 6. M. Khounlotham, S. Subbian, R. Smith III, S.L.G. Cirillo, J.D. Cirillo (2009). Mycobacterium tuberculosis modulates the host response to infection through the murine EphA2 receptor. J. Infect. Dis. 199:1797-1806. PMCID: PMC2687327. 7. Y. Kong, H. Yao, H. Ren, S. Subbian, S.L.G. Cirillo, J.C. Sacchettini, J. Rao, J.D. Cirillo 2010. Imaging tuberculosis with endogenous β-lactamase reporter enzyme fluorescence. PNAS 107:12239-12244. PMCID: PMC2901431. 8. Y. Kong, J.D. Cirillo (2010). Reporter enzyme fluorescence (REF) imaging and quantification of tuberculosis in live animals. Virulence. 1(6):558-562. PMCID: PMC3073363. 9. L. Alibaud, Y. Rombouts, X. Trivelli, A. Burguiere, S.L.G. Cirillo, J.D. Cirillo, J.-F. Dubremetz, Y. Guerardel, G. Lutfalla, L. Kremer (2011). A Mycobacterium marinum mutant defective for major cell wall associated lipids is highly attenuated in Dictyostelium discoideum and zebrafish embryos. Mol. Microbiol. 80:919-934. PMID:21375593 10. R. Kapoor, P.R. Eimerman, J.W. Hardy, J.D. Cirillo, C.H. Contag, A.E. Barron (2011). Efficacy of antimicrobial peptoids against Mycobacterium. Antimicrob. Agents Chemother. 55:3058-3062. PMID:21464254. 11. H.K. Janagama, H. Hassounah, S.L.G. Cirillo, J.D. Cirillo (2011). Random inducible controlled expression (RICE) for identification of mycobacterial virulence genes. Tuberculosis. 91:S66-S68. PMCID: in process. 12. Y. Zhou, Y. Kong, S. Kundu, J.D. Cirillo, H. Liang (2012). Antibacterial activities of gold and silver nanoparticles against Escherichia coli and bacillus Calmette-Guérin. J. Nanobiotech. 10:19. PMCID: PMC3405418. 13. H. Xie, J. Mire, Y. Kong, M.H. Chang, H.A. Hassounah, C.N. Thornton, J.C. Sacchettini, J.D. Cirillo, J. Rao (2012). Designing BlaC-specific probes for rapid fluorescence detection of tuberculosis. Nature Chem. 4:802-809. PMID:23000993. 14. V.E. Calderon, G.A. Valbuena, Y. Goez-Rivillas, B.M. Judy, M.B. Huante, P. Sutjita, R.K. Johnston, D.M. Estes, R.L. Hunter, J. Actor, J.D. Cirillo, J.J. Endsley (2013). A humanized mouse model of tuberculosis. PLoS One. 8:e63331. PMCID: PMC3656943. 15. Y. Zheng, T. Sambou, J.D. Cirillo, M. McClelland, H. Andrews-Polymenis (2013). EAL-domain containing protein STM2215 (rtn) is a cyclic di-GMP phosphodiesterase that is needed during Salmonella infection. Mol. Microbiol. June 5, Epub ahead of print. PMID:23734719. C. Research Support Ongoing Research Support Animal Models of Infectious Diseases PI: Jeffrey D. Cirillo Type: Contract HHSN2722010000241 Period: 03/22/10-03/21/17 The objectives of this contract are to provide services under contract to NIH for investigators who wish to utilize animal models for the study of infectious disease virulence mechanisms, vaccines and therapeutics.

Application of Imaging to Development of Tuberculosis Interventions PI: Jeffrey D. Cirillo Type: R01 (AI104960) Period: 03/01/13-02/28/19 The objectives of this project are to improve imaging strategies for tuberculosis research and use imaging to evaluate vaccine efficacy.

Real-time Optical Imaging Solutions for Tuberculosis Infections PI: Jeffrey D. Cirillo Type: Grant, Bill & Melinda Gates Foundation Period: 12/01/07-04/01/15 The objectives of this project are to develop novel real-time imaging technologies to allow visualization of tuberculosis infections directly in live animals.

PHS 398/2590 (Rev. 06/09) Page Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle): COATES, Craig, J.

NAME POSITION TITLE Coates, Craig, J. Assistant Professor eRA COMMONS USER NAME cjcoates EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Australian National University, Canberra, Biochemistry and B.Sc. (Hons) 1988-1991 Australia Molecular Biology Australian National University, Canberra, Biochemistry and Ph.D. 1992-1996 Australia Molecular Biology Postdoctoral University of California, Irvine, Irvine, California 1996-1998 Insect Molecular Biology Training

A. Positions and Honors

Employment

1996-1998 Postdoctoral Research Associate, UCI, Irvine California 1999 - 2005 Assistant Professor, Texas A&M University 2005 - Associate Professor, Texas A&M University Member, Faculty of Genetics Member, Faculty of Biotechnology

Other Experience and Professional Memberships

March 2005 Chair, Session VI at the 4th International Workshop on Transgenesis and Genomics of Invertebrate Organisms June 2005 Study Section Member, NIH - IDM-M July 2005 Study Section Member, NIH – VB

Entomological Society of America (ESA)

Honors

2002 Texas A&M University Center for Teaching Excellence Montague Scholar

B. Selected peer-reviewed publications (Postdocs and Graduate Students as shown)

Jasinskiene, N., C.J. Coates, A. Ashikyan and A.A. James (2003). High efficiency, site-specific excision of a marker gene by the phage P1 cre-loxP system in the yellow fever mosquito, Aedes aegypti. Nucleic Acids Res. 31: e147.

O’Brochta, D.A., N. Sethuraman, R. Wilson, R.H. Hice, A.C. Pinkerton, C.S. Levasque, D.K. Bideshi, N. Jaskinskiene, C.J. Coates, A. A. James, M.J. Lehane and P.W. Atkinson (2003). Gene vector and transposable element behavior in mosquitoes. Journal of Experimental Biology, 206: 3823-3834.

Tu, Z. & Coates, C.J. (2004) Mosquito Transposable Elements. Insect Biochem. Mol. Biol. 34:631-44. PHS 398/2590 (Rev. 09/04) Page Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle): COATES, Craig, J.

Cônsoli, F.L., Tian, H., Vinson, S.B. and Coates, C.J.* (2004) Differential gene expression during wing morph differentiation of the ectoparasitoid Melittobia digitata (Hym., Eulophidae). Comp. Biochem. Physiol. A. Mol. Integr. Physiol. 138: 229-39.

Tian, H., Vinson, S.B., and Coates, C.J.* (2004) Differential gene expression between alate and dealate queens in the red imported fire ant, Solenopsis invicta Buren (Hymenoptera: Formicidae) Insect Biochemistry and Molecular Biology 34: 937-49.

Pledger, D.W., Fu, Y.Q. and Coates, C.J.* (2004) Analyses of cis-acting elements that affect the transposition of MosI mariner transposons in vivo. Molecular Genetics and Genomics 272: 67-75

Gray, C. and Coates, C.J.* (2004) High-level gene expression in Aedes albopictus cells using a baculovirus Hr3 enhancer and IE1 transactivator. BioMed Central 5: 8.

Mohammed, A. and Coates, C.J. (2004) Promoter and piggyBac activities within embryos of the potato tuber moth, Phthorimaea operculella, Zeller (Lepidoptera: Gelechiidae). Gene, 342: 293-301.

Chowdhury, M.H., Julian, A.M., Coates, C.J. and Cote, G.L. (2004) Detection of differences in oligonucleotide influenced aggregation of colloidal gold nanoparticles using absorption spectroscopy. Journal of Biomedical Optics, 9: 1347-1357.

Adelman, Z.N., Jasinskiene, N., Vally, K.J.M., Peek, P., Travanty, E.A., Olson, K.E., Brown, S.E., Stephens, J.L., Knudson, D.L., Coates, C.J. and James, A.A. (2004) Formation and loss of large, unstable tandem arrays of the piggyBac transposable element in the yellow fever mosquito, Aedes aegypti. Transgenic Research 13:411-25.

Gray, C.E. & Coates, C.J. (2005) Cloning and characterization of cDNAs encoding putative CTCFs in the mosquitoes, Aedes aegypti and Anopheles gambiae. BMC Molecular Biology 6:16

Pledger, D.W. & Coates, C.J. (2005) Mutant MosI mariner transposons are hyperactive in Aedes aegypti. Insect Biochem. Mol. Biol.,35:1199-207

Li, H., Medina, F., Vinson, S.B. & Coates, C.J. (2005) Isolation, Characterization and Molecular Identification of Bacteria from the Red Imported Fire Ant (Solenopsis invicta) Midgut. Journal of Invertebrate Pathology 89:203-9

Li, H., Medina, F., Vinson, S.B. & Coates, C.J. (in press) Genetic Transformation of Midgut Bacteria from the Red Imported Fire Ant (Solenopsis invicta). Current Microbiology.

Kolb, A.F., Coates, C.J., Kaminski, J.M., Summers, J.B., Miller, A.D. & Segal, D.J. (2005) Site-directed genome modification: nucleic acid and protein modules for targeted integration and gene correction. Trends in Biotechnology 23:399-406

Coates, C.J., Kaminski, J.M., Summers, J.B, Segal, D.J., Miller, A.D., & Kolb, A.F. (2005) Site-directed genome modification: derivatives of DNA modifying enzymes as targeting tools. Trends in Biotechnology 23:407-19

Maragathavally, K.J., Kaminski, J.M., Coates, C.J. (2006) Chimeric Mos1 and piggyBac transposases result in site-directed integration. FASEB J. 20:1880-2.

PHS 398/2590 (Rev. 09/04) Page Continuation Format Page Principal Investigator (Cohen, Noah D.) BIOGRAPHICAL SKETCH Provide the following information for collaborators listed on this application. Follow this format for each person. DO NOT EXCEED TWO PAGES NAME POSITION TITLE Dr. Noah D. Cohen Professor and Associate Department Head for Research and Graduate Studies

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of Pennsylvania, Philadelphia, PA A.B 1979 Oriental Studies/Biology Univ ersity of Pennsylvania, Philadelphia, PA V.M.D. 1983 Veterinary Medicine Johns Hopkins University, Baltimore, MD M.P.H. 1986 Epidemiology Johns Hopkins University, Baltimore, MD Ph.D. 1988 Epidemiology

Texas A&M University, College Station, TX Residency 1989-1991 Large Animal Medicine

A. Positions and Honors. POSITIONS 1991-1997 Assistant Professor, Department of Large Animal Medicine & Surgery College of Veterinary Medicine, Texas A&M University, College Station, Texas 1998-2003 Associate Professor, Department of Large Animal Medicine & Surgery College of Veterinary Medicine, Texas A&M University, College Station, Texas 2004-Present Professor, Department of Large Animal Clinical Sciences College of Veterinary Medicine, Texas A&M University, College Station, Texas 2012-Present Associate Department Head for Research and Graduate Studies Department of Large Animal Clinical Sciences College of Veterinary Medicine & Biomedical Sciences Texas A&M University, College Station, Texas

HONORS & AWARDS 1977-1979 Dean's List, University of Pennsylvania 1979 Zion Award, Department of Oriental Studies, University of Pennsylvania 1979 A.B. Magna Cum Laude, University of Pennsylvania 1983 Pennsylvania Veterinary Medical Auxiliary Award for Excellence in Large Animal Clinics, School of Veterinary Medicine, University of Pennsylvania 1991 Texas Veterinary Medical Association Auxiliary Clinical Resident Award, College of Veterinary Medicine, Texas A&M University 1995 John H. Milliff Award, College of Veterinary Medicine, Texas A&M University 1997 Society of Phi Zeta (Veterinary Honor Society), Texas A&M University 2001 Pfizer Award for Excellence in Research, Texas A&M University 2002 Texas Veterinary Medical Association Research Award 2002 John Hickman Memorial Lecture, British Equine Veterinary Association 2002 Faculty Fellow Award, Texas A&M University 2008 World Equine Veterinary Association/Schering-Plough Applied Equine Research Award 2008 Honorary Diplomate, American Veterinary Epidemiology Society 2011 Frank J. Milne Honorary Lecture, American Association of Equine Practitioners 2013 Texas A&M University Distinguished Service Award for Research 2013 Keynote Speaker, Veterinary Research Symposium, College of Veterinary Medicine, University of Georgia

CPRIT Research Programs (Rev 5/10/10) Biographical Sketch p.1/2 Principal Investigator (Cohen, Noah D.)

B. Selected (from 225) peer-reviewed publications, in chronological order (earliest to recent). Cohen ND, Munoz A, Reitz BA, et al. Transmission of retroviruses by transfusion in patients undergoing cardiac surgery. New Engl J Med 1989; 320:1172-6. Nelson KE, Donahue JG, Munoz A, Cohen ND, et al. Transmission of retroviruses from seronegative donors by transfusion during cardiac surgery. Ann Int Med 1992; 117:554-559. Cohen ND, Neibergs HL, Wallis DE, et al. Genus-specific detection of salmonellae in equine feces using the polymerase chain reaction (PCR). Am J Vet Res 1994; 8:1049-1054. Cohen ND, Carter GK, Mealey RH, Taylor TS. Medical management of right dorsal colitis in 5 horses (1987- 1993). J Vet Int Med 1995; 9:272-276. Pokorny R, Hofmeister A, Galandiuk S, Dietz A, Cohen ND, Neibergs HL. Crohn's disease and ulcerative colitis are associated with the DNA repair gene MLH1. Annals Surg 1997; 225:718-725. Cole DJ, Cohen ND, Snowden KJ, et al. Prevalence of and risk factors for fecal shedding of Cryptosporidium parvum oocysts in horses. J Am Vet Med Assoc 1998;213: 1296-1302. Cohen ND, Gibbs P, Woods AM. Dietary and other management factors associated with equine colic in Texas. J Am Vet Med Assoc 1999;215:53-60. Kim I, Cohen ND, Carrol RJ. Graphical representation of effect modification by a matched covariate in matched case-control studies using data from a study of colic in horses. Am J Epidemiol 2002; 156:463-470. Cohen ND, Harrington J, Gros P, et al. Nramp1 deletion does not confer susceptibility to Rhodococcus equi infection in mice. Immunogenetics 2004;56:65-67. Cohen ND, Lester GD, Sanchez LC, Merritt AM, Roussel AJ. Prospective study of risk factors for postoperative ileus in horses. J Am Vet Med Assoc 2004;225:1070-1078. Martens RJ, Cohen ND, Jones SL, Moore TA, Edwards JF. Protective role of neutrophils in mice experimentally infected with Rhodococcus equi. Infect Immunity 2005;73:740-742. Hewetson M, Cohen ND, Love S, et al. AJ. Sucrose concentration in blood: a new method for assessment of gastric permeability in horses with gastric ulceration. J Vet Int Med 2006;20:388-394. Cohen ND, Toby E, Roussel AJ, Murpehy EL, Wang N. Are feeding practices associated with duodenitis- proximal jejunitis? Equine Vet J 2006; 38(6):526-531. Liu T, Nerren JR, Liu M, Martens RJ, Cohen ND. Basal and stimulus-induced cytokine expression is selectively impaired in peripheral blood mononuclear cells of newborn foals. Vaccine 2009;27:674-683. Liu M, Liu T, Bordin A, Nerren J, Cohen ND. Activation of foal neutrophils at different ages by CpG oligodeoxynucleotides and Rhodococcus equi. Cytokine 2009;48:280-289. Liu M, Bordin AI, Liu T, Russell K, Cohen ND. Gene expression of innate Th1-, Th2-, and Th17-type cytokines during early life of neonatal foals in response to Rhodococcus equi. Cytokine 2011; 56(2):356-364. Furr M, Cohen ND, Sanchez LC, Axon C, et al. Treatment with histamine-type 2 receptor antagonists and omeprazole increase the risk of diarrhoea in neonatal foals. Equine Vet J 2012;44(Suppl 41):80-86. Doan R, Cohen ND, Harrington JR, Vezie KJ, Juras R, Cothran G, McCue M, Skow L, Dindot SV. Identification of copy number variants in horses. Genome Research 2012;22(5):899-907. Kachroo P, Ivanov I, Seabury AG, Liu M, Chowdhary BP, Cohen ND. Age-related changes following in vitro stimulation with Rhodococcus equi of peripheral blood leukocytes from neonatal foals. PLoS ONE 2013 8(5):e62879; doi: 10.1371/journal.pone.0062879 Rossi G, Pengo G, Caldin M, Palumbo Piccionello A, Steiner JM, Cohen ND, Jergens AE, Suchodolski JS. Comparison of microbiological, histological, and immunomodulatory parameters in response to treatment with either combination therapy with prednisone and metronidazole or probiotic VSL#3 strains in dogs with idiopathic inflammatory bowel disease. PLoS One 2014; 9(4):e94699. Levine JM, Cohen ND, Heller M, et al. Efficacy of a metalloproteinase inhibitor in spinal cord-injured dogs. PLos One 2014; 9(5):e96408. McQueen CM, Doan R, Dindot SV, Bourquin JR, Zlatev ZZ, Chaffin MK, Blodgett GP, Ivanov I, Cohen ND. Identification of genomic loci associated with Rhodococcus equi susceptibility in foals. PLoS One 2014; 9(6):e98701

CPRIT Research Programs (Rev 5/10/10) Biographical Sketch p.2/2 Principal Investigator/Program Director CRISCITIELLO, Michael Frederick

BIOGRAPHICAL SKETCH Provide the following information for the key personnel and other significant contributors.

NAME Criscitiello, Michael Frederick POSITION TITLE Assistant Professor of Veterinary Pathobiology

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION (if YEAR(S) FIELD OF STUDY applicable) University of North Carolina, Chapel Hill, NC B.S. 1989-1993 Biology East Carolina University, Greenville, NC M.S. 1995-1997 Molecular Biology Microbiology and University of Miami, Miami, FL Ph.D. 1997-2003 Immunology University of Maryland, Baltimore, MD Postdoctoral 2003-2008 Immunology

The Comparative Immunogenetics Laboratory studies immunology, molecular genetics and evolution. Most of my group’s research focuses on the natural history of the vertebrate adaptive immune system, with particular attention given to the genetics of lymphocyte antigen receptors, mucosal immune mechanisms in the gut and antigen presentation, as well as applied shrimp immunogenomics in mariculture. A focus of my lab has been antigen receptor immunogenetics in aquatic vertebrates, and we are well-poised to investigate the adaptive immune loci of these two manatee species. 2008-present; Assistant Professor in Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University (TAMU) 2008-present; Ecology and Evolutionary Biology Interdisciplinary Research Program (TAMU) 2008-present; Interdisciplinary Faculty of Genetics (TAMU) 2009-present; Whole Systems Genomics Initiative (TAMU) 2010-present; Interdisciplinary Faculty of Toxicology (TAMU) 2010-present; Professional Program in Biotechnology (TAMU) Peer Reviewed Publications from last three years (total n=26, h index=9) Romoser A.A., P.L. Chen, J.M. Berg, C. Seabury, I. Ivanov, M.F. Criscitiello, and C.M. Sayes. “Quantum dots trigger modulation of the NFkappaB pathway in human skin cells”. Molecular Immunology 48:1349- 1359, 2011. PMID: 21481475 Owen, J.L., M.F. Criscitiello, S. Libreros, R. Garcia-Areas, K. Guthrie, M. Torroella-Kouri, and V. Iragavarapu- Charyulu. “Expression of the inflammatory chemokines CCL2, CCL5 and CXCL2 and their receptors CCR1-3 and CXCR2 in T lymphocytes from mammary tumor-bearing mice.” Cellular Immunology 270:172-182, 2011. PMID: 21621198 Criscitiello M.F., Y. Ohta, M.D. Graham, J.O. Eubanks, P.L. Chen, and M.F. Flajnik. “Shark class II invariant chain reveals ancient conserved relationships with cathepsins and MHC class II.” Developmental and Comparative Immunology 36:521-533, 2012. PMID: 21996610 Du, C.C., S.M. Mashoof, and M.F. Criscitiello. “Oral immunization of the African clawed frog (Xenopus laevis) upregulates the mucosal immunoglobulin IgX.” Veterinary Immunology and Immunopathology 145:493- 498, 2012. PMID: 22100190 Principal Investigator/Program Director CRISCITIELLO, Michael Frederick

Romoser A.A., D.E. Figueroa, A. Sooresh, K. Scribner, P.L. Chen, W. Porter, M.F. Criscitiello, and C.M. Sayes. “Distinct immunomodulatory effects of a panel of nanoparticles in human dermal fibroblasts.” Toxicological Letters 210:293-301, 2012. PMID: 22342292 Flajnik, M.F., T. Tlapakova, M.F. Criscitiello, V. Krylov, and Y. Ohta. “Evolution of the B7 family: co-evolution of B7H6 and NKp30, identification of a new B7 family member, B7H7, and of B7’s historical relationship with the MHC.” Immunogenetics 64:571-590, 2012. PMID: 22488247 Pohlenz, C., A. Buentello, M.F. Criscitiello, W. Mwangi, R. Smith, and D. Gatlin. “Synergies between vaccination and dietary arginine and glutamine supplementation improve the immune response of channel catfish against Edwardsiella ictaluri.” Fish and Shellfish Immunology 33:543-551, 2012. PMID: 22728565 Criscitiello, M.F. and P. de Figueiredo. “Fifty shades of immune defense.” PLoS Pathogens 9(2): e1003110, 2013. PMID 2340888 Zimmer, D.B., J.O. Eubanks, D. Ramakrishnan, and M.F. Criscitiello. “Evolution of the S100 family of calcium sensor proteins.” Cell Calcium 53(3):170-9, 2013. PMID: 23246155 Mashoof, S., A. Goodroe, C.C. Du, J.O. Eubanks, N. Jacobs, J.M. Steiner, I. Tizard, J.S. Suchodolski, and M.F. Criscitiello. “Ancient T-independence of mucosal IgX/A: gut microbiota unaffected by larval thymectomy in Xenopus laevis.” Mucosal Immunology 6(2):358-68, 2013. PMID: 22929561 Wang F., D.C. Ekiert, I. Ahmad, W. Yu, Y. Zhang, O. Bazirgan, A. Torkamani, T. Raudsepp, W. Mwangi, M.F. Criscitiello, I.A. Wilson, P.G. Schultz, V.V. Smider. “Reshaping antibody diversity.” Cell (153)6:511-8, 2013. PMID: 23746848 Criscitiello, M.F., M.B. Dickman J.E. Samuel and P. de Figueiredo. “Tripping on acid: trans-kingdom perspectives on biological acids in immunity and pathogenesis.” PLoS Pathogens 9(7):e1003402, 2013. PMID: 23874196 López-Zavala, A.A., J.S. Carrasco-Miranda, K.D. Garcia-Orozco, R. Sugich-Miranda, J.M. Hernandez-Flores, M.F. Criscitiello, Luis G. Brieba, Rogerio R. Sotelo-Mundo and Enrique Rudiño-Piñera. “Crystal structure of shrimp arginine kinase in binary complex with arginine - a molecular view of the phosphagen precursor binding to the enzyme.” Journal of Bioenergetics and Biomembranes 45(6):511- 8, 2013. PMID: 23746848 Mashoof, S.M., C. Pohlenz, P.C. Chen, D. Gatlin, A. Buentello and M.F. Criscitiello. “Expressed IgH µ and τ transcripts share diversity segment in ranched Thunnus orientalis.” Developmental and Comparative Immunology 43(1):76-86, 2014.PMID: 24231183 Romoser, A.A., D.E. Figueroa, M.F. Criscitiello, and C.S. Sayes. “Engineered nanoparticles induce DNA damage in primary human skin cells, even at low doses.” In press at NanoLIFE, accepted September 22, 2013.

Federal Research Support as PI Ongoing Research Support NSF Criscitiello (PI) 2013-2016 Evolution of loci critical in antigen recognition Role: PI $655,000 (to Criscitiello)

INAPESCA Criscitiello (PI) 2011-2015 RNA Sequencing for Annotation of a Reference Genome for Augmentation of Shrimp Disease Resistance (renewal) Role: Co-PI $96,420 (to Criscitiello)

Recently Completed Research Support National Institutes of Health (AI73888) Criscitiello (PI) 2008-2011 Origins of Specialized Mucosal Lymphocyte Subsets and Immunoglobulin Isotypes Role: PI $270,000 (to Criscitiello) Principal Investigator DATTA, Sumana

NAME POSITION TITLE Datta, Sumana Associate Professor of Biochemistry and Biophysics eRA COMMONS USER NAME at Texas A&M University (TAMU)

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of Michigan-Ann Arbor B.Sc. 1980 Molecular & Cell. Biology University of California San Diego Ph.D. 1987 Biology Yale University Postdoc. 1987-1992 Vertebrate Genetics

Personal Statement: Dr. Datta is the Executive Director of Honors and Undergraduate Research at the flagship campus of the Texas A&M system. As such, she organizes the university-wide programs in undergraduate research both during the academic year and during the summer months. The summer research program provides brown bag seminars, GRE prep, discussions of graduate school, presentation skills, and other topics culminating in a poster session to approximately 100-140 students who come to the TAMU campus to carry out summer research projects. There is also a special series of seminars aimed at under-represented minorities that runs weekly during the summer period. Dr. Datta is leading the process of developing and implementing an application process for the University Honors Program, designing a new Honors Distinction and initiating programmatic changes that will take the place of the previous distinctions, facilitating ways for faculty to easily offer Honors opportunities and promoting better communication and coordination between University, College and Departmental Honors Programs. Dr. Datta is a faculty member in Biochemistry and Biophysics as well as Genetics with an active research program for the past 17 years prior to becoming a full-time administrator. In that period, over 50 undergraduates conducted research projects in her laboratory and went on to graduate or professional school as well as positions in various industries.

A. Positions and Honors. Positions and Employment 2010-present Executive Director of Honors and Undergraduate Research, Office of Undergraduate Studies, Texas A&M University 2008-2010 Assistant Dean of Undergraduate Research, Office of Graduate Studies and Office of the Vice President for Research, Texas A&M University 2008-present Associate Professor, Department of Biochemistry and Biophysics, Faculty of Genetics, Texas A&M University 2005-2006 Visiting Professor, Department of Urology, Emory Medical School 1999-2009 Associate Professor, Department of Biochemistry and Biophysics, Department of Biology, Faculty of Genetics, Faculty of Neuroscience, Texas A&M University 1993-1999 Assistant Professor, Department of Biochemistry and Biophysics, Department of Biology, Faculty of Genetics, Faculty of Neuroscience, Texas A&M University

Other Experience and Professional Membership 2013 Society for Neuroscience, member 2003-2013 Genetics Society of America, member 2010-present TAMU Genetics and TAMU Neuroscience (TAMIN) graduate program faculty member. 2003-2005 Pittsburgh Supercomputing Center collaboration to development 3D models of sexually dimorphic neural tissues in C. elegans based on electron micrograph reconstructions. 2003-2005 Co-editor and author of the C. elegans Male Atlas on the wormatlas.org website. PHS 398/2590 (Rev. 09/04) Page 1 Biographical Sketch Format Page Principal Investigator DATTA, Sumana 2003-2007 Contributed chapters to the wormatlas.org hermaphrodite atlas and textbook: “C. elegans Altas” (2008). eds. David H. Hall and Z. Altun. Cold Spring Habor Laboratory Press, NY. 2014-present Collaboration with Jun Kameoka (TAMU Engineering) to develop microfluidic devices for visualizing mitochondria in C. elegans neurons. Honors 1993 Muscular Dystrophy Association of America Fellowship 2000 National Alliance for Schizophrenia and Depression (NARSAD), Young Investigators Award.

B. Selected peer-reviewed publications (in chronological order).

Selected Publications: (bold = undergraduate co-authors)

1. Ferguson, B. and Datta, S. (2011). Stress regulation of 2OST expression in human prostate cancer. In press, Prostate Cancer. 2. Barrett, A., Kreuger, S., Perry, T. L. and Datta, S. (2008). Curable genetic instability of a GAL4 transgene in Drosophila. Fly 2(2): 67-73. 3. Barrett, A., Kreuger, S. and Datta, S. (2008). Bnl and Hedgehog operate in a positive feedback loop to regulate the initiation of neuroblast division in the Drosophila larval brain. Developmental Biology 317: 234-245. 4. Lindner, J., Hillman, P., Barrett, A., Jackson, M., Perry, T., Park, Y. and Datta, S. (2007). The Drosophila Perlecan gene trol regulates multiple signaling pathways in different developmental contexts. BMC Developmental Biology, 7: 121. 5. Datta, M. W., Hernandez, A. M., Schlicht, M., Kahler, A. J., DeGueme, A. M., J., Dhir, R., Shah, R., Farach-Carson, M. C., Barrett, A. and Datta, S. (2006). Perlecan, a candidate gene for the CABP locus, regulates cancer cell growth via the Sonic Hedgehog pathway. Molecular Cancer 5(1): 9. 6. Datta, S. and Datta, M. (2006). Sonic Hedgehog signaling in advanced prostate cancer. Cellular and Molecular Life Sciences, 63:435-448. 7. Sanchez, P., Hernández, A. M., Stecca, B., Kahler, A. J., DeGueme, A. M., Barrett, A., Beyna, M., Datta, M. W., Datta, S. and Ruiz i Altaba, A. (2004). Inhibition of prostate cancer proliferation by interference with Hedgehog-GLI1 signaling. Proc. Natl. Acad. Sci., 101: 12561-12566. 8. Park, Y, Ng, C. and Datta, S. (2003). Induction of String rescues the neuroblast proliferation defect in trol mutant animals. Genesis, 36(4): 187-195. 9. Park, Y., Rangel, C., Reynolds, M., Caldwell. M. C., Johns, M., Nayak, M., Welsh, C. J. R., McDermott, S. and Datta, S. (2003). Drosophila Perlecan modulates FGF and Hedgehog signals to activate stem cell division. Developmental Biology, 253(2): 247-257.

PHS 398/2590 (Rev. 09/04) Page 2 Continuation Format Page

BIOGRAPHICAL SKETCH

NAME Paul de Figueiredo POSITION TITLE Associate Professor eRA COMMONS USER NAME (credential, e.g., agency login) PDEFIGUEIREDO EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) Rice University, Houston TX B.A. 1986 Mathematics & Political Science Stanford, Palo Alto CA M.A. 1989 Religious Studies Cornell, Ithaca NY Ph.D. 1997 Biochemistry, Molecular & Cell Biology MIT, Cambridge MA Postdoc 1998-1999 Vertebrate genetics U. Washington, Seattle WA Postdoc 2000-2005 Microbiology

A. PERSONAL STATEMENT N/A

B. POSITIONS AND HONORS SELECTED RECENT PROFESSIONAL EXPERIENCE 2006 Member, Faculty of Genetics, Texas A&M University 2010 Investigator, Norman Borlaug Center, Texas A&M University 2013 Assoc. Professor, Dept. of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center

SELECTED OTHER EXPERIENCE AND PROFESSIONAL ACTIVITIES 2008, 2010 Panel Member, NSF Integrated and Organismal systems (IOS) 2008-2012 Panel Member, NIH Special Emphasis Panel/Scientific Review Group ZRG1 IDM-A, Intracellular bacterial pathogenesis 2009-2012 Panel Member, NSF Chemical, Bioengineering, Environmental, and Transport Systems (CBET) 2011 Panel Member, CDC-NIH Family History and Diamond Blackfan Anemia 2005-present Member, American Association for the Advancement of Science 2010-present Associate Editor, Frontiers in Cellular and Infection Microbiology 2013-present Associate Editor, Frontiers in Cell and Developmental Biology

C. SELECTED SERVICE TEXAS A&M UNIVERSITY 2006-2013 Co-Director, Research Experience for Undergraduates, Texas A&M Agrilife Research 2008-present Faculty mentor, University Scholars Program 2009-present Faculty Mentor, “Invisible Jungle”, a weekly National Public Radio broadcast 2009-2012 Member, Graduate Student Recruiting Committee, Faculty of Genetics 2009-2012 Member, Curriculum Committee, Biotechnology Program 2012-present Member, Institutional Biosafety Committee 2013-present Member, Faculty of Genetics Graduate Mentoring Committee

D. PUBLICATIONS (30 total, 1 in press, 1 in review) SELECTED RECENT PUBLICATIONS 1. Qin QM, Pei J, Ancona V, Shaw BD, Ficht TA, de Figueiredo P. RNAi screen of endoplasmic reticulum- associated host factors reveals a role for IRE1a in supporting Brucella replication. PLOS PATHOG. 2008 Jul 25;4(7):e1000110 PMID: 18654626 2. Qin, Q, Luo J, Lin X, Pei J, Ficht TA, de Figueiredo P. Functional analysis of host factors that mediate Cryptococcus neoformans intracellular trafficking. PLOS PATHOG. 2011. Jun;7(6):e1002078. Epub 2011 Jun 16. PMID: 21698225 3. Bechler M., de Figueiredo P, Brown WJ. A PLA1-2 punch regulates the Golgi complex.

PHS 398/2590 (Rev. 06/09) Page Biographical Sketch Format Page

TRENDS CELL BIOL. 2011 Nov 28, PMID: 22130221 4. Criscitiello M, de Figueiredo P. Fifty shades of immune defense. PLOS PATHOG. 2013 9(2): e1003110. doi:10.1371/journal.ppat.1003110 PMID: 23408882 5. Han A, Hou H, Li L, Kim HS, de Figueiredo P. Microfabricated devices in microbial bioenergy sciences. TRENDS IN BIOTECHNOL. 2013. pii: S0167-7799(12)00221-1. PMID: 23453527 6. Criscitiello M, Dickman MB, Samuel JE and de Figueiredo P. Tripping on acid: trans-Kingdom perspectives on biological acids in immunity and pathogenesis PLOS PATHOG. 2013. 9(7): e1003402. doi:10.1371/journal.ppat.1003402. PMID: 23874196 7. Dickman and de Figueiredo. Death be not proud––cell death control in host fungal interactions PLOS PATHOG. 2013. 9(9): e1003542. doi:10.1371/journal.ppat.100354

D. RESEARCH SUPPORT Current support 1. Texas A&M––CAPES Program (PI: de Figueiredo; co-PIs: de Lima Santos, Ficht, Rice-Ficht), Brucella spp. neuropathogenesis and vaccine development, 5/2014-5/2015 2. The Bill & Melinda Gates Foundation (PI: de Figueiredo; co-PIs: McMurray, Ficht), Defeating antibiotic resistance before it emerges, 5/2012-11/2014 3. Qatar National Research Fund (QNRF) (PI: Sadr; co-PI: Han; co-PI: de Figueiredo), Microfluidic Platforms for High-Throughput Screening of Microbes Utilizing Wastewater, 9/11/2012-9/10/2015 4. Texas A&M-–Weizmann Research Program (PI: Ficht, co-PIs: de Figueiredo, Elazar), Mechanisms mediating intracellular parasitism by Cryptococcus neoformans, 7/2012-7/2014 5. Texas A&M AgriLife Research (PI: de Figueiredo, co-PI: Dickman), A Universal Small Molecule System for the Non-lytic Secretion of Oils from Living Cells. 9/13-9/15 Prior support (last 4 years) 6. Shwachman Diamond Research Foundation (PI: de Figueiredo), Development of small molecule therapeutics for Shwachman Diamond Syndrome, 11/2011-4/2013 7. NSF DBI (PI: Gonzalez; co-PI: de Figueiredo), REU: The Plant-Microbe Interface, 4/2011-4/2014 8. The Bill & Melinda Gates Foundation (PI: Han; co-PI: de Figueiredo), Hybrid Microbial-Electrochemical System for Waste Utilization, 11/2011-11/2013 9. Defense Threat Reduction Agency (PI: Han; co-PI: de Figueiredo), Microfuidics Based High Throughput Analysis of Polymicrobial Interactions, 6/2011-6/2013 10. Leaf Energy, Inc. (PI: Dickman; co-PI: de Figueiredo), Microdiesel–– a next generation biofuel platform, 6/2012-6/2013 11. Texas A&M Genomics and Bioinformatics Seed Grant Program (PI: Ficht; co-PI: de Figueiredo), Subcellular pathogenomics, 7/2012-7/2013 12. Congressionally Directed Medical Research Program (PI: de Figueiredo), Shwachman Diamond Syndrome: Linking Bone Marrow Failure to Global Acetylome Dysregulation, 11/2011-11/2012 13. NSF/CBET (PI: Paul de Figueiredo; co-PI: Han), Microbe-mediated electricity generation, 8/2009-8/2012 14. Shwachman Diamond Syndrome Foundation (SDSF) (PI: de Figueiredo), Development of small molecule therapeutics for Shwachman Diamond syndrome, 11/2010-11/2011 15. Diamond Blackfan Anemia Foundation (DBAF) (PI: de Figueiredo), Discovery of therapeutics for treating Diamond Blackfan Anemia. 5/2010-5/2011 16. Department of Defense Army Research Office (PI: de Figueiredo; co-PIs–– Samuel, Ficht, Rice-Ficht, Adams), Confocal microscopy instrumentation for biodefense research 17. USDA APHIS (PI: de Figueiredo; Appel, co-PI), Cyclic di-GMP regulation Xylella fastidiosa virulence, 3/2007-3/2010 18. NIH NIAID (PI: de Figueiredo), Microscopy for infectious disease research, 1/2010 19. NIH NIDDK (PI: de Figueiredo), Supplement for undergraduate research, 6/2009-8/2010 20. NIH MLPCN (PI: de Figueiredo), Drug discovery for bone marrow failure diseases, 6/2009-6/2011, No monies, resources only 21. NIH NIAID, (PI: de Figueiredo; co-PI: Ficht), Identification and analysis of host factors that support Brucella infection, 2/08-1/2010 22. NSF IOS (PI: de Figueiredo; co-PI: Ficht), Molecular analysis of Brucella host factors, 8/2008-8/2011

PHS 398/2590 (Rev. 06/09) Page Biographical Sketch Format Page Principal Investigator/Program Director: DERR, JAMES N.

BIOGRAPHICAL SKETCH

NAME DERR, James N. POSITION TITLE Professor

EDUCATION/TRAINING INSTITUTION AND LOCATION DEGREE YEAR FIELD OF STUDY CONFERRED Cameron University B.S. 1980 Biology Sul Ross State University M.S. 1982 Zoology Texas A&M University Ph.D. 1990 Genetics

Professional Experience

1985-1987 Graduate Teaching Assistant, WFSC, TAMU 1987-1989 Tom Slick Research Fellow, WFSC, TAMU 1989-1990 Staff Research Assistant, WFSC, TAMU 1990-1993 Post-Doc Research Associate, ANSC, TAMU 1993-1999 Assistant Professor, VTPB, TAMU 1995- Director, DNA Technologies Laboratory, VTPB, TAMU 1999- 2006 Associate Professor, VTPB, TAMU 2000-2002 Chair, Graduate Faculty of Genetics, TAMU 2001-2003 President-Elect and President, Texas Genetics Society 2006 - Professor, VTPB. TAMU

Honors and Awards

Phi Kappa Phi Distinguished Alumnus Award, Cameron University, 2000. Outstanding Doctoral Student, Department of Wildlife and Fisheries Sciences, TAMU, 1987-1988. Outstanding Student in Training, The Texas Genetics Society. April, 1987, College Station, Texas. Recipient of the Tom Slick Research Fellowship, by the College of Agriculture, TAMU 1987-1988. President, Association of Graduate Wildlife and Fisheries Scientists, TAMU, 1985-1986.

Peer-reviewed publications (last 10 years).

Seabury, C.M., and J.N. Derr. 2004. Identification of a novel ovine PrP polymorphism and scrapie resistance genotypes for St. Croix White and a related composite breed. Cytogenetic and Genome Research. 102: 85-88. Schnabel, R.D., J.F. Taylor and J.N. Derr. 2004. Development of a linkage map and QTL scan for growth traits in North American bison. Cytogenetic and Genome Research. 102:59-64. Seabury, C.M., J.E. Womack, J. Piedrahita, and J.N. Derr. 2004. Comparative PRNP genotyping of U.S cattle sires for potential association with BSE. Mammalian Genome.15:828-833.Seabury, C.M., R.L. Honeycutt, A.P. Rooney, N.D. Halbert and J.N. Derr. 2004. Novel prion protein gene (PRNP) variants and evidence for strong purifying selection in functionally important regions of bovine exon 3. Proceedings of the National Academy of Sciences. 101(42):15142-15147. Halbert, N., Raudsepp, T., Chowdhary, B., and J.N. Derr. 2004. The legacy of Charles Goodnight: Conservation genetic analysis of the Texas State Bison Herd. Journal of Mammalogy. 85(5):925-931. Halbert, N.R., W.E. Grant, and J.N. Derr. 2005. Genetic and demographic consequences of importing animals into a small population: A simulation model of the Texas State Bison Herd (U.S.A.). Ecological Modeling. 181:263-276. Seabury, C. M., N. D. Halbert, P. J. P. Gogan, J. W. Templeton, and J. N. Derr. 2004. An evaluation of PRNP exon 3 variation and association with seroprevalence of Brucella spp. antibodies in Yellowstone bison. Animal Genetics 36:104-110.

Halbert, N., T. Ward, R. Schnabel, J. Taylor, and J. Derr. 2005. Conservation genomics: Principal Investigator/Program Director: DERR, JAMES N. disequilibrium mapping of domestic cattle chromosomal segments in North American bison populations. Molecular Ecology 14:2343-2362. White, S.N., N.D. Halbert, K.H. Taylor, J.N. Derr, and J.E. Womack. 2005. Comparison of segregating TLR4 variation in American bison and cattle. Animal Genetics 36:511 – 542. Solomon K.M., N.D. Halbert, D.T. Redden, D.B. Allison, J.N. Derr. 2006. Marker genotypes, population admixture, and their association with body weight, height, and relative body mass in U.S. federal bison herds. Genetics 174:775-783. Freese, C.H., K. E. Aune, D.P. Boyd, J. N. Derr, S.C. Forrest, C.C. Gates, PJ.P. Gogan, S.M. Grassel, N.D. Halbert, K. Kunkel and K.H. Redford. 2007. Second Chance for the plains bison. Biological Conservation 136(2):175-184. Halbert, N., and J. Derr. 2007. A Comprehensive Evaluation of Cattle Introgression into U.S. Federal Bison Herds. Journal of Heredity 98(1):1-12. Vogel, A.B., K. Tenggardjaja, S. Edmands, N.D. Halbert, J.N. Derr, and D. Hedgecock. 2007. Introgression of cattle mtDNA into Santa Catalina Island American bison. Animal Genetics 38: 410 – 412 Halbert, N., P. Gogan, R. Hiebert, and J. Derr. 2007. Where the buffalo roam: federal bison history and role in species conservation. National Park Service. Park Science 24 :(2) 22-29. Seabury, C., J. E. Womack, C. A. Gill, J. B. Dyar, J. W. Templeton, D. L. Adelson, K. E. Owens, J. N. Derr, D. C. Kraemer. 2007. Molecular characterization of the Rocky Mountain Elk (Cervus elaphus nelsoni) PRNP putative promoter. Journal of Heredity. 98(7): 678-686. Osterstock, J., G. Fosgate, J. Derr, N. Cohen and A. Roussel. 2008. Assessing familial aggregation of paratuberculosis in beef cattle of unknown pedigree. Preventive Veterinary Medicine. 84: 121-134. Osterstock, JB; Fosgate, GT; Cohen, ND; Derr, JN; Manning, EJB; Collins, MT; Roussel, AJ. 2008. Familial associations with paratuberculosis ELISA Results in Texas Longhorn cattle. Veterinary Microbiology.129 (1-2), 131-138. Sanderson, E., K. Redford, B. Weber, K. Aune, D. Baldes, J. Berger, D. Carter, C. Curtin, J. Derr, S. Dobrott, E. Fearn, C. Fleener, S. Forrest, C. Gerlach, j C.C. Gates, J. Gross, P. Gogan, S. Grassel, J. Hilty, M. Jensen, K. Kunkel, D. Lammers, R. List, K. Minkowski, T. Olson, C. Pague, P. Robertson, and B. Stephenson. 2008. The Ecological Future of the North American Bison: Conceiving long-term, large-scale conservation of a species. Conservation Biology 22(2): 252 – 266. Osterstock, JB., G T Fosgate, N D Cohen, J N Derr, A J Roussel. 2008. Familial and herd-level associations with paratuberculosis ELISA status in beef cattle. Journal of Animal Science. 2008 May 9. Halbert, N.D., J.N. Derr (2008) Patterns of genetic variation in U.S. federal bison herds. Molecular Ecology (in press). Douglas, K.C., N.D. Halbert, C.Kolinda, C. Childers, D.L. Hunter and J.N. Derr. 2010. Complete Mitochondrial DNA Sequence Analysis of Bison bison A Bison-Cattle Hybrids: Function and Phylogeny. Mitochondrion. 11. 166-175. Halbert, N.D. J.P. Gogan, P.W. Hedrick, J.M. Wahl and J.N. Derr. 2012. Genetic population substructure in bison at Yellowstone National Park. Journal of Heredity. 103(3):360-370. Derr, J.N., P. W. Hedrick, N.D. Halbert, L. Plough, L.K. Dobson, J. King, C. Duncan, D.L. Hunter, N.D. Cohen, D. Hedgecock. 2012. Phenotypic Effects of Cattle Mitochondrial DNA in American Bison. Conservation Biology 26(6):1130 – 1136. Halbert, N.D. J.P. Gogan, P.W. Hedrick, J.M. Wahl and J.N. Derr. 2012. Yellowstone Bison Genetics - Let us Move Forward. J Hered first published online August 21, 2012 doi:10.1093/jhered/ess051 Raudsepp, T., McCue, M.M., Das, P.J., Dobson, L., Vishnoi, M., Fritz, K.L., Schaefer, R., Rendahl, A.K., Derr, J.N., Love, C.C., Varner, D.D., Chowdhary, B.P. 2012. Genome-Wide Association Study Implicates Testis-Sperm Specific FKBP6 as a Susceptibility Locus for Impaired Acrosome Reaction in Stallions. PLoS GENETICS, Dec; 8(12):e1003139. Epub 2012 Dec 20. Cronin, M.A., M.D. MacNeil, N. Vu, V. Leesburg, H.D. Blackburn, and J.N. Derr. 2013. Genetic variation and differentiation of bison (Bison bison) subspecies and cattle (Bos taurus) breeds and subspecies. J Hered first published online May, 2012 doi:10.1093/jhered/ess030. Su, H., J. McKelvey, D. Rollins, M. Zhang, D. J. Brightsmith, J. Derr, and S. Zhang. 2014. Cultivable Bacterial Microbiota of Northern Bobwhite (Colinus virginianus): A New Reservoir of Antimicrobial Resistance? PLoS ONE 9:e99826.

Principal Investigator/Program Director (Last, First, Middle): EBBOLE, Daniel, J.

NAME POSITION TITLE Ebbole, Daniel, J. Professor eRA COMMONS USER NAME Ebbole EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Indiana University, Bloomington B.A. 1979-1983 Microbiology Indiana University, Bloomington B.S. 1979-1983 Biochemistry

Purdue University, West Lafayette Ph.D. 1983-1988 Biochemistry

Postdoctoral Stanford University 1988-1991 Biology Training

A. Positions and Honors

Employment

1988 - 1991 Postdoctoral Research Associate, Stanford University 1991 - 1997 Assistant Professor, Texas A&M University 1997 - 2004 Associate Professor, Texas A&M University 2004 – present Professor, Texas A&M University, Department of Plant Pathology & Microbiology Member, Faculty of Genetics

Other Experience and Professional Memberships

Adjunct Professor, Fujian Agriculture & Forestry University, Fuzhou, Fujian, P.R.C. Genetics Society of America (GSA) America Phytopathological Society (APS)

Honors

1988 - 1991 NIH NRSA Postdoctoral Fellow 2013 – present Minjiang Scholar, Fujian Province, P.R.C.

B. Selected peer-reviewed publications (Postdocs and Graduate Students as shown)

Chen S, Songkumarn P, Venu RC, Gowda M, Bellizzi M, Hu J, Liu W, Ebbole D, Meyers B, Mitchell T, Wang GL. 2013. Identification and characterization of in planta-expressed secreted effector proteins from Magnaporthe oryzae that induce cell death in rice. Mol Plant Microbe Interact. 26:191-202. Hollister EB, Forrest AK, Wilkinson HH, Ebbole DJ, Tringe SG, Malfatti SA, Holtzapple MT, Gentry TJ. 2012, Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion. PLoS One. 7(6):e39689. Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, PHS 398/2590 (Rev. 09/04) Page Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle): EBBOLE, Daniel, J. Deshpande N, von Doehren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gomez-Rodriguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernandez-Onate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lubeck M, Lubeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV. 2011. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol. 12:R40. Chung DW, Greenwald C, Upadhyay S, Ding S, Wilkinson HH, Ebbole DJ, Shaw BD. 2011. acon-3, the Neurospora crassa ortholog of the developmental modifier, medA, complements the conidiation defect of the Aspergillus nidulans mutant. Fungal Genet. Biol. 48:370-376. Hollister EB, Forrest AK, Wilkinson HH, Ebbole DJ, Malfatti SA, Tringe SG, Holtzapple MT, Gentry TJ. 2010. Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production. Appl Microbiol Biotechnol. 88:389-399 Greenwald, CJ., Kasuga, T., Glass, NL., Shaw, BD., Ebbole, DJ., Wilkinson, HH. 2010. Temporal and Spatial Regulation of Gene Expression During Asexual Development in Neurospora crassa. Genetics. 186:1217-1230. Zhou J, Lin CZ, Zheng XZ, Lin XJ, Sang, SH., Wang ZH., Ebbole D.J., Lu GD. 2009. Functional analsyis of an α-1,2-mannosidase from Magnaporthe oryzae. Curr. Genet. 55:485-496. Meng S, Brown DE, Ebbole DJ, Torto-Alalibo T, Oh YY, Deng J, Mitchell TK, Dean RA. 2009. Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae. BMC Microbiol. 19:S8. Zhou J, Zheng XZ, Lan L, Lin CZ, Wu YB, Lin XJ, Ebbole D.J., Lu GD, Wang ZH. 2008. Biochemical and molecular characterization of a putative endoglucanase in Magnaporthe grisea. Curr. Genet. 53:217-224. Perkins DD, Freitag M, Pollard VC, Bailey-Shrode LA, Selker EU, Ebbole DJ. 2007. Recurrent locus- specific mutation resulting from a cryptic ectopic insertion in Neurospora. Genetics 175:527-544. Soderlund, C., Haller, K., Pampanwar, V., Ebbole, DJ., Farman, M., Orbach, MJ., Wang, GL., Wing, R., Xu, JR., Brown, D., Mitchell, T., Dean, R. 2006. MGOS: A resource for studying Magnaporthe grisea and Oryza sativa interactions. Mol. Plant Microbe Interact. 19:1055-1061. Li, D., Bobrowicz P., Wilkinson, HH., and Ebbole, DJ. 2005. A mitogen-activated protein kinase pathway essential for mating and contributing to vegetative growth in Neurospora crassa. Genetics 170:1091-1104. Rerngsamran, P., Murphy, MB., Doyle, SA., and Ebbole. DJ. 2005. Fluffy, the major regulator of conidiation in Neurospora crasa directly activates a developmentally regulated hydrophobin gene. Mol. Microbiol. 56:282-297. Dean RA, Talbot NJ, Ebbole DJ, Farman ML, Mitchell TK, Orbach MJ, Thon M, Kulkarni R, Xu JR, Pan H, Read ND, Lee YH, Carbone I, Brown D, Oh YY, Donofrio N, Jeong JS, Soanes DM, Djonovic S, Kolomiets E, Rehmeyer C, Li W, Harding M, Kim S, Lebrun MH, Bohnert H, Coughlan S, Butler J, Calvo S, Ma LJ, Nicol R, Purcell S, Nusbaum C, Galagan JE, Birren BW. 2005. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434:980-986

PHS 398/2590 (Rev. 09/04) Page Continuation Format Page Program Director/Principal Investigator: FUCHS-YOUNG, Robin BIOGRAPHICAL SKETCH

NAME POSITION TITLE Fuchs-Young, Robin Professor eRA COMMONS USER NAME (credential, e.g., agency login) ROBINFY EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) Emory University, Atlanta, GA B.S. 1978 Biology/English Vanderbilt University, Nashville, TN Ph.D. 1988 Pathology University of Chicago, Chicago, IL (Ben May Institute) Post-doc 1988-1991 Biology of Breast Cancer A. Personal Statement Dr. Fuchs-Young brings over 25 years of experience in investigations of the basic mechanisms of mammary tumorigenesis. Her research focuses on interacting signaling networks involving the estrogen receptor (ERα), p53 and IGF-1 and includes studies of the impact of energy balance and refined carbohydrates on breast cancer susceptibility. Studies in her lab use a broad array of in vitro and in vivo models, including mammary epithelial and breast cancer cells and genetically modified animals. Using a unique transgenic model of IGF-1 overexpression, she and her team recently reported that developmentally regulated, nongenomic (membrane and cytoplasmic) ERα actions determine the impact of IGF-1 on normal and transformed mammary epithelium and susceptibility to mammary carcinogenesis. Dr. Fuchs-Young’s laboratory also studies breast cancer health disparities and the bio- physiological mechanisms underlying disproportionately poor cancer outcomes in women of color. Dr. Fuchs-Young has also directed a community outreach and engagement program for over 15 years. She has developed and implemented a wide variety of high impact programs providing science education and career development for K-16 students, particularly underrepresented minorities in science, and professional development for K-12 teachers. The goal of these programs is to enhance preparation for and stimulate excitement about careers in EHS, medicine and technology. Her community engagement efforts are also aimed at enhancing EHS literacy and promoting community capacity to achieve environmental justice. B. Positions and Honors. Research and Professional Experience: 1991-1992 Research Associate, Ben May Institute, University of Chicago, Chicago IL 1992-1996 Senior Scientist, Endocrine Research, Lilly Research Laboratories, Indianapolis IN 1996-2003 Assistant Professor, Department of Carcinogenesis, Science Park - Research Division (SPRD), The University of Texas MD Anderson Cancer Center (UT MDACC), Smithville TX 2004-2011 Associate Professor, Department of Carcinogenesis, SPRD, UT MDACC 2011-2012 Professor, Department of Molecular Carcinogenesis, SPRD, UT MDACC 2012-pres. Professor, Department of Molecular and Cellular Medicine, College of Medicine and the Institute for Bioscience and Technology (IBT), Texas A&M Health Science Center, TAMU Patents: US Patent #5604248 Method for minimizing the utertrophic effect of tamoxifen and tamoxifen analogs. Issue: 2/18/97 US Patent #5658931 Method for inhibiting mammalian breast carcinoma with tamoxifen and analogs thereof, and certain naphthyl compounds. Issue: 8/19/97 C. Selected peer-reviewed publications or manuscripts in press (relevant to this proposal). 1. Hodges LC, Hunter DS, Bergerson JS, Fuchs-Young R and Walker CL. An in vivo/in vitro model to assess endocrine disrupting activity of xenoestrogens in uterine leiomyoma. Ann NY Acad Sci, 948:100-111, 2001. 2. Hodges LC, Houston KD, Hunter DS, Fuchs-Young R, Zhang ZM, Wineker RC, Walker CL. Transdominant suppression of estrogen receptor signaling by progesterone receptor ligands in uterine leiomyoma cells. Mol Cell Endocrinol 196 (1-2): 11-20, 2002. 3. Yakar S, Nunez N, Pennisi P, Brodt P, Fallavollita L, Sun H, Stannard B, East-Palmer J, Scavo L, Smith N, Perkins S, Fuchs-Young R, Barrett JC, Hursting SD, LeRoith D. Increased tumor growth in mice with diet- induced obesity: Impact of ovarian hormones. Endocrinology 147: 5826-34, 2006.

PHS 398/2590 (Rev. 06/09) Page Biographical Sketch Format Page Program Director/Principal Investigator: Houston, Kevin 4. de Ostrovich KK, Lambertz I, Colby J, Tian J, Rundhaug J, Johnston D, Conti CJ, DiGiovanni J and Fuchs- Young R. Paracrine overexpression of IGF-1 enhances mammary tumorigenesis in vivo, Am J Path173(3): 824- 34, 2008, PMCID: PMC2527085. 5. Harkey SH, Rundhaug J, Tian J, Cullinan-Ammann N, Lambertz I, Conti CJ and Fuchs-Young R. “Transcriptional Regulation of Estrogen Receptor-a by p53 in Human Breast Cancer Cells. Cancer Res, 69(8): 3405-14, 2009, PMCID: PMC Journal-In Process. 6. Sullivan J, Parras, B, St. Marie R, Subra W, Petronella S, Gorenstein J, Fuchs-Young R, Santa RK, Chavarria A, Ward J, and Diamond P. Public Talks and Science Listens: A Community-Based Participatory Approach to Characterizing Environmental Health Risk Perceptions and Assessing Recovery needs in the Wake of Hurricanes Katrina and Rita. Environmental Health Insights, 3: 37-51, 2009. 7. Colbert JH, Westerlind KC, Perkins SN, Haines DC, Berrigan D, Donehower LA, Fuchs-Young R and Hursting SD. Exercise Effects on Tumorigenesis in a Transgenic Mouse Model of Breast Cancer. Med Science Sports Exercise, 41(8): 1597-605, 2009, PMCID: PMC Journal-In Process. 8. King D, Miranda P, Gor B, Fuchs-Young R, Chilton J, Hajek R, Torres-Vigil I, Hernández MA, Snipes SA, Jones L. Addressing cancer health disparities using a global biopsychosocial approach. Cancer, 116(2):264-9, 2010. 9. Fuchs-Young R, Shirley SH, Lambertz I, Colby J, Tian J, Johnston D, Gimenez-Conti I, Donehower LA, Conti CJ, and Hursting SD. P53 genotype as a determinant of ER expression and tamoxifen response in the MMTV- Wnt-1 model of mammary carcinogenesis. Breast Cancer Res Treat, 130(2):399-408, 2011. PMCID: PMC3202603. 10. Tian, J, Lambertz I, Berton TR, Rundhaug JE, Kiguchi K, Shirley SH, DiGiovanni J, Conti CJ, Fischer SM, and Fuchs-Young R. Transgenic Insulin-like Growth Factor-1 Stimulates Activation of COX-2 Signaling in Mammary Glands. Mol Carcinog, 51(12):973-983, 2012. 11. Tian J, Berton TR, Shirley SH, Lambertz I, Gimenez-Conti IB, DiGiovanni J, Korach KS, Conti CJ, and Fuchs- Young R. Developmental stage determines estrogen receptor alpha expression and non-genomic mechanisms that control IGF-1 signaling and mammary proliferation in mice. J Clin Invest, 122(1):192-204, 2012. PMCID: PMC3248275.

D. Current Research and Outreach Support R01MD006228 (Fuchs-Young, PI) 03/01/11–02/29/16 1.44 calendar month NIH/NIMHHD $250,000 Role of p53 polymorphisms in disparities in breast carcinogenesis and outcome. This project will investigate the role of racially disparate p53 polymorphisms in mediating the lack of pregnancy protection and increased susceptibility of minority women to early onset breast cancer. RP130639 (Shippen, Fuchs-Young, Co-PIs) 12/1/13-11/31/15 0.6 Calendar Months CPRIT $100,000 A role for non-coding RNA in the regulation of telomerase in breast cancer. Specific aims are: 1. To examine the effect of DNA damage on telomerase enzyme activity in mammary cancer cell lines. 2. To identify DNA damage- induced non-coding RNAs that associate with human telomerase. 3. To investigate the expression profile and biochemical interactions of TERT-associated non-coding RNAs. BC123455 (Fuchs-Young, PI) 09/01/13 – 08/31/15 1.2 Calendar Months DOD/BCRP – IDEA Expansion Undoing the damage: reprogramming the effects of early high sugar/high fat diets through exercise. This project will investigate the potential of exercise to counteract the effects of exposure to hyperinsulinemia/hyperglycemia- inducing diet, during early development, by changing the “metabolic programming” induced by these early dietary exposures.

P30 ES023512 (Walker, C., PI) 4/2014-3/2018 2.6 Calendar Months NIEHS/NIH Center for Translational Environmental Health Research (CTEHR). The goal of this project is to develop a Center to support environmental health research projects at Texas A&M. Role: Director of the Community Outreach and Engagement Core; Co-director, Career Development Program.

Training Grants NIH/NCI R25T (PI: R. Carroll) 8/1/11 – 7/31/16 unspecified effort Post-doc in Nutrition, biostatistics and bioinformatics $2,467,870 direct costs/5 years Role: Faculty Mentor PHS 398/2590 (Rev. 06/09) Page Continuation Format Page Principal Investigator/Program Director (Last, First, Middle): GARCIA, L. Rene.

NAME POSITION TITLE Garcia, Luis Rene Professor eRA COMMONS USER NAME HHMI Investigator GARCIALR EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of Texas at Austin BS Honors 1986-1990 Microbiology University of Texas at Austin Ph.D. 1990-1996 Microbiology California Institute of Technology Post Doc 1996-2002 Development/Behavior

A. Positions and Honors

Employment

1. 1990: Research Intern. NIH, Bethesda, Maryland. Supervisor: Dr. Rose Mage. 2. 1990-1996: Graduate Student. University of Texas at Austin, Dept of Microbioloy. Supervisor: Dr. Ian J. Molineux 3. 1997-2000: Postdoctoral Scholar and NRSA Fellow. California Institute of Technology, Division of Biology. Supervisor: Dr. Paul W. Sternberg 4. 2000-2002: Howard Hughes Postdoctoral Scholar. California Institute of Technology, Division of Biology and Associate, Howard Hughes Medical Institute. Supervisor: Dr. Paul W. Sternberg 5. 2002-2008 Assistant Professor, Department of Biology; Texas A&M University 6. 2008- present Associate Professor, Howard Hughes Medical Institute Investigator, Home Institute, Department of Biology; Texas A&M University

Honors

1. The Texas Achievement Award (5 year undergraduate scholarship) 2. NSF minority pre-doctoral fellowship (accepted) 3. Ford Foundation pre-doctoral fellowship (declined in order to accept the NSF Award) 4. University of Texas Ex Students' Asociation Ethel and Robert L. Terry Memorial Scholarship. 5. National Research Service Award Postdoctoral fellowship. 6. Searle scholars Award 7. Presidential Early Career Award for Scientists and Engineers 8. Howard Hughes Medical Institute investigator

B. Selected peer-reviewed publications (Postdocs and Graduate Students as shown)

Leboeuf, B and García, LR. 2014. A network of sensory-motor neurons and dopaminergic support cells couples ejaculation and satiation in C. elegans males. eLife in press. Guo, X and García, LR. 2014. SIR-2.1 integrates metabolic homeostasis with the reproductive neuromuscular excitability in aging male C. elegans. eLife:3:e01730 Markert, M and García, LR. 2013. Virgin Caenorhabditis remanei females are attracted to a coital pheromone released by con-specific copulating males. Worm. (2):e24448. Correa, P., LeBoeuf, B., and García, LR. 2012. C. elegans dopaminergic D2-like receptors delimit recurrent cholinergic-mediated motor programs during a goal-oriented behavior. PLoS Genetics. (11):e1003015.

PHS 398/2590 (Rev. 09/04) Page Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle): GARCIA, L. Rene. Leboeuf, B and García, LR. 2012. Genetic interactions between BK channels and EAG family K+ channels regulate the neuromuscular circuitry that controls C. elegans male mating behavior. Genetics. 190(3):1025-41. Guo, X, Navetta, A., Gualberto, D.G., and García, LR. 2012. Behavioral decay in aging male C. elegans correlates with increased cell excitability. Neurobiology of Aging. (7):1483.e5-23. Liu Y, LeBeouf B, Guo X, Correa PA, Gualberto DG, Lints, R and García, LR. 2011. A cholinergic- regulated circuit coordinates the maintenance and bi-stable states of a sensory-motor behavior during Caenorhabditis elegans male copulation. PLoS Genetics. 7(3);e1001326. Leboeuf, B, Guo X, and García, LR. 2011 The effects of transient starvation persist through direct interactions between CaMKII and ether-a-go-go K+ channels in C. elegans males. Neuroscience. 175:1- 17. Gruninger, T.R., Gualberto, D.G.and García, LR. 2008. Sensory Perception of Food and Insulin-like Signals Influence Seizure Susceptibility. PloS Genetics. 4(7):e1000117. *LeBoeuf, B., *Gruninger, T.R., (*Co-first Authors) and García, LR. 2007. Food deprivation suppresses defective ERG K+ channel-induced muscle seizures through CaMKII and EAG K+ channels. PloS Genetics. 3(9): e156. García, LR., LeBoeuf, B and Koo, P. 2007. Diversity in Mating Behavior of Hermaphroditic and Male- Female Caenorhabditis Nematodes. Genetics. 175:1761-1771. Liu Y, LeBoeuf, B, and García, LR. 2007. Gαq-coupled Muscarinic Acetylcholine Receptors Enhance Nicotinic Acetylcholine Receptor Signaling in C. elegans Mating Behavior. J. Neurosci. 27: 1411- 1421. Reiner, DJ., Weinshenker, D., Tian, H., Thomas, J.H., Hishiwaki, K., Miwa, J., Gruninger, T., LeBoeuf, B., García, LR. 2006. Behavioral Genetics of Caenorhabditis elegans unc-103- encoded ERG- like K+ Channel. J. Neurogenetics. 20:41-46. Gruninger, T.R., Gualberto, D.G., LeBoeuf, B., and García, LR. 2006. Integration of Male Mating and Feeding Behaviors in Caenorhabditis elegans. J. Neurosci. 26:169-179. Kemp, P., García, LR., and Molineux, I.J. 2005. Changes in bacteriophage T7 virion structure at the initiation of infection. Virology. 2:307-317. *Moghal, N., *García, LR. (*Co-first Authors), Khan, L.A., Iwasaki, K., Sternberg, P.W. 2003 Modulation of EGF receptor-mediated vulval development by Gαq and excitable cells in C. elegans. Development. 130:4553-4566. García, LR. and P.W. Sternberg. 2003 C. elegans UNC-103 ERG-like potassium channel regulates contractile behaviors of sex muscles in males prior to and during mating. J. Neurosci. 23:2696- 270. García, LR., Mehta, P., and P.W. Sternberg. 2001. Regulation of distinct muscle behaviors controls the C. elegans male’s copulatory spicules during mating. Cell 107: 777-788 García, LR. and I. J. Molineux. 1999. Translocation and cleavage of bacteriophage T7 DNA by the type I restriction enzyme EcoKI in vivo. PNAS. 96:12430-12435. García, LR. and I. J. Molineux. 1996. Transcription-independent DNA translocation of bacteriophage T7 DNA into Escherichia coli. J. Bacteriol. 178:6921-6929. García, LR.and I. J. Molineux. 1995. Incomplete entry of bacteriophage T7 into F plasmid containing Escherichia coli. J. Bacteriol. 177:4077-4083. García, LR. and I. J. Molineux. 1995. Rate of translocation of bacteriophage T7 DNA across the membranes of Escherichia coli. J. Bacteriol 177:4066-4076. Hole, N. J. K., N. Harindranath, G. O. Young-Cooper, García, LR., and R. G. Mage. 1991. Identification of enhancer sequences 3' of the rabbit Ig Kappa l chain loci. J. Immunol. 146:4377-4384.

PHS 398/2590 (Rev. 06/09) Page Continuation Format Page Program Director/Principal Investigator: GILL, Clare A.

BIOGRAPHICAL SKETCH

NAME POSITION TITLE Gill, Clare A. Professor EDUCATION/TRAINING

INSTITUTION AND LOCATION DEGREE YEAR(s) FIELD OF STUDY Flinders University of South Australia, Australia B.Biot. 1995 Biotechnology University of Adelaide, Australia Ph.D. 2001 Molecular Genetics

Texas A&M University, College Station, TX Post-doc. 1999 Animal Genomics

A. Positions and Honors Positions and Employment: 1995 - 1998: Graduate Student; University of Adelaide, South Australia, Australia. 1999 - 2000: Post-Doctoral Fellow; Texas A&M University. 2000 - 2001: Associate Research Scientist; Texas A&M University. 2001 - present: Member of the Graduate Faculty, Texas A&M University. 2001 - 2007: Assistant Professor of Animal Genomics; Texas A&M University. 2002 - present: Member of the Interdisciplinary Faculty of Genetics, Texas A&M University. 2003 - present: Member of the Interdisciplinary Faculty of Biotechnology, Texas A&M University. 2007 - 2013: Associate Professor of Animal Genomics; Texas A&M University. 2011 - present: Associate Vice President for Diversity; Texas A&M University. 2013 - present: Professor of Animal Genomics; Texas A&M University. 2013 - present: Faculty Ombuds Officer; Texas A&M University.

Professional Memberships and Honors: Memberships: American Society of Animal Science, International Society of Animal Genetics, Texas Genetics Society, American Association for the Advancement of Science

1995: AMGEN Australia prize for excellence in biotechnology research 1995: Flinders University Chancellor’s letter of commendation 1998 & 1999: Finalist in the Young Australian of the Year Awards: nominated for The SA Water Science and Technology award for outstanding achievement 2009: Vice Chancellor’s Award in Excellence for Research (The McGregor Bovine Genomics Team) 2011: ADVANCE Administrative Fellow

Patent: Gill, C. A., B. Woodward, S. Bauck, and N. Voss. 2008. Breed specific haplotypes for the polled phenotype in cattle. 12/338,835 and PCT/US08/87522. Filed December 18, 2008. Patent 8,105,776 issued, 1/31/12 by US Patent Trademark Office. B. Selected Peer-Reviewed Publications (2009-2014) 1. Goldammer, T., R. M. Brunner, A. Rebl, C. H. Wu, K. Nomura, T. Hadfield, C. Gill, B. P. Dalrymple, J. E. Womack, and N. E. Cockett. 2009. A high-resolution radiation hybrid map Program Director/Principal Investigator: GILL, Clare A.

of sheep chromosome x and comparison with human and cattle. Cytogenet Genome Res 125: 40-45. 2. Kochan, K. J., R. N. Vaughn, T. S. Amen, C. A. Abbey, J. O. Sanders, D. K. Lunt, A. D. Herring, J. E. Sawyer, C. A. Gill, and P. K. Riggs. 2009. Expression of mitochondrial respiratory complex genes in liver tissue of cattle with different feed efficiency phenotypes. Proc. Assoc. Advmt. Anim. Breed. Genet. 18: 175-178. 3. Smith, S. B., C. A. Gill, D. K. Lunt, and M. A. Brooks. 2009. Regulation of fat and fatty acid composition in beef cattle. Asian-Aust. J. Anim. Sci. 22: 1225-1233. 4. The Bovine Genome Sequencing and Analysis Consortium. 2009. The genome sequence of taurine cattle: A window to ruminant biology and evolution. Science 324: 522-528. 5. The Bovine HapMap Consortium. 2009. Genome-wide survey of snp variation uncovers the genetic structure of cattle breeds. Science 324: 528-532. 6. *Villa-Angulo, R., L. Matukumalli, C. Gill, J. Choi, C. Van Tassell, and J. Grefenstette. 2009. High-resolution haplotype block structure in the cattle genome. BMC Genetics 10: 19. 7. Riggs, P. K., and C. A. Gill. 2009. Molecular mapping and marker-assisted breeding for muscle growth and meat quality. In: Applied Muscle Biology and Meat Science, M. Du and R. J. McCormick, eds. CRC press. 8. *Stafuzza, N. B., C. A. Abbey, C. A. Gill, J. E. Womack, and M. E. J. Amaral. 2012. Construction and preliminary characterization of a river buffalo bacterial artificial chromosome library. Genet. Mol. Res. 11: 3013-3019. 9. Brinkmeyer-Langford, C. L., J. J. Cai, C. A. Gill, L. C. Skow. 2013. Microsatellite variation in the equine MHC. Anim. Genet. 44:267-275. 10. *Stafuzza, N. B., A. J. Greco, J. R. Grant, C. A. Abbey, C. A. Gill, T. Raudsepp, L. C. Skow, J. E. Womack, P. K. Riggs, and M. E. J. Amaral. 2013. A high-resolution radiation hybrid map of the river buffalo major histocompatibility complex and comparison with BoLA. Anim. Genet. 44:369-376. 11. Riley, D. G., T. H. Welsh, Jr., C. A. Gill, A. D. Herring, P. K. Riggs, J. E. Sawyer, and J. O. Sanders. 2013. Whole genome association of SNP with newborn calf cannon bone length. Livestock Sci. 155: 186-196. 12. *†Hulsman Hanna, L. L., J. O. Sanders, D. G. Riley, C. A. Abbey, and C. A. Gill. 2014. Identification of a major locus interacting with MC1R and modifying black coat color in an F2 Nellore-Angus population. Gen. Sel. Evol. 46:4. Highly Accessed. 13. *Hulsman Hanna, L. L., D. J. Garrick, C. A. Gill, A. D. Herring, P. K. Riggs, R. K. Miller, J. O. Sanders, and D. G. Riley. 2014. Genome-wide association study of temperament and tenderness using different Bayesian approaches in a Nellore-Angus crossbred population. Livestock Sci. 161: 17-27. 14. *Ingram, C. M., N. J. Troendle, C. A. Gill, and R. L. Honeycutt. 2014. Characterization of 12 new microsatellite markers for the naked mole-rate, Heterocephalus glaber. Conserv. Genet. Resour. doi:10.1007/s12686-014-0147-2 Epub ahead of print. * Graduate student as first author *† Graduate student that I advised as first author Program Director/Principal Investigator: GOMER, Richard H.

BIOGRAPHICAL SKETCH Provide the following information for the Senior/key personnel and other significant contributors. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Gomer, Richard H Professor of Biology eRA COMMONS USER NAME (credential, e.g., agency login) RGomer EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) Pomona College, Claremont, CA B.A. 05/77 Physics

California Institute of Technology, Pasadena, CA Ph.D. 02/83 Biology

University of California, San Diego, CA Postdoctoral 09/88 Biology

A. Personal Statement Our lab studies the genetics and biochemistry of tissue size regulation in Dictyostelium discoideum. Work from this project led to the finding that the human serum protein Serum Amyloid P (SAP) is a potential therapeutic for fibrosing diseases. I co-founded a company to develop SAP as a therapeutic for fibrosis, and SAP is currently in Phase 2 clinical trials. As a PI on five NIH grants, several smaller grants, and as a HHMI Investigator for 15 years, I have successfully supervised research projects, trained students and postdocs, published research papers, and moved some of our basic research into clinical trials.

B. Positions and Honors Positions and Employment 3/1983-8/1983 Visiting Scientist, Carnegie Institution of Washington Observatories, Pasadena, CA 9/1983-9/1988 Postdoctoral Fellow, Biology Department, UCSD, San Diego, CA 4/1986-7/1999 Consultant, Terrapin Diagnostics 9/1988-6/1994 Assistant Professor of Biochemistry and Cell Biology, Rice University, Houston, TX 4/1990-8/2005 Adjunct Assistant Professor of Cell Biology, Baylor College of Medicine, Houston, TX 6/1990-6/1996 Assistant Investigator, Howard Hughes Medical Institute 7/1994-3/2000 Associate Professor of Biochemistry and Cell Biology, Rice University 7/1996-9/2000 Associate Investigator, Howard Hughes Medical Institute 4/2000-1/2010 Professor of Biochemistry and Cell Biology, Rice University 9/2000-8/2005 Investigator, Howard Hughes Medical Institute 1/2010-present Adjunct Professor of Biochemistry and Cell Biology, Rice University 1/2010-present Professor of Biology, Texas A&M University, College Station, TX 5/2011-present Member, Faculty of Genetics, Texas A&M University

Honors, Awards and Other Professional Activities: 1977 Pomona College Tileston Physics Prize 1977-1982 NIH Predoctoral Traineeship 9/l983-8/l986 NIH Postdoctoral Fellowship 9/1986-8/1988 American Cancer Society California Chapter Senior Postdoctoral Fellowship 4/2001-4/2003 Member, NIH Surgery, Radiology and Bioengineering special study section 8 7/2001-present Member, Faculty of 1000 9/2004-present Science Advisory Board member, Trellis Bioscience 5/2006-present Co-founder and Science Advisory Board member, Promedior 2007-2010 Chair, IACUC, Rice University 5/2008-present Editorial board member, International Journal of Cell Biology Program Director/Principal Investigator: GOMER, Richard H.

11/2008-present Editorial board member, Journal of Biomedicine and Biotechnology 2/2010-present Member, Global Fibrosis Foundation Medical Advisory Council 1/2011-present Editorial board member, Advances in Molecular Imaging 6/2011 State Bar of Texas Inventor of the Year award (with Darrell Pilling) 5/2012-present Editorial board member, F1000 Research 2013-2014 National Academies Education Fellow in the Life Sciences

C. Selected peer-reviewed publications (From 120 peer-reviewed publications in genetics and biology, 15 peer-reviewed publications in astronomy, and 13 issued patents) (Postdocs and Graduate Students as shown)

1. Crawford, J.R., Bjorklund, N.L., Taglialatela, G., and Gomer, R.H. Brain Serum amyloid P levels are reduced in individuals that lack dementia while having Alzheimer’s disease neuropathology. Neurochemical Research, 37, 795-801 (2012). 2. Kolonin, M.G., Evans, K.W., Mani, S.A., and Gomer, R.H. Alternative origins of stroma in normal organs and disease. Stem Cell Research, 8, 312-323 (2012). 3. Phillips, J.E. and Gomer, R.H. A secreted protein is an endogenous chemorepellant in Dictyostelium discoideum. Proc. Natl. Acad. Sci. USA, 109, 10990-10995 (2012). 4. Pilling, D. and Gomer, R.H. Differentiation of circulating monocytes into fibroblast-like cells. Methods in Molecular Biology, 904, 191-206 (2012). 5. Crawford, J.R., Pilling, D., and Gomer, R.H. FcγRI mediates serum amyloid P inhibition of fibrocyte differentiation. Journal of Leukocyte Biology, 92, 699-711 (2012). 6. Cox, N., Pilling, D., and Gomer, R.H. NaCl potentiates human fibrocyte differentiation. PLoS ONE, 7, e45674 (2012). 7. Maharjan, A.S., Roife, D., Brazill, D., and Gomer, R.H. Serum Amyloid P inhibits granulocyte adhesion. Fibrogenesis & Tissue Repair, 6, 2 (2013). 8. Herlihy, S.E., Tang,Y., and Gomer, R.H. A Dictyostelium secreted factor requires a PTEN-like phosphatase to slow proliferation and induce chemorepulsion. PLoS ONE, 8, e59365 (2013). 9. Herlihy, S.E., Pilling, D., Maharjan, A.S., and Gomer, R.H. Dipeptidyl-peptidase IV is a neutrophil chemorepellent. Journal of Immunology, 190, 6468-6477 (2013). 10. White, M.J.V., Glenn, M., and Gomer, R.H. Trypsin potentiates human fibrocyte differentiation. PLoS ONE, 8, e70795 (2013). 11. Gomer, R.H. New approaches to modulating idiopathic pulmonary fibrosis. Current Allergy and Asthma Reports, 13, 607-612 (2013). 12. Bakthavatsalam, D., White, M.J.V., Herlihy, S.E., Phillips, J.E., and Gomer, R.H. A Retinoblastoma orthologue is required for the sensing of a chalone in Dictyostelium. Eukaryotic Cell, 13, 376-382 (2014). 13. Pilling, D. and Gomer, R.H. Persistent lung inflammation and fibrosis in Serum Amyloid P (Apcs-/-) knockout mice. PLoS ONE, 9, e93730 (2014). 14. Phillips, J.E. and Gomer, R.H. The p21-activated kinase (PAK) family member PakD is required for chemorepulsion and proliferation inhibition by autocrine signals in Dictyostelium discoideum. PLoS ONE, 9, e96633 (2014). 15. DeBord, J.D., Smith, D.F., Anderton, C.R., Heeren, R.M.A., Paša-Tolić, L., Gomer, R.H., and Fernandez- Lima, F.A. Secondary ion mass spectrometry imaging of Dictyostelium discoideum aggregation streams. PLoS ONE, 9,e99319 (2014). 16. Pilling, D., Crawford, J.R., Verbeek, J.S., and Gomer, R.H. Inhibition of murine fibrocyte differentiation by cross-linked IgG is dependent on FcγRI. Journal of Leukocyte Biology, 96, 275-282 (2014). 17. Cox, N., Pilling, D., and Gomer, R.H. Serum Amyloid P: a systemic regulator of the innate immune response. Journal of Leukocyte Biology, in press. 18. Cox, N., Pilling, D., and Gomer, R.H. Distinct Fcγ receptors mediate the effect of Serum Amyloid P on neutrophil adhesion and fibrocyte differentiation. Journal of Immunology, 193, 1701-8 (2014).

D. Ongoing Research Support R01 GM102280 Gomer (PI) 9/01/12-8/31/16 R01 HL118507 Gomer (PI) 4/01/14-3/31/18 Principal Investigator/Program Director (Last, First, Middle): GONZALEZ, Carlos F.

NAME POSITION TITLE Gonzalez, Carlos F. Professor eRA COMMONS USER NAME cf-gonzalez EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable)

Texas A&M University BS 1970 Microbiology Texas A&M University MS 1972 Microbiology University of Nebraska-Lincoln PhD 1978 Plant Pathology University of California-Davis Postdoctoral 1978-1979 Plant Pathology University of Michigan-Medical School Postdoctoral 1979-1980 Microbiology

A. Positions and Honors

Employment

Professor, Department of Plant Pathology and Microbiology and Faculty of Genetics, Texas A&M University, 2003-Present Associate Professor, Tenured, Department of Plant Pathology and Microbiology and Faculty of Genetics, Texas A&M University, 1992-Present Associate Professor, Non-Tenured, Department of Plant Pathology and Microbiology and Faculty of Genetics, Texas A&M University, 1986-1992 Unilever (Microlife Genetics), Microbiologist, 1980-1986 U.S. Army Reserve, Captain, 1972-1982 (Honorable Discharge)

Professional Memberships

American Phytopathological Society American Society for Microbiology Society for Minorities in Agriculture, Natural Resources, and Related Sciences

Honors

Ford Foundation Fellowship, University of Nebraska 1974-78 Phi Sigma Sigma Xi, Charter member of Texas A&M University Chapter, 1971 Vice Chancellor’s Award in Excellence, Texas A&M University, 1994. Award for Exemplary Service and Leadership 1994. Society for Minorities in Agriculture Natural Resources and Related Sciences Award for Exemplary Service and Leadership 2000. Society for Minorities in Agriculture Natural Resources and Related Sciences Award for Exemplary Service as Finance Chair for 2000-2006. Society for Minorities in Agriculture Natural Resources and Related Sciences Diversity Award-2011-Texas A&M University-Division of Student Affairs-Multicultural Services

PHS 398/2590 (Rev. 09/04) Page Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle): GONZALEZ, Carlos F.

US PATENTS: 9 issued, one pending

B. Selected peer-reviewed publications

Gill, J.J, E. J. Summer, W. K. Russell, S. M. Cologna, T. M. Carlile, A. C. Fuller, K. Kitsopoulos, L. M. Mebane, B. N. Parkinson, D. Sullivan, L. A. Carmody, C. F. Gonzalez, J. J. LiPuma, R. Young. 2011. Genome and characterization of phages Bcep22 and BcepIL02, founders of a novel phage type in Burkholderia cenocepacia. J. Bacteriol.193:5300-5313.

Summer, E. J., C. J. Enderle, S. J. Ahern, J. J. Gill, C. P. Torres, D. N. Appel, M. C. Black, R. Young, and C. F. Gonzalez. 2010. Genomic and Biological Analysis of Phage Xfas53 and Related Prophages of Xylella fastidiosa. J Bacteriol 192:179-190.

Carmody, L. A, J.J. Gill, E.J. Summer,U. S. Sajjan,C. F. Gonzalez, R. F. Young, and J. J. LiPuma. 2010. Efficacy of Bacteriophage Therapy in a Model of Burkholderia cenocepacia Pulmonary Infection. J Infect Dis 201:264-271.

Zhang, R., J. J. LiPuma, and C. F. Gonzalez. 2009. Two type IV secretion systems with different functions in Burkholderia cenocepacia K56-2. Microbiology 155:4005-13.

Sajjan, S. U., Carmody, L. A. Gonzalez, C.F. and LiPuma, J. J. 2008. A Type IV Secretion System Contributes to Intracellular Survival and Replication of Burkholderia cenocepacia. Infect. Immun. 76:5447-5455.

Summer, E.J., Gill, J. J., Upton, C., Gonzalez, C.F. and Young, R. F. 2007. Role of phages in the pathogenicity of Burkholderia, or, ‘where are the toxin genes in Burkholderia phages?’ Current Opinion in Microbiology 10:410-17.

Summer, E.J., C. F. Gonzalez, M. Bomer, T. Carlile, A.Embry, A. M. Kucherka, J. Lee, L. Mebane, W. C. Morrison, L. Mark, M. D. King, J.J. LiPuma, A. K. Vidaver, and R. Young. 2006. Divergence and mosaicism among virulent soil phages of the Burkholderia cepacia complex. J. Bacteriol. 188:255-268.

Engledow, A. S., E.G. Medrano, E. Mahenthiralingam, J. J. LiPuma and C.F. Gonzalez. 2004. Involvement of a Plasmid Encoded Type IV Secretion System in the Plant Tissue Watersoaking Phenotype of Burkholderia cenocepacia. J. Bacterol.186:6015-6024.

Summer, E., C. F. Gonzalez, T. Carlisle, L. M. Mebane, A. M. Cass, C.G. Savva, J. J. LiPuma and R. Young. 2004. Burkholderia cenocepacia phage BcepMu and a family of Mu-like phages encoding potential pathogenesis factors. J. Mol. Biol. 340: 49-65.

PHS 398/2590 (Rev. 09/04) Page Continuation Format Page Program Director/Principal Investigator (Last, First, Middle): Hall, Timothy C.

NAME POSITION TITLE HALL, Timothy C. Dist. Prof.of Biology Emeritus & Director, IDMB eRA COMMONS USER NAME (credential, e.g., agency login) Hall 1100181 EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) University of Nottingham, U.K. B.Sc. (Hons) I 06/1962 Botany, Chemistry University of Nottingham, U.K. Ph. D. 06/1965 Protein Synthesis University of Minnesota, St. Paul Postdoc 1965-66 Stress Physiology

Please refer to the application instructions in order to complete sections A, B, C, and D of the Biographical Sketch. Professional Experience 1992 - present Distinguished Professor and Director, institute of Developmental and Molecular Biology 1984 - 1992 Distinguished Professor and Head, Biology Department, Texas A&M University, College Station, TX 1982 - 1984 Adjunct Professor of Biophysics and Genetics, University of Wisconsin, Madison 1981 - 1984 Director of Advanced Research, Agrigenetics Corporation, Madison, Wisconsin 1966 - 1982 Assistant, Associate (1970) and Full Professor (1975), University of Wisconsin, Madison 2009 Organizer, Bush Foundation Symposium on "A New Look at Transgenic Plants", Peking University, China 2002 - 2005 Member of Scientific Advisory Committee of the China National Center for Biotechnology Development 2005 - present Member of Advisory Board for Program of Excellence, Chinese University of Hong Kong 1998 Organizer, Juan March Meeting on Chromatin and DNA Modification, Madrid, Spain (Oct) 1996 - 2005 Member of the Editorial Board, Journal of Virology 1996 - 1999 Member, NIH Reviewers Reserve; NIH Shared Equipment Grants

Research Chromatin is the association of DNA with histones, vital to the packaging of DNA in the chromosomes. We were able to demonstrate experimentally that the phas promoter is rotationally and translationally positioned relative to a nucleosome. This architecture is known to confer epigenetic reduction of expression. Chemical changes to residues in the N-terminal tails of nucleosomal histones can be followed by chromatin immunoprecipitation (ChIP) assays, and we have used these to decipher orderly changes in nucleosomal structure during potentiation and activation, two major steps in obtaining expression from.the phas promoter. These, and other, studies identified PvALF as a major effector protein for phas expression, with a central role in recruiting accessory proteins to build the SWI/SNF chromatin remodeling complex. Recent experiments using high-throughput sequencing have revealed that over 300 genes contribute to seed protein expression, probably as members of gene networks. This is truly an exciting new approach that promises to reveal much information regarding control of expression from the phas promoter, placing our plant system on competitive par with human and other systems for studying gene regulation.

PHS 398/2590 (Rev. 06/09) Page Biographical Sketch Format Page Program Director/Principal Investigator (Last, First, Middle):Hall, Timothy C.

Selected Reviews and Book Chapters: Li, G., Chandrasekharan, M.B., Wolffe, A.P. and Hall, T.C. 2001. Chromatin structure and phaseolin gene regulation. Plant Mol. Biol. 46:121-129. C. Kole and T.C. Hall (editors). 2008. Compedium of Transgenic Crop Plants. Volumes 1-10. Wiley-Blackwell. C. Kole, C.H. Michler, A.G. Abbott, T.C. Hall (editors). 2010. Transgenic Crop Plants, Volumes 1-2. Springer. p. 487.

Selected publications on Phaseolin project: Ng D., Hall T.C. 2008. PvALF and FUS3 activate expression from the phaseolin promoter by different mechanisms. Plant Mol Biol. 66(3):233-44. Ng D., Chandrasekharan M.B., Hall T.C. 2006. Ordered histone modifications are associated with transcriptional poising and activation of the phaseolin promoter. Plant Cell. 18(1):119-32. Carranco R.., Chandrasekharan M.B., Townsend J.C., Hall T.C. 2004. Interaction of PvALF and VP1 B3 domains with the beta -phaseolin promoter. Plant Mol Biol. 255(2):221-37. Grace M.L., Chandrasekharan M.B., Hall T.C., Crowe A.J. 2004 Sequence and spacing of TATA box elements are critical for accurate initiation from the beta-phaseolin promoter. J Biol Chem. 279(9):8102-10. Chandrasekharan M.B., Li G., Bishop K.J., Hall T.C. 2003. S phase progression is required for transcriptional activation of the beta-phaseolin promoter. J Biol Chem. 278(46):45397-405. Chandrasekharan M.B., Bishop K.J., Hall T. 2003. Module-specific regulation of the beta-phaseolin promoter during embryogenesis. Plant J. 33(5):853-66. Li G., Hall T.C., Holmes-Davis R. 2002. Plant chromatin: development and gene control. Bioessays. 24 (3):234-43. Review. Li G., Chandrasekharan M.B., Wolffe A.P., Hall T.C. 2001. Chromatin structure and phaseolin gene regulation. Plant Mol Biol. 46(2):121-9. Review. Li G., Bishop K.J., Hall T.C. 2001. De novo activation of the beta-phaseolin promoter by phosphatase or protein synthesis. J Biol Chem. 76(3):2062-8. Li G, Bishop KJ, Chandrasekharan MB, Hall TC. 1999. beta-Phaseolin gene activation is a two-step process: PvALF- facilitated chromatin modification followed by abscisic acid-mediated gene activation. Proc Natl Acad Sci U S A. 96(12):7104-9. Li G., Chandler S.P., Wolffe A.P., Hall T.C. 1998. Architectural specificity in chromatin structure at the TATA box in vivo: nucleosome displacement upon beta-phaseolin gene activation. PNAS USA. 95(8):4772-7. Yang, G. and Hall, T.C. 2003. MAK, a computational tool kit for automated MITE analysis. Nucleic Acids Res. 31: 3659-3665. Teerawanichpan, P., Chandrasekharan, M.B., Jiang, Y., Narangajavana, J. and Hall, T.C. 2004. Characterizati on of two rice DNA methyltransferase genes and RNAi-mediated restoration of promoter activity in silence rice callus. Planta 218: 337-349. Yang, G., Lee, Y-H., Jiang, Y., Shi, X., Kertbundit, S. and Hall, T.C. 2005. A two-edged role for the transposabl element Kiddo in the rice ubiquitin2 promoter. Plant Cell 17: 1559-1568. Van Der Geest A., Frisch D.A., Kemp J.D., Hall T.C. 1995. Cell Ablation Reveals That Expression from the Phaseolin promoter Is Confined to Embryogenesis and Microsporogenesis. Plant Physiol. 09(4):1151-1158

PHS 398/2590 (Rev. 06/09) Page Biographical Sketch Format Page Program Director/Principal Investigator (Last, First, Middle): HARDIN, Paul E.

NAME POSITION TITLE Hardin, Paul E. Distinguished Professor of Biology eRA COMMONS USER NAME (credential, e.g., agency login) PHARDIN EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) Southern Methodist University B.S. 1982 Biology Indiana University Ph.D. 1987 Genetics Brandeis University Postdoc 1991 Neurogenetics

A. Positions and Honors

Positions and Employment 1991-1995 Assistant Professor, Department of Biology and the Center for Advanced Invertebrate Molecular Sciences, Texas A&M University. 1995-2000 Associate Professor, Department of Biology and Biochemistry, University of Houston. 2000-2005 Professor, Department of Biology and Biochemistry, University of Houston. 2004-2005 John and Rebecca Moores Professor, Department of Biology and Biochemistry, University of Houston. 1996-2005 Adjunct Professor, Department of Biology, Texas A&M University. 2005-2008 John W. Lyons ‘59 Chair and Professor, Department of Biology, Texas A&M University. 2005- Adjunct Professor, Department of Biology and Biochemistry, University of Houston. 2006- Member, Faculty of Genetics, Texas A&M University. 2006- Member, Faculty of Neuroscience, Texas A&M University. 2008- John W. Lyons Jr. ‘59 Chair and Distinguished Professor, Department of Biology, Texas A&M University.

Other Experience and Professional Memberships 2000-2001 NIH Conte Center study section (ad hoc) 2002-2008 NIH Integrative, Functional and Cognitive Neuroscience D study section (ad hoc) 2004- Associate Editor, Journal of Biological Rhythms 2004-2006 Secretary, Society for Research on Biological Rhythms 2004-2007 NIH Neurogenesis and Cell Fate Study Section (ad hoc) 2008-2010 Treasurer, Society for Research on Biological Rhythms 2010-2012 Comptroller, Society for Research on Biological Rhythms 2005- Member, Society for Research on Biological Rhythms 2009-2010 NIH Biological Rhythms and Sleep Study Section, member 2010-2013 NIH Neuronal Development, Plasticity and Rhythms Study Section, member 2012-2014 President-elect, Society for Research on Biological Rhythms 2014-2016 President, Society for Research on Biological Rhythms 2013- Member, Society for Neuroscience 2013- Member, Genetics Society of America

Honors 1985 M.D. Anderson Biochemistry and Molecular Biology Fellowship 1988 National Research Service Award PHS 398/2590 (Rev. 06/09) Page Biographical Sketch Format Page Program Director/Principal Investigator (Last, First, Middle): HARDIN, Paul E. 2003 Aschoff-Honma Prize, Honma Life Science Foundation 2003 Sigma Xi Faculty Research Achievement Award, University of Houston 2004 Research Excellence Award, University of Houston 2004 John and Rebecca Moores Professor of Biology 2005 John W. Lyons Jr. ’59 Endowed Chair in Biology

B. Selected peer-reviewed publications (of 91 total; Post-docs and Graduate Students as shown).

1. Hardin, P.E., J.C. Hall and M. Rosbash (1990) Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels. Nature 343, 536-540. 2. Hao, H., D.L. Allen and P.E. Hardin (1997) A circadian enhancer mediates PER-dependent mRNA cycling in Drosophila. Mol. Cell. Biol. 17, 3687-3693. 3. Glossop, N.R.J., L.C. Lyons and P.E. Hardin (1999) Interlocked feedback loops within the Drosophila circadian oscillator. Science 286, 766-768. 4. Krishnan, B., S.E. Dryer and P.E. Hardin (1999) Circadian rhythms in olfactory responses of Drosophila melanogaster. Nature 400, 375-378. 5. Krishnan, B., J. D. Levine, K. Sisson, H. B. Dowse, P. Funes, J. C. Hall, P. E. Hardin and S. E. Dryer (2001) A novel role for cryptochrome in a Drosophila circadian oscillator. Nature 411, 313-317. 6. Glossop, N. R. J., J. H. Houl, H. Zheng, F. S. Ng, S. M. Dudek and P. E. Hardin (2003) VRI feeds back to control circadian transcription of Clock in the Drosophila circadian oscillator. Neuron 37, 249-261. 7. Cyran, S.A., A.M. Buchsbaum, K.L. Reddy, M.-C. Lin, N.R.J. Glossop, P.E. Hardin, M.W. Young, R.V. Storti and J. Blau (2003) vrille, Pdp1 and dClock form a second feedback loop in the Drosophila circadian clock. Cell 112, 329-341. 8. Tanoue, S., P. Krishnan, B. Krishnan, S. E. Dryer and P. E. Hardin (2004) Circadian clocks in antennal neurons are necessary and sufficient for olfaction rhythms in Drosophila. Curr. Biol. 14, 638-649. PMC2176154 9. Yu, W., H. Zheng, J. H. Houl and P. E. Hardin (2006) PER dependent rhythms in CLK phosphorylation and E-box binding regulate circadian transcription. Genes Dev. 20, 723-733. PMC1434787 10. Benito, J., H. Zheng and P. E. Hardin (2007) PDP1e functions downstream of the circadian oscillator to mediate behavioral rhythms. J. Neurosci. 27, 2539-2547. PMC1828026 11. Taylor, P., and P. E. Hardin (2008) Rhythmic E-box binding by CLK-CYC controls daily cycles in per and tim transcription and chromatin modifications. Mol. Cell. Biol. 28, 4642-4652. PMC2447118 12. Tanoue, S., A. Chatterjee, P. Krishnan and P. E. Hardin (2008) G-protein-coupled Receptor Kinase 2 is required for rhythmic olfactory responses in Drosophila. Curr. Biol. 18, 787-794. PMC2474769 13. Krishnan, P., A. Chatterjee and P. E. Hardin (2008) Spike amplitude and single unit responses in antennal sensillae is controlled by the Drosophila circadian clock. Curr. Biol. 18, 803-807. 14. Houl, J. H., F. Ng, P. Taylor and P. E. Hardin (2008) CLOCK expression identifies developing circadian oscillator neurons in the brains of Drosophila embryos. BMC Neurosci. 9, 119. PMC2628352 15. Yu, W., H. Zheng, J. L. Price and P. E. Hardin (2009) DOUBLETIME functions to bridge CLK phosphorylation by other kinases. Mol. Cell. Biol. 29, 1452-1458. PMC2648245 16. Chatterjee, A., S. Tanoue, J. H. Houl and P. E. Hardin (2010) Regulation of gustatory physiology and appetitive behavior by the circadian clock in Drosophila melanogaster. Curr. Biol. 20, 300-309. 17. Yu, W., J. H. Houl, and P. E. Hardin (2011) NEMO kinase contributes to core period determination by slowing the pace of the Drosophila circadian oscillator. Curr. Biol. 21, 756-761. PMC3090582 18. Hardin, P. E. and S. Panda (2013) Circadian timekeeping and output mechanisms in animals. Curr. Opin. in Neurobiol. 23, 724-731. 19. Mahesh, G., E. H. Jeong, F. S. Ng, Y. Liu, K. Gunawardhana, J. H. Houl, E. Yildirim, R. Amunugama, R. Jones, D. L. Allen, I. Edery, E. Y. Kim and P. E. Hardin (2014) Phosphorylation of the transcription activator CLOCK regulates progression through a ~24h feedback loop to influence circadian period in Drosophila. J. Biol. Chem. 289, 19681-19693. 20. Lee, E., E. H. Jeong, H. J. Jeong, E. Yildirim, J. T. Vanselow, F. S. Ng, Y. Liu, G. Mahesh, A. Kramer, P. E. Hardin, I. Edery and E. Y. Kim (2014) Phosphorylation of a central clock transcription factor is required for thermal but not photic entrainment. PLOS Genetics 10, e1004545.

PHS 398/2590 (Rev. 06/09) Page 2 Biographical Sketch Format Page Program Director/Principal Investigator: HERRING, Andy D.

BIOGRAPHICAL SKETCH

NAME POSITION TITLE Herring, Andy D. Associate Professor EDUCATION/TRAINING

INSTITUTION AND LOCATION DEGREE YEAR(s) FIELD OF STUDY Tarleton State University, Stephenville, TX B.S. 1988 Animal Science Texas A&M University, College Station, TX M.S. 1991 Animal Breeding

Texas A&M University, College Station, TX Ph.D. 1994 Genetics

A. Positions and Honors Professional Experience: Associate Professor and Holder of John K. Riggs ’41 Beef Cattle Professorship Department of Animal Science Texas A&M University, 2002 - present Associate Professor (2000 - 2002), Assistant Professor (1994-2000) Department of Animal and Food Sciences, Texas Tech University, Graduate Teaching and Research Assistant Department of Animal Science, Texas A&M University, 1988 to 1994

Selected Honors and Awards: • 2009 Vice Chancellor’s Award in Excellence for Graduate Teaching • 2009 Vice Chancellor’s Award in Excellence for Research Team “McGregor Bovine Genomics Team” • Outstanding Young Animal Scientist – Education (2000), Southern Region, American Society of Animal Science • Texas Tech University Teaching Academy (Inducted 1999) • 1998 NACTA National Teacher Fellow Award

B. Selected Peer-Reviewed Publications (2009-2014)

1. Thrift, F.A., J.O. Sanders, M.A. Brown, A.H. Brown, Jr., A.D. Herring, D.G. Riley, S.M. DeRouen, J.W. Holloway, W.E. Wyatt, R.C. Vann, C.C. Chase, Jr., D.E. Franke, L.V. Cundiff, and J.F. Baker. 2010. Review: Preweaning, Postweaning, and Carcass Trait Comparisons for Progeny Sired by Subtropically Adapted Beef Sire Breeds at Various US Locations. Prof. Anim. Sci. 26:451-473. 2. *Cleere, J.J., F.M. Rouquette Jr., A.D. Herring, J.W. Holloway, H. Lippke, B.G. Warrington, C.R. Long, K.R. Pond, M.F. Miller, and G.E. Aiken. Stocker growth on rye and ryegrass pastures affects subsequent feedlot gains and carcass traits. Forage and Grazinglands. Online. doi:10.1094/FG-2012-0524-01-RS. 3. *Rhone, J.A., D.F. Waldron, and A.D. Herring. 2013. Performance of Boer-Spanish and Spanish does in Texas I: Body weights, fertility, prolificacy, and number of kids weaned. Journal of Animal Science 91:4679-4683. Program Director/Principal Investigator: HERRING, Andy D.

4. Riley, D.G., T.H. Welsh Jr., C.A. Gill, L.L. Hulsman, A.D. Herring, P.K. Riggs, J.E. Sawyer, and J.O. Sanders. 2013. Whole genome association of SNP with newborn calf cannon bone length. Livestock Science 155:186-196. 5. Hulsman Hanna, L.L., D.J. Garrick, C.A. Gill, A.D. Herring, P.K. Riggs, R.K. Miller, J.O. Sanders, and D.G. Riley. 2014. Genome-wide association study of temperament and tenderness using different Bayesian approaches in a Nellore-Angus crossbred population. Livestock Science 161:17-27.

Books and Chapters: 1. Herring, Andy D. 2014. North American Beef Production (Chapter 5). In: Cottle, D.J., and L. Kahn (eds.) Beef Cattle Production and Trade. CSIRO Publishing in conjunction with Meat & Livestock Australia, Brisbane, QLD. 2. Herring, Andy D. 2014. Beef Cattle, Chapter 130 in Encyclopedia of Agriculture and Food Systems, to be published in print and online by Elsevier in 2014, Editor-in-Chief Neal K. Van Alfen. Submitted December 2013, proofs accepted April 2014. 3. Beef Cattle Production Systems by Andy D. Herring (2014) 14-chapter text book for global beef production courses, published by CABI, Oxfordshire, UK (typesetting in April 2014).

Selected Relevant Scientific Abstracts 1. *Runyan, C.A., A.D. Herring, J.F. Ridpath, M.S. Cabaniss, C.T. Muntean, J.E. Sawyer. 2010. Health measures in beef steers of known genetic background following BVDV challenge. J. Anim. Sci. 88(E-Suppl. 3): 2(Abstr.). 2. *Runyan, C.A., A.D. Herring, J.F. Ridpath, M.S. Cabaniss, C.T. Muntean, J.E. Sawyer. 2010. Feed intake and weight gain in beef steers of known genetic background following BVDV challenge. J. Anim. Sci. 88(E-Suppl. 3): 2(Abstr.). 3. *Downey, E., X. Fang, C.A. Runyan, J.E. Sawyer, T.B. Hairgrove, J.F. Ridpath, C.A. Gill, and A.D. Herring. 2012. Sire and vaccine treatment effects on immune response to BVDV 1b challenge. J. Anim. Sci. 90(Suppl. 3): 403(Abstr.). 4. *Fang, X., E. Downey, C.A. Runyan, J.E. Sawyer, T.B Hairgrove, J.F. Ridpath, C.A. Gill, W. Mwangi, and A.D. Herring. 2012. Correlations of Temperament with Titer and Hematological Responses of Crossbred Steers Challenged with Bovine Viral Diarrhea Virus. J. Anim. Sci. 90(Suppl. 3): 223(Abstr.). 5. *Downey, E.D., X. Fang, C.A. Runyan, J.E. Sawyer, T.B. Hairgrove, J.F. Ridpath and A.D. Herring. 2013. Anamnestic antibody response to in BVDV 1b challenge in Angus-Nelore steers. J. Anim. Sci. 91(Suppl. 3): (Abstr.). 6. *Runyan, C.A., X. Fang, E.D. Downey, T.B. Hairgrove, J.E. Sawyer, J.G. Moreno, J.F. Ridpath, and A.D. Herring. 2013. Interactions of rectal temperature status and vaccine type with sire on weight gain and feed intake in Bos indicus crossbred steers following Bovine Viral Diarrhea virus challenge. J. Anim. Sci. 91(Suppl. 3): (Abstr.). 7. *Fang, X., E. Downey, C.A. Runyan, J.E. Sawyer, T.B Hairgrove, J.F. Ridpath, W. Mwangi , C.A. Gill, and A.D. Herring. 2013. Relationships of temperament, exit velocity and rectal temperature of crossbred steers challenged with Bovine Viral Diarrhea Virus. J. Anim. Sci. 91(Suppl. 3): (Abstr.). *Graduate student directed or advised Program Director/Principal Investigator: HU, James C.

BIOGRAPHICAL SKETCH Provide the following information for the key personnel in the order listed on Form Page 2. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Hu, James C Professor

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Stanford University, Stanford, CA B.S 1975 Biological Sciences University of Wisconsin, Madison, WI M.S. 1982 Molecular Biology University of Wisconsin, Madison, WI Ph.D. 1987 Molecular Biology Mass. Inst. of Technology, Cambridge, MA Postdoc. 1987-1992

A. Positions and Honors Employment 1992-1998 Assistant Professor Dept. of Biochemistry and Biophysics, Texas A&M Univ. 1998-2011 Associate Professor Dept. of Biochemistry and Biophysics, Texas A&M Univ. 2011-present Professor Dept. of Biochemistry and Biophysics, Texas A&M Univ. 1994-present Member Graduate Faculty of Genetics, Texas A&M Univ. 2000-2005 Chair of the steering Program in Microbial Genetics and Genomics, Texas A&M Univ. committee 2003-2006 Steering committee Chemistry-Biology Interface Training Program

Other Experience and Professional Memberships NIH MBC-2 Study Section, 1998-2002. Reviews Editor, Protein Science, 2002-2006 EcoliHub Steering Committee 2006-2009 NSF Microbial Molecular Genetics Advisory Panel 2005-2009 Organizer, Molecular Genetics of Bacteria and Phage Meeting. 2008-2010 Organizer, Texas Protein Function and Folding Conference 1993-present Genetics Society American Society for Microbiology ASBMB Protein Society International Society of Biocurators

Honors Graduation with distinction and departmental honors, Stanford 1975 Support on NIH Cell and Molecular Biology Training Grant, University of Wisconsin 1975-7 NIH Postdoctoral Fellowship, 1987-1990 Biochemistry Graduate Association Faculty Recognition Award, Texas A&M, 1996, 2000

B. Selected Peer-reviewed Publications (Postdocs and Grad students as shown) 1. Hu, J.C, Karp, P. Keseler, I, Krummenacker, M, and Siegele DA (2009) What we can learn about Escherichia coli through application of Gene Ontology. Trends in Microbiology. 7:269-78 2. Renfro DP, McIntosh BK, Venkatraman A, Siegele DA & Hu JC (2012) GONUTS: the Gene Ontology Normal Usage Tracking System. Nucleic Acids Res 40: D1262-9. PMCID: PMC3245169

3. McIntosh BK, Renfro DP, Knapp GS, Lairikyengbam CR, Liles NM, Niu L, Supak AM, Venkatraman A, Zweifel AE, Siegele DA & Hu JC (2012) EcoliWiki: a wiki-based community resource for Escherichia coli. Nucleic Acids Res 40: D1270-7. PMCID: PMC3245172 4. Brister JR, Le Mercier P, Hu JC. (2012) Microbial virus genome annotation - mustering the troops to fight the sequence onslaught. Virology 434:175-80 PMCID: PMC3518702 5. Hu, JC, Sherlock, G, Siegele, DA, Aleksander, SA, Ball, CA, Demeter, J, Gouni, S, Holland, TA, Karp, PD, Lewis, JE, Liles, NM, McIntosh, BK, Mi, H, Muruganujan, A, Wymore, F, Thomas, PD (2014) PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. Nucleic Acids Res. 42: D677-84 PMCID: PMC3965092 6. Siegele, D.A., & Hu, J.C. (1997) Gene expression from ParaBAD plasmids at subsaturating inducer concentrations represents mixed populations. Proc. Natl. Acad. Sci. USA 94: 8168-8172. PMCID: PMC21575 7. Kopytek, S.J., Dyer, J.C.D., Knapp, G.S., and Hu, J.C. (2000) Resistance to Methotrexate due to AcrAB- dependent export from Escherichia coli. Antimicrobial Agents and Chemotherapy 44:3210-3212. PMCID: PMC101636 8. Champion, M., Campbell, C., Siegele, D., Russell, D., and Hu, J.C. (2003) Protein analysis of Escherichia coli K-12 by two-dimensional native-state chromatography and MALDI-MS. Molecular Microbiology 47(2): 383-396. 9. Mariño-Ramírez, L., Minor J.L., Reading, N and Hu, J.C. (2004) Identification and mapping of self- assembling protein domains encoded by the Escherichia coli K-12 genome by use of λ repressor fusions. J. Bact 186:1311-9. PMCID: PMC344411 10. Fischer TB, Holmes JB, Miller IR, Parsons JR, Tung L, Hu JC, Tsai J.(2006) Assessing methods for identifying pair-wise atomic contacts across binding interfaces. J Struct Biol.153:103-12. 11. Knapp, G, Tsai, J, and Hu JC. (2009) The oligomerization of OxyR in Escherichia coli. Protein Science, 18:101-7. PMCID: PMC2708027 12. Knapp, G and Hu JC. (2009) The oligomerization of CynR in Escherichia coli. Protein Science. 18:2307- 15. PMCID: PMC2788285 13. Knapp GS & Hu JC (2010) Specificity of the E. coli LysR-type transcriptional regulators. PLoS One 5: e15189. PMCID: PMC3004787 14. Rajagopala SV, Yamamoto N, Zweifel AE, Nakamichi T, Huang HK, Mendez-Rios JD, Franca-Koh J, Boorgula MP, Fujita K, Suzuki K, Hu JC, Wanner BL, Mori H, and Uetz P. (2010) The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology. BMC Genomics. 11:470. PMCID: PMC3091666 15. Reference Genome Group of the Gene Ontology Consortium (2009) The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLoS Comput Biol. 2009 Jul;5(7):e1000431. PMCID: PMC2699109

Principal Investigator/Program Director (Last, First, Middle): HURTADO-CLAVIJO, Luis A.

NAME POSITION TITLE Hurtado-Clavijo, Luis A. Assistant Professor eRA COMMONS USER NAME

Universidad Nacional de Colombia, Bogotá, Colombia B. Sc. 1986-1992 Biology

Instituto Tecnológico y de Estudios Superiores Conser., Ecol. and Manag. de Monterrey, Campus Guaymas, México M.Sc. 1994-96 of Natural Resources

Rutgers University, New Jersey, USA Ph.D. 1997-2002 Ecology and Evolution

University of Arizona, Tucson, Arizona Postdoc. 2002-2005 Evolution

A. Positions and Honors

Employment 2006-08 Research Assistant Professor, Department of Wildlife and Fisheries Sciences, Texas A&M University 2005-06 Research Assistant Professor, Department of Biological Sciences, University of Texas at El Paso 2002-05 Postdoctoral Associate, Arizona Research Labs/ Department of Ecology and Evolutionary Biology, University of Arizona

Other Experience and Professional Memberships

2010 Organizer International Symposium: Multidisciplinary vision for the study of the Sea of Cortez: Research perspectives. XII Congress of the Asociación de Investigadores del Mar de Cortés, March 2010, Guaymas, Mexico.

2009 NSF Panelist, Population and Evolutionary Processes Society for the Study of Evolution Honors

1996 Award from the Mexican Government Environmental Agency ‘Procuraduría Federal de Protección al Medio Ambiente del Gobierno de México (PROFEPA)’ for research on massive mortality of dolphins occurred in 1995 in the Gulf of California

B. Selected peer-reviewed publications [C = corresponding author; * = graduate student in my lab; ** = undergraduate student working in my lab; + = graduate student in another lab]

Santamaria CA*, Mateos MC, Hurtado LAC. 2014. Diversification at the narrow sea-land interface in the Caribbean: phylogeography of endemic supralittoral Ligia isopods. Frontiers in Ecology and Evolution 2:42. DOI: 10.3389/fevo.2014.00042

PHS 398/2590 (Rev. 09/04) Page Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle): HURTADO-CLAVIJO, Luis A. Smolensky NC+, Hurtado LA, Fitzgerald LA. 2014. DNA barcoding of Cameroon samples enhances our knowledge on the distributional limits of putative species of Osteolaemus (African dwarf crocodiles). Conservation Genetics (Online First) DOI: 10.1007/s10592-014-0639-3

Hurtado LAC, Santamaria CA*, Fitzgerald LA. 2014. The phylogenetic position of the Critically Endangered Saint Croix ground lizard Ameiva polops: revisiting molecular systematics of West Indian Ameiva. Zootaxa 3794 (2): 254–262. DOI: http://dx.doi.org/10.11646/zootaxa.3794.2.4

Hurtado LAC, Lee EJ*, Mateos M, Taiti S. 2014. Global diversification at the harsh sea-land interface: Mitochondrial phylogeny of the supralittoral isopod genus Tylos (Tylidae, Oniscidea). PLoS ONE 9(4): e94081. DOI: 10.1371/journal.pone.0094081 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0094081

Santamaria CA*, Mateos M, Taiti S, DeWitt TJ, Hurtado LAC. 2013. A complex evolutionary history in a remote archipelago: phylogeography and morphometrics of the Hawaiian endemic Ligia isopods. PLoS ONE 8(12): e85199. DOI:10.1371/journal.pone.0085199 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0085199

Liu S*, Sun J, Hurtado LAC. 2013. Genetic differentiation of Portunus trituberculatus, the world’s largest crab fishery, among its three main fishing areas. Fisheries Research 148: 38-46. DOI: 10.1016/j.fishres.2013.08.003

Eberl RC+, Mateos M, Grosberg RK, Santamaria CA*, Hurtado LAC. 2013. Phylogeography of the supralittoral isopod Ligia occidentalis around the Point Conception marine biogeographic boundary. Journal of Biogeography 40: 2361-2372. DOI: 10.1111/jbi.12168

Hurtado LAC, Carrera E*, Adite A, Winemiller K. 2013. Genetic differentiation of a primitive teleost, the African bonytongue (Heterotis niloticus), among river basins and within a floodplain river system in Benin, West Africa. Journal of Fish Biology 83: 682-690. DOI: 10.1111/jfb.12198

Hurtado LAC, Lee EJ*, Mateos M. 2013. Contrasting phylogeography of sandy vs. rocky supralittoral isopods in the megadiverse and geologically dynamic Gulf of California and adjacent areas. PLoS ONE 8(7): e67827. DOI: 10.1371/journal.pone.0067827

Mateos M†C, Hurtado LA†C, Santamaria CA*, Leignel V., Guinot D. 2012. Molecular systematics of the deep- sea hydrothermal vent endemic brachyuran family Bythograeidae: a comparison of three Bayesian Species tree methods. PLoS ONE 7(3): e32066. DOI:10.1371/journal.pone. 0032066

Hurtado LAC, Santamaria CA*, Fitzgerald LA. 2012. Conservation genetics of the Critically Endangered Saint Croix ground lizard (Ameiva polops Cope 1863). Conservation Genetics 13 (2): 665-679. DOI: 10.1007/s10592-012-0316-3

Kelley SW, Ransom D C, Butcher JA, Schulz GG, Surber BW, Pinchak WE, Santamaria CA*, Hurtado LA. 2011. Home range dynamics, habitat selection, and survival of Greater Roadrunners. Journal of Field Ornithology 82 (2): 165-174. DOI: 10.1111/j.1557-9263.2011.00319.x

Hurtado LAC, Mateos M, Santamaria CA*. 2010. Phylogeography of supralittoral rocky intertidal Ligia isopods in the Pacific region from Central California to Central Mexico. PLoS ONE 5(7): e11633. DOI:10.1371/journal.pone.0011633

Santamaria CA*, Kelley S, Schulz GG, Ransom D, Hurtado LAC. 2010. Polymerase Chain Reaction-Based sex identification in the Greater Roadrunner. Journal of Wildlife Management 74 (6): 1395-1399. DOI: 10.1111/j.1937-2817.2010.tb01263.x. http://onlinelibrary.wiley.com/doi/10.1111/j.1937- 2817.2010.tb01263.x/abstract (Times cited = 7) 13(3): 427–445.

PHS 398/2590 (Rev. 09/04) Page Continuation Format Page Program Director/Principal Investigator: ING, Nancy H.

NAME POSITION TITLE Ing, Nancy Hughes Associate Professor of Animal Science and eRA COMMONS USER NAME (credential, e.g., agency login) Veterinary Integrated Biosciences NANCYING EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of Florida B.S. 1979 Zoology University of Florida D.V.M. 1984 Veterinary Medicine University of Florida Ph.D. 1988 Biochemistry Mol. Biology Baylor College of Medicine Post-doctoral 1992 Cell Biology

A. Personal Statement

My research focuses on steroid hormone-regulated gene expression in mammalian reproductive tissues. My independent laboratory discovered the post-transcriptional mechanism by which estradiol up-regulates estrogen receptor expression to enhance estrogen responsiveness in the uterus: estradiol stabilizes estrogen receptor mRNA via specific sequence elements in the 3’untranslated region of the message. These studies are leading to investigations of microRNAs regulating gene expression via steroid hormones in responsive tissues. I am excited to extend my studies to glucocorticoid repression of testosterone synthesis in stallion testes, expected to have high relevance to man. I am dedicated to mentoring diverse students at undergraduate as well as graduate levels and my track record extends throughout my career.

B. Positions and Honors.

Positions and Employment 1986-1988 Research Assistant Department of Animal Science University of Missouri 1988-1992 Post-Doctoral Fellow Department of Cell Biology Baylor College of Medicine 1992- Assistant Professor Department of Animal Science Texas A&M University 1992- Joint Appointment Department of Veterinary Anatomy and Public Health (renamed Veterinary Integrative Biosciences) Texas A&M University 1998- Associate Professor Department of Animal Science Texas A&M University

Other Experience and Professional Memberships 1986 Member, Publication and Membership Committees Society for the Study of Reproduction 1993 - Member, Exec. Comm., Faculty of Genetics Texas A&M University 1996- Member Endocrine Society 1999 - Member, Exec. Comm., Faculty of Reproductive Biology Texas A&M University 1997 - 2001 Editorial Board Biology of Reproduction 2000 - Member, Exec. Comm., Faculty of Biotechnology Texas A&M University 1998 - 2002 Editorial Board Domestic Animal Endocrinology 2007- Member Texas Faculty Association

2009 - Member Am. Society for Reproductive Medicine

Honors 1979 Rita McTigue O'Connell Award Gainesville Women's Club 1979 Phi Beta Kappa 1980 ERF Award American Medical Association 1980 Graduate Fellowship for Women Entering Non-Traditional Careers University of Florida 1995 American Registry of Professional Animal Scientists 2000 Gamma Sigma Delta (Agricultural Honor Society) Texas A&M University 2005 Phi Zeta (Veterinary Medicine Honor Society) Texas A&M University 2012 Dean’s Outstanding Achievement Award for Faculty Mentoring Texas A&M University

C. Peer-reviewed publications (Selected from 45 peer-reviewed publications)

1. Ing, N. H., A. Laughlin, D. D. Varner, T. H. Welsh Jr., D. W. Forrest, T. L.Blanchard and L. Johnson (2004) Gene expression in the spermatogenically inactive “dark” and the maturing “light” testis tissue of the prepubertal colt. J. Androl. 25:535-44. PMID:15223842 2. Ing, N.H., R.L. Wolfskill, S. Clark, J.A. deGrauuw, C.A. Gill (2006) Steroid hormones acutely regulate expression of a nudix protein-encoding gene in the endometrial epithelium of sheep Mol. Reprod. Devel. 73:967-76. http://www3.interscience.wiley.com/cgi-bin/fulltext/112613568/PDFSTART 3. Ing, N. H., D.A. Massuto, L.A. Jaeger (2008) Estradiol regulates A+U-rich RNA-binding factor 1 p45 binding to stabilizing regions within the 3' untranslated regions of estrogen receptor-α mRNA. J. Biol. Chem. 283:1764-72. PMID:18029355 4. Laughlin, A., T. H. Welsh Jr., C. C. Love, D. D. Varner, A. R. Parrish, D. W. Forrest, N. H. Ing (2009) In vitro culture of precision-cut testicular tissue as a novel tool for the study of responses to LH. In Vitro Cell Dev. Biol. – Animal 46:45-53. PMID:19915939 5. Ing, N. H. (2010) Estradiol up-regulates expression of the A + U-rich binding factor 1 gene in the sheep uterus. J. Steroid Biochem. Mol. Biol. 122: 172-179. PMID:20621185 6. Loux, S., K. R. Crawford, N. H. Ing, L. Gonsalez-Fernandez, B. Macias-Garcia, C. C. Love, D. D. Varner, I. C. Velez, Y.-H Choi, K. Hinrichs (2013) CatSper and the relationship of hyperactivated motility to calcium and pH kinetics. Biol Reprod 89:123 7. Ing, N. H., D. W. Forrest, C. C. Love, D. D. Varner (2014) Dense spermatozoa in stallion ejaculates contain lower concentrations of mRNAs encoding the sperm specific calcium channel 1, ornithine decarboxylase antizyme 3, aromatase and estrogen recptor alpha than less dense sperm. Theriogenology DOI: 10.1016/j.theriogenology.2014.04.016. 8. Ing, N.H., D. Abi-Ghanem, M.M.K Abbas, A. Kaushik, L. Berghman, J. B. Puschett (2014) Marinobufagenin regulates permeability and gene expression of human brain microvascular endothelial cells. J. Am. Phys. 306:R918-924. 9. Ing. N. H., D. W. Forrest, P. K. Riggs, S. Loux, C. C. Love, S. P. Brinsko, D. D. Varner, T. H. Welsh, Jr. (2014) Dexamethasone acutely down-regulates genes involved in steroidogenesis in stallion testes. J. Steroid Biochem. Mol. Biol. (in press). 10. Ing, N. H., S. P. Brinsko, K. O. Curley, D. W. Forrest, C. C. Love, K. Hinrichs, M. M Vogelsang, D. D. Varner, T. H. Welsh, Jr. (2014) Dexamethasone acutely regulates endocrine parameters in stallions and subsequently affects gene expression in testicular germ cells. Anim Reprod Sci (in press). 11. Faucette, A. N., V. A. Maher, M. A. Gutierrez, J. M. Jucker, D. C. Yates, T. H. Welsh, Jr., M. Amstalden, G. R. Newton, L. C. Nuti, D. W. Forrest, N. H. Ing (2014)Temporal changes in histomorphology and gene expression in goat testes during postnatal development. J. Anim. Sci. (in press)

Program Director/Principal Investigator: JI, Jun-yuan

NAME POSITION TITLE Ji, Jun-yuan Assistant Professor, eRA COMMONS USER NAME (credential, e.g., agency login) Department of Molecular and Cellular Medicine JITAMHSC Texas A&M University Health Science Center EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) Lanzhou University, China B.S. 06/94 Cell Biology Institute of Genetics and Developmental Biology, M.S. 06/97 Developmental Biology Chinese Academy of Sciences, Beijing University of Washington, Seattle, WA Ph.D. 12/03 Zoology Massachusetts General Hospital Cancer Center, Postdoctoral 08/09 Molecular Oncology Harvard Medical School, Dept. of Pathology

Positions and Employment 2004-2009 Research Fellow, Massachusetts General Hospital Cancer Center and Harvard Medical School, Department of Pathology, Boston, Massachusetts; 2009- Assistant Professor, Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, Texas; 2009- Assistant Professor, Faculty of Genetics, Texas A&M University, College Station, Texas. 2012- Member, Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas. Other Experience and Professional Memberships: 2004- Genetics Society of America 2011- American Association for Cancer Research

Honors and Awards: 2011 The American Heart Association NCRP Spring 2011 Scientist Development Award 2011 The AHA SCA Spring 2011 Beginning Grant-in-Aid (Declined) 2009 MGH Fund for Medical Discovery (FMD) Postdoctoral Fellowship Award 2006 Tosteson Postdoctoral Fellowship Award from Massachusetts Biomedical Research Corporation 2005 Drosophila Image Award Finalists 1997 Di-Ao Award for Excellent Graduate Student of Chinese Academy of Sciences 1994 Excellent Graduate Award of Lanzhou University

Selected Publications (reverse chronological order) 1. Zheng, Y., Hsu, F.N., Xu, W., Xie, X.J., Ren, X., Gao, X., Ni, J.Q., and Ji, J.Y.# (2014) A Developmental Genetic Analysis of the Lysine Demethylase KDM2 in Drosophila melanogaster. Mechanisms of Development, submitted. (# Corresponding author) 2. Zhao, X., Xiaoli, Zong, H., Abdulla, A., Yang, E.S.T., Ji, J.Y., Pessin, J.E., Bhaskar C. Das, B.C., Yang, F. (2014) Inhibition of SREBP transcriptional activity by a boron-containing compound improves lipid homeostasis in diet- induced obesity. Diabetes, in press. 3. Xu, H., Li, H., Woo, S.L., Kim, S.M., Shende, V.R., Neuendorff, N., Guo, X., Guo, T., Qi, T., Chen, L., Ji, J.Y., Alaniz, R.C., Earnest, D.J., Wu, C. (2014) Myeloid cell-specific Circadian Clock Disruption Exacerbates Diet-induced Inflammation and Insulin Resistance. Journal of Biological Chemistry, 289, 16374-16388. 4. Xu, W.#, Amire-Brahimi, B., Xie, X.J., Huang, L., Ji, J.Y.# (2014) All-atomic Molecular Dynamic Studies of Human CDK8: Insight on A-loop, Point Mutations and Binding with Its Partner CycC. Computational Biology and Chemistry, 51, 1-14. (# Corresponding authors) Program Director/Principal Investigator: JI, Jun-yuan

5. Zhang, T., Liao, Y., Hsu, F.N., Zhang, R., Searle, J.S., Pei, X., Li, X., Ryoo, H.D., Ji, J.Y., Du, W. (2014) Elevated TORC1 activity mediates synthetic lethal interaction between deregulated Wnt signaling and Rb inactivation. PLoS Genetics, 10(5):e1004357. 6. Wang, C., Ji, J.Y., Tian, L., and Pestell, R.G. (2014) Transcriptional regulation of lipogenesis as a therapeutic target for cancer treatment. R. Kumar (ed.) Nuclear Signaling Pathways and Targeting Transcription in Cancer, Cancer Drug Discovery and Development, pp 259-275. DOI 10.1007/978-1-4614-8039-6_10; Springer New York 7. Ren, X., Sun, J., Housden, B.E., Hu, Y., Roesel, C., Lin, S., Liu, L.P., Yang, Z., Mao, D., Sun, L., Wu, Q., Ji, J.Y., Xi, J., Mohr, S.E., Xu, J., Perrimon, N., Ni, J.Q. (2013) Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9. Proc. Natl. Acad. Sci. USA 110, 19012-19017. 8. Gu, W., Wang, C., Li, W., Hsu, F.N., Zhou, J., Yuan, C., Xie, X.J., Jiang, T., Addya, S., Kong, B.# and Ji, J.Y.# (2013) Tumor suppressive effects of CDK8 in endometrial cancer cells. Cell Cycle, 12, 987-999. (# Corresponding authors) 9. Ji, J.Y. #, Miles, W.O. Korenjak, M., Zheng, Y., and Dyson, N.J. (2012) In vivo regulation of E2F1 by Polycomb group genes in Drosophila. G3: Genes, Genomes, Genetics 2, 1651-1660. (# Corresponding author) 10. Zhao, X.*, Feng, D.*, Wang, Q.*, Abdulla, A., Xie, X.J., Zhou, J., Sun, Y., Yang, E.S., Liu, L.P., Vaitheesvaran, B., Bridges, L., Kurland, I., Strich, R., Ni, J., Wang, C., Ericsson, J., Pessin, J., Ji, J.Y.#, and Yang, F.# (2012) Regulation of lipogenesis by Cyclin-dependent kinase 8–mediated control of SREBP1. Journal of Clinical Investigation 122, 2417-2427. (* Equal contribution authors; # Corresponding authors) 11. Ren, X., Sun, J., Housden, B.E., Hu, Y., Roesel, C., Lin, S., Liu, L.P., Yang, Z., Mao, D., Sun, L., Wu, Q., Ji, J.Y., Xi, J., Mohr, S.E., Xu, J., Perrimon, N., Ni, J.Q. (2013) Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9. Proc Natl Acad Sci USA 110,19012-19017. 12. Li, W., Tai, Y., Zhou, J., Gu, W., Bai, Z., Zhou, T., Zhong, Z., McCue, P.A., Sang, N., Ji, J.Y., Kong, B., Jiang, J., and Wang, C. (2012) Repression of endometrial tumor growth by targeting SREBP1 and lipogenesis. Cell Cycle 11, 2348-2358. 13. Herr, A., Longworth, M. Ji, J.Y., Korenjak, M., Macalpine, D.M., and Dyson, N.J. (2012) Identification of E2F target genes that are rate limiting for dE2F1-dependent cell proliferation. Developmental Dynamics 241, 1695-1707. 14. Miles, W.O., Tschop, K., Herr, A.*, Ji, J.Y.*, Dyson, N.J. (2012) Pumilio facilitates miRNA regulation of the E2F3 oncogene. Genes & Development 26: 356-368. (* Equal contribution authors) PMID: 22345517 15. Mulligan, P., Yang, F., Di Stefano, L.*, Ji, J.Y.*, Ouyang, J.*, Nishikawa, J.L., Toiber, D., Kulkarni, M., Wang, Q., Najafi-Shoushtari, S.H., Mostoslavsky, R., Gygi, S.P., Gill, G., Dyson, N.J., and Näär, A.M. (2011) A SIRT1-LSD1 Corepressor Complex Regulates Notch Target Gene Expression and Development. Mol Cell. 42, 689-699 (* Equal contribution authors.) PMID: 21596603 16. Xu, W., and Ji, J.Y.* (2011) Dysregulation of CDK8 and Cyclin C in tumorigenesis. Journal of Genetics and Genomics 38, 439-452. (*Corresponding author) PMID: 22035865. 17. Ji, J.Y., and Dyson, N.J. (2010) Interplay between Cyclin-dependent kinases and E2F-dependent transcription. In Cell Cycle Deregulation in Cancer, edited by Enders, G., Springer Science, pp.23-41. 18. Walker, A.K., Yang, F., Jiang, K., Ji, J.Y., Watts, J.L., Purushotham, A., Boss, O., Hirsch, M.L., Ribich, S., Smith, J.J., Israelian, K., Westphal, C.H., Rodgers, J.T., Shioda, T., Mulligan, P., Najafi-Shoushtari, H., Thakur, J.K., Kadyk, L.C., Mostoslavsky, R., Puigserver, P., Li, X., Dyson, N.J., Hart, A.C., and Näär, A.M. (2010) Conserved role of SIRT1 orthologs in fasting-dependent inhibition of the lipid and cholesterol regulator SREBP. Genes & Development, 24, 1403-1417. PMCID: PMC2895199. 19. Zhang, J., Ji, J.Y., Yu, M., Overholtzer, M., Smolen, G.A., Wang, R., Brugge, J.S., Dyson, N.J., Haber, D.A. (2009) YAP-dependent induction of amphiregulin identifies a non-cell-autonomous component of the Hippo pathway. Nature Cell Biology 11, 1444-1450. PMCID: PMC2819909. Program Director/Principal Investigator (Last, First, Middle): JOHNSTON, J. Spencer BIOGRAPHICAL SKETCH Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Johnston, J. Spencer Professor of Entomology/Genetics eRA COMMONS USER NAME JSPENCERJ EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION (if YEAR(s) FIELD OF STUDY applicable) University of Washington, Seattle, WA B. S. 1967 Zoology University of Arizona, Tucson, AZ Ph. D. 1972 Genetics

University of Texas, Austin, TX Post 1975 Genetics Doctoral

A. Personal Statement I am interested in arthropod genome size evolution, and to this end, have examined genome size of a number of insect species. Recent work includes the relationship of genome size and Drosophila life history traits. To address this, we produced high-resolution estimates of the average female genome size of the 205 DGRP isolines of D. melanogaster. Three important published findings from that work are first; genome size varies among Drosophila lines that were extracted from nature, second, genome size correlates with development time in a temperature-dependent fashion, and third, chromosomal inversions affect both average genome size and the magnitude of genome size variation. Our goal is to extend this work to naturally occurring populations. To this end, we have measured a small subset of the D. melanogaster and D. simulans populations studied by Begun et al., and found significant genome size variation – which variation is more than sufficient to achieve, in a timely fashion, the goals of the proposed research. I have a great deal of experience estimating genome size and have utilized flow cytometry to determine the total genome size for most, if not all, complete arthropod genome projects, and continue to provide genome size estimates for scientists and genome centers across the world. With M. Bennett et al. in 2005 we established the genome size standard for D. melanogaster by comparison against the fully sequenced genome of Caenorhabditis elegans. With Ryan Gregory, I published the genome size for 78 Drosophila species. For the DGRP we measured genome size for more than 1000 D. melanogaster . Most recently, I published evidence that the majority of nuclei from the thorax of D. melanogaster are underreplicated. The underreplication peak can be compared to the 2C peak from the same individual, allowing an estimation of the replicated (and unreplicated) portions of the genome with very high accuracy and precision. Within a given line, the standard error of this measurement (N = 5) is less than 0.0001 Mb. Between lines there are very significantly different proportions, providing thereby a powerful new tool to help successfully address the objectives in the proposal in a timely fashion.

B. Positions and Honors Positions and Employment 1975 - 1979 Assistant Professor of Biology, Biology, Baylor University 1980 - 1986 Associate Professor of Genetics, Plant Sciences, Texas A&M University 1986 – 1997 Associate Professor of Entomology, Entomology, Texas A&M University 1997 – Professor of Entomology, Dept. Entomology, Texas A&M University

PHS 398/2590 (Rev. 11/07) Page Biographical Sketch Format Page Program Director/Principal Investigator (Last, First, Middle): JOHNSTON, J. Spencer Other Experience and Professional Memberships 1980- Faculty of Genetics, TAMU 1991- Director of Cytometry, Center for Sytematics and Biodiversity, TAMU 1999 Visiting Senior Research Fellow, Department of Zoology, Oxford University 2003 Visiting Senior Fellow, St. Hugh's College, Oxford University

Honors 1992 Outstanding Undergraduate Genetics Professor 1996 Outstanding Undergraduate Genetics Professor 2005 Paper in Ann. Botany listed in Science Citation Index as most cited in its field. 2005 Two papers in Ann. Botany listed among 50 most cited in the journal history. 2006 Author of the year: Jn. Insect Molecular Biology - (865 citations). 2006 Four papers in Ann. Botany listed among 10 most cited in the journal history.

C. Selected peer-reviewed publications. Kapheim KM, et al. 2014. Genomic Signatures of Repeated Social Evolution in Bees. Nature 10/3/14. Ellis LL, et al. 2014. Intrapopulation genome size variation in D. melanogaster reflects life history variation and plasticity. PLoS Genet. 10(7): e1004522. doi:10.1371/journal.pgen.1004522

Soria-Carrasca, et. al. 2014. Stick Insect genomes reveal natural selection’s role in parallel speciation. Science 334(6185):738-742.

Kelley, J.L et al. 2014. Insights into evolution of the small genome of the Antarctic midge: Environmental extremes constrain genome architecture, not gene content. Nature. 35.2

Boussau, B., et. al. 2014. Strepsiptera, phylogenomics and the long branch attraction problem. PLoS One 10.1371/journal.pone.0107709

DGRP Consortium, JS Johnston one of 4 senior authors: 2014. Natural variation in genome Architecture among 205 Drosophila melanogaster Genetic Reference Panel lines . Genome Res. 04/2014; doi:10.1101/gr.171546.113.

Chávez-Galarza et al.. 2013. Signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) revealed by a genome scan analysis of single nucleotide polymorphisms. Mol. Ecol. 22(23):5890-907 DOI. 10.1111/mec.12537.

Johnston, JS, Schoener, M & McMahon, DP. 2013. DNA Underreplication in the Majority of Nuclei in the Drosophila melanogaster Thorax: Evidence from Suur and Flow Cytometry. Journal of Molecular Biology Research, 3(1), 47-54. 2.5

Jacobson,AL, Johnston, JS et al.. 2012. Genome size and ploidy of Thysanoptera. Insect Molecular Biology 1165:12-17. doi: 10.1111/j.1365-2583.2012.01165 3.0 Hanrahan SJ, Johnston JS. 2011. New genome size estimates of 134 species of Arthropods. Chromosome Research 19:809-23. Sirviö A,Johnston JS.2011. A high recombination rate in the common wasp Vespula vulgaris adds independent support to the theory that advanced sociality selected for increased recombination rates. BMC Genetics 2011, 12:95doi:10.1186/1471-2156-12-95. Baxter SW, Davey JW, J. S. Johnston JS et al. Linkage Mapping and Comparative Genomics Using Next-

PHS 398/2590 (Rev. 11/07) Page Continuation Format Page BIOGRAPHICAL SKETCH Provide the following information for the key personnel and other significant contributors. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Geoffrey Kapler Professor and Chair eRA COMMONS USER NAME Department of Molecular and Cellular Medicine [email protected] Texas A&M Health Science Center EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of Connecticut, Storrs CT B.S. 1979 Biology

Genetics Harvard University, Cambridge MA Ph.D. 1989

Microbiology and University of California, San Francisco CA Postdoctoral 1900-1994 Immunology

A. PERSONAL STATEMENT For the past 20 years the Kapler lab has used the model eukaryote Tetrahymena thermophila, to gain insights into the genetic and epigenetic control of DNA replication. Aberrations in replication initiation (gene amplification) and elongation (fork collapse) induce genome instability, a hallmark of all cancer cells. My lab has exploited genetically programmed and environmentally induced conditions to address fundamental questions in the DNA replication field. We discovered a novel mechanism for the selective recruitment of the origin recognition complex (ORC) to sites for gene amplification, in which a novel RNA component of ORC binds to amplified origins through Watson-Crick RNA:DNA base pairing. We identified a novel single strand DNA binding protein, TIF1p, that regulates the intra-S phase DNA damage/replication stress checkpoint response, and provided the first evidence for epigenetic control of replication fork elongation. Most recently, we discovered a robust unconventional DNA replication program that operates in the virtual absence of conserved initiator proteins (ORC and the MCM2-7 replicative helicase). This cell cycle program is activated by environmental agents that damage DNA. Genotoxic agents arrest the cell cycle at the G1/S border and trigger the ATR-dependent degradation of ORC and MCM complexes. Remarkably, upon removal of these agents, the entire genome is replicated before the initiator proteins are replenished. The molecular underpinnings of this ‘alternative DNA replication program’ are being assessed by nascent strand deep sequencing. Finally, we have identified a role for histone H3 K27 monomethylation in the regulation of replication fork elongation. TXR1 methyltransferase mutant strains exhibit profound genome instability that is associated with gross genome rearrangements (microhomology induced inverted repeats) proximal to replication initiation sites.

B. POSITIONS AND HONORS 1990-1993 Damon Runyon-Walter Winchell Postdoctoral Fellow, UCSF, mentor: Elizabeth Blackburn 1994 California Cancer Research Coordinating Board Committee Postdoctoral Fellow, University of California, San Francisco, mentor: Elizabeth Blackburn 1994-2002 Assistant Professor, Medical Biochemistry and Genetics, Texas A&M Health Science Center 1994-present Member, Interdisciplinary Faculty of Genetics, Texas A&M University 1997-present Member, Department of Biochemistry and Biophysics, Texas A&M University 1999-2004 Member, Tetrahymena Genome Project Steering Committee 2001-present Board of Reviewers, Current Genetics 2002-2005 Chair, Interdisciplinary Faculty of Genetics, Texas A&M University 2002-2006 Associate Professor, Dept. of Medical Biochemistry and Genetics, TAMHSC 2003 Ad hoc reviewer, NIH Study Section in Comparative Medicine (October 2003) 2003/2004 Ad hoc member, NIH Study Section in Genetics (June 2003, February 2004) 2006-present Professor, Dept. of Molecular and Cellular Medicine, Texas A&M Health Science Center 2007 Ad hoc member, NSF Study Section, Eukaryotic Genetics (April 2007) 2007-2009 Associate Chair, Dept. of Molecular and Cellular Medicine, Texas A&M Health Science Center 2009 Recipient, Texas A&M Health Science Center Excellence in Research Award 2009-2011 Meeting Organizer, 2011 FASEB Ciliate Molecular Biology Conference, Crete, Greece 2010-2011 Interim Chair, Dept. of Molecular and Cellular Medicine, Texas A&M Health Science Center 2011 Ad hoc member, NSF Study Section, Eukaryotic Genetics (April 2011) 2011-present Tetrahymena Research Advisory Board (Chair, 2013-2015) 2012- Chair, Dept. of Molecular and Cellular Medicine, Texas A&M Health Science Center 2012- Tom and Jean McMullin Endowed Chair in Genetics 2013-2016 Coordinating Committee, Genetics Society of America, 2016 Genetics Conference, TAGC (GSA 100th anniversary meeting), Orlando, FLA

C. SELECTED PEER-REVIEWED PUBLICATIONS (in reverse chronological order) Gao S, Xiong J, Zhang C, Berquist BR, Yang R, Zhao M, Molascon AJ, Kwiatkowski SY, Yuan D, Qin Z, Wen J, Kapler GM, Andrews PC, Miao W and Y (2013). Impaired replication elongation in Tetrahymena mutants deficient in histone H3 Lys 27 monomethylation. Genes and Development 27:1662-1679.

Donti TR, Datta S, Sandoval PY and GM Kapler (2009). Differential targeting of Tetrahymena ORC to ribosomal DNA and non-rDNA replication origins. EMBO Journal 28:223-33.

Mohammad, MM, Smith, AG, Donti, TR and GM Kapler (2007). Tetrahymena ORC contains a ribosomal RNA fragment that participates in rDNA origin recognition. EMBO Journal 26:5048-5060.

Yakisich, JS, Sandoval, PY, Morrison, TL and GM Kapler (2006). TIF1 activates the intra-S phase checkpoint response in the diploid micronucleus and amitotic macronucleus of Tetrahymena. Mol Biol Cell 17:5185-5197.

Yakisich, JS and GM Kapler (2006). Deletion of the T thermophila rDNA replication fork barrier region creates a fragile site in micronuclear chromosome 1 and affects macronuclear rDNA excision. Nucleic Acids Res 34:620-634.

Morrison, T, Cassidy-Hanley, D and GM Kapler (2005). TIF1 represses rDNA replication initiation, but promotes normal S phase progression and chromosome transmission in Tetrahymena. Mol Biol Cell 16:2624-2635.

Smith, JJ, Yakisich, JS * (co-first author), Cole, E, Kapler, GM and DP Romero (2004). A β-tubulin mutation selectively uncouples nuclear division and cytokinesis in Tetrahymena. Eukaryotic Cell 3:1217-1226.

Yakisich, JS and GM Kapler (2004) Role of the PI3-kinase pathway in programmed nuclear death and the fate of pharmacologically-induced survival nuclei in Tetrahymena thermophila. Cell Death and Diff 10: 1146-1149.

Mohammad, M, York RD, Hommel, J and G.M. Kapler (2003). Characterization of a novel ORC-like complex: implications for DNA recognition, cell cycle control and locus-specific gene amplification. Mol Cell Biol 23:5005-5117

Saha S, Nicholson, A, and GM Kapler (2001). Cloning and Biochemical Analysis of the Tetrahymena Origin Binding Protein TIF1: Competitive DNA binding in vitro and in vivo to critical rDNA replication determinants. J. Biol. Chem. 276: 45417-45426

Saha, S and GM Kapler (2000). Allele-specific DNA-protein interactions between ssA-TIBF and cis-acting determinants for replication of the T. thermophila rDNA minichromosome. Journal of Molecular Biology 295:423-439.

Mohammad, M, Saha, S and GM Kapler (2000). Three different proteins recognize a multifunctional determinant that controls replication initiation, fork arrest and transcription in Tetrahymena. Nucleic Acids Research 28:843-851.

MacAlpine, DM, Zhang, Z and GM Kapler (1997). Type I elements mediate replication fork pausing at conserved upstream sequences in the Tetrahymena thermophila rDNA minichromosome. Molecular and Cellular Biology 17:4517-4525.

Zhang, Z, MacAlpine, DM and GM Kapler (1997). Developmental regulation of DNA replication: replication fork barriers and programmed gene amplification in Tetrahymena. Molecular and Cellular Biology 17: 6147-6156.

D. RESEARCH SUPPORT Source: TAMU/National Science Foundation of China Research Grant Program Title: Transcriptome analysis of a novel stress-induced DNA replication program in Tetrahymena. Funding Period: 9/01/13 – 8/31/14 PI: GM Kapler, Co-PI, Wei Miao (Institute of Hydrobiology, Chinese Academy of Science, Wuhan, China) Funding Period: 8/01/14 – 7/31/18 (effort: 1.0 month) Budget: $25,000 (direct cost to GMK)

Source: National Science Foundation (Division of Molecular and Cellular Biosciences) Title: Dissecting the role of histone lysine 27 mono-methylation in DNA replication. PI: Y Liu, Univ. of Michigan; Co-PI, GM Kapler Funding Period: 8/01/14 – 7/31/17 (effort 1.0 month) Sub-contract budget for Kapler lab: (cumulative direct cost to Kapler lab: $61,585, total cost $89,299 (direct and indirect))

Source: Jean and Tom McMullin Endowed Professorship in Genetics (annual direct costs ~$60,000) Program Director/Principal Investigator: KUNKEL, Gary R.

BIOGRAPHICAL SKETCH Provide the following information for the Senior/key personnel and other significant contributors. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Kunkel, Gary R. Associate Professor of Biochemistry EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) University of California, Davis B.S. 06/75 chemistry University of California, Los Angeles Ph.D. 12/81 biochemistry Worcester Foundation for Biomedical Research postdoc 04/82-12/88 cell & mol. biology

A. Personal Statement I have directed research projects involving efforts of graduate students, undergraduate students and technicians in the general field of eukaryotic transcriptional control for over 20 years. My laboratory is skilled in transcription assays, transfection of cultured cells, protein expression, and manipulation/analysis of DNA and RNA. Starting in 2005, we began work using zebrafish as a model organism, collaborating with Prof. A. Lekven’s laboratory at Texas A&M. To hone those skills, both technical and conceptual, I performed sabbatical research in 2009 with Prof. D. Raible’s laboratory at the University of Washington.

B. Positions and Honors Positions Research Associate, Worcester Foundation for Experimental Biology, Shrewsbury, MA, 1982-1985 Senior Research Associate, Worcester Foundation, 1985-1988 Assistant Professor of Biochemistry, Texas A&M University, 1989-1994 Visiting Associate Professor, Department of Molecular Genetics, M.D. Anderson Cancer, Houston, TX, Fall 1997-Spring 1998 Associate Professor of Biochemistry, Texas A&M University, 1994-present Visiting Scholar, Department of Biological Structure, University of Washington, 2009

Honors Robert E. Wood Foundation National Merit Scholarship, 1971-1975 University of California Regent's Fellowship, UCLA NIH NRSA Predoctoral Trainee, UCLA, 1977-1979 NIH NRSA Postdoctoral Fellowship, 1983-1985 Outstanding Faculty Award, Undergraduate Biochemistry Society, Texas A&M University, 1993 Outstanding Teacher Award, Undergraduate Genetics Society, Texas A&M University, 1993 Faculty Recognition Award, Biochemistry Graduate Student Association, 2004

C. Selected Peer-reviewed Publications 1) The transcriptional activator ZNF143 is essential for development in zebrafish. K.M. Halbig, A.C. Lekven, and G.R. Kunkel, 2012, BMC Mol. Biol. 13:3. (PMID: 22268977) 2) Adhesion-dependent regulation of skp2 transcription and cell proliferation by selenocysteine tRNA gene transcription activating factor (STAF). Hernandez-Negrete, I., Sala-Newby, G.B., Perl, A., Kunkel, G.R., Newby, A.C., and Bond, M., 2011. Biochem J. 436:133-143. (PMID: 21352097) Program Director/Principal Investigator: KUNKEL, Gary R.

3) Interplay between Foxd3 and Mitf regulate cell fate plasticity in the zebrafish neural crest. Curran, K., Lister, J.A., Kunkel, G.R., Prendergast, A., Parichy, D.M., and Raible, D.W. 2010. Dev. Biol. 344:107-118. (PMID: 20460180) 4) Zebrafish U6 Small Nuclear RNA Gene Promoters Contain a SPH Element in an Unusual Proximal Location. K.M. Halbig, A.C. Lekven, and G.R. Kunkel. 2008. Gene 421:89-94. (PMID: 18619527) 5) Regulation of Aldehyde Reductase Expression by STAF and CHOP. O.A. Barski, V.Z. Papusha, G.R. Kunkel, and K.H. Gabbay. 2004. Genomics 83:119-129. (PMID: 14667815) 6) Multiple, Dispersed Human U6 Small Nuclear RNA Genes with Varied Transcriptional Efficiencies. A.M. Domitrovich and G.R. Kunkel. 2003. Nucleic Acids Res. 31:2344-2352. (PMID: 12711679) 7) The Small RNA Gene Activator Protein, SPH-binding Factor/Selenocysteine tRNA Gene Transcription Activating Factor, Stimulates Transcription of the Human Interferon Regulatory Factor-3 Gene. C.M. Mach, B.W. Hargrove, and G.R. Kunkel. 2002. J. Biol. Chem. 277:4853-4858. (PMID: 11724783) 8) The Novel Zinc Finger-Containing Transcription Factor Osterix Is Required for Osteoblast Differentiation and Bone Formation. K. Nakashima, X. Zhou, G. Kunkel, Z. Zhang, J.M. Deng, R.R. Behringer, and B. de Crombrugghe. 2002. Cell 108:17-29. (PMID: 11792318) 9) Identification of an essential proximal sequence element in the promoter of the telomerase RNA gene of Tetrahymena thermophila. B.W. Hargrove, A. Bhattacharyya, A.M. Domitrovich, G.M. Kapler, K. Kirk, D.E. Shippen, and G.R. Kunkel. 1999. Nucleic Acids Res. 27:4269-4275. (PMID: 10518620) 10) Molecular cloning of a cDNA encoding human SPH-binding factor, a conserved protein that binds to the enhancer-like region of the U6 small nuclear RNA gene promoter. J.C. Rincon, S.K. Engler, B.W. Hargrove, and G.R. Kunkel. 1998. Nucleic Acids Res. 26:4846-4852. (PMID: 9776743) 11) The distal elements, OCT and SPH, stimulate the formation of preinitiation complexes on a human U6 snRNA promoter in vitro. G.R. Kunkel and J.D. Hixson. 1998. Nucleic Acids Res. 26:1536-1543. (PMID: 9490803) 12) Identification of a SPH Element in the Distal Region of a Human U6 Small Nuclear RNA Gene Promoter and Characterization of the SPH Binding Factor in HeLa Cell Extracts. G.R. Kunkel, T.C. Cheung, J.H. Miyake, O. Urso, K.J. McNamara-Schroeder, and W.E. Stumph. 1996. Gene Expression 6:59-72. (PMID: 8979085) 13) A complex that contains proteins binding to the PSE and TATA sites in a human U6 small nuclear RNA promoter. R.S. Goomer, O. Urso and G.R. Kunkel. 1994. Gene 148:269-275. (PMID: 7958954) 14) Functional Characterization of Elements in a Human U6 Small Nuclear RNA Gene Distal Control Region. D.A. Danzeiser, O. Urso, and G.R. Kunkel. 1993. Mol. Cell. Biol. 13:4670-4678. (PMID: 8336708) 15) Formation of a Template Committed Complex on the Promoter of a Gene for the U6 Small Nuclear RNA from the Human Requires Multiple Sequence Elements, Including the Distal Region. G.R. Kunkel and D.A. Danzeiser. 1992. J. Biol. Chem. 267:14250-14258. (PMID: 1378440)

D. Research Support Ongoing NSF DBI-1358941, 04/01/2014-03/31/2019, “REU Site – Summer Undergraduate Research Program in Biochemistry” The goals of this project are to recruit participants and administer a summer undergraduate research program in the Department of Biochemistry and Biophysics at Texas A&M University. G.R. Kunkel is the P.I. for this grant and co-director of the program.

American Heart Association SWA Winter 2014 Grant-in-Aid: 14GRNT20460146, 07/01/2014-06/30/2016, “Mechanism of Control of Zebrafish Heart Development by a Multifunctional Transcriptional Activator Protein” The goals of this project are to perform experiments to understand the mechanism of zebrafish heart development under transcriptional control by ZNF143 activator protein. Aims are to perform a detailed phenotypic analysis of heart marker gene expression after knockdown of ZNF143 and to determine molecular steps controlled by ZNF143 at one or more such gene promoters.

Program Director/Principal Investigator:LEIBOWITZ, Julian

NAME POSITION TITLE Leibowitz, Julian Professor of Microbial and Molecular Pathogenesis eRA COMMONS USER NAME JLeibowitz EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Alfred University, Alfred, NY B.A. 1964-1968 Chemistry Albert Einstein College of Medicine, Bronx, NY Ph.D. 1970-1975 Cell Biology Albert Einstein College of Medicine, Bronx, NY M.D. 1968-1975 Medicine University of California, San Diego, CA 1975-1977 Intern/Resident Pathology University of California, San Diego, CA 1977-1979 Exptl Neuropathology

A. Positions and Honors.

Positions: 1970-75. Medical Scientist Trainee, Albert Einstein College of Medicine, Bronx, N.Y. 1975-77. Intern and Resident, Department of Pathology, University of California, San Diego. 1977-79. USPHS Trainee and Post-doctoral Fellow in Neuropathology, University of California, San Diego. 1979-83. Assist. Prof. of Pathology in Residence, University of California, San Diego. 1983-95. Assist. Prof., Assoc. Prof., Prof. of Pathology and Laboratory Medicine, University of Texas Medical School-Houston. June, 1995-December, 2005. Prof. of Pathology and Laboratory Medicine, Texas A&M College of Medicine, College Station, TX. Jan. 2006-present. Prof. of Microbial and Molecular Pathogenesis, Texas A&M College of Medicine, College Station, TX. July 1998-present. Prof. of Veterinary Pathobiology, Texas A&M University, College Station, TX.

Other Experience and Professional Memberships Member, American Society of Virology, 1981-present Member, American Society for Microbiology, 1977-present Member, American Association for the Advancement of Science, 1975-present Member, Association of University Pathologists, 1991 Member, Veteran's Administration Merit Grant, Infectious Diseases Panel, 1994 -1997 NIH Ad hoc Peer Reviewer for Virology, Path B, CBNT, Neurology, and 7 Special Study Sections, 1987-2013 Peer Reviewer for Medical Research Council, UK, 2008 External Reviewer, Qatar National Research Fund, March 2013

Honors and Awards: Eta Mu Alpha, College Honor Society New York State Regents Medical School Scholarship Elected to the Pluto Club (Association of University Pathologists), 1991

B. Selected peer-reviewed publications (Selected from 100 peer-reviewed publications) Graduate students and post-docs are underlined.

Liu, Q, Johnson, RF, and Leibowitz, JL. (2001) Secondary structural elements within the 3' untranslated region of mouse hepatitis virus strain JHM genomic RNA. J. Virol. 75:12105–12113. PMCID: PMC116106 Program Director/Principal Investigator:LEIBOWITZ, Julian

Nanda, SK, Johnson, RF, Liu, Q, and Leibowitz, JL. (2004). Mitochondrial HSP70, and HSP60 bind to the 3’ untranslated region of the mouse hepatitis virus genome. Arch. Virol., 149:93-111. PMID: 14689278 Johnson, RF, Feng, M, Liu, P, Millership, JJ, Yount, B, Baric, RS, Leibowitz, JL. (2005).The effect of mutations in the mouse hepatitis virus 3'(+)42 protein binding element on RNA replication. J. Virol., 79:14570-14585. PMCID: PMC1287598 Youn, S, Leibowtiz, JL, and Collisson, EW. (2005) In vitro assembled, recombinant infectious bronchitis viruses demonstrate that the 5a open reading frame is not essential for replication. Virology 332:206-215. PMID: 15661153. Kang, K, Feng, M, Schroeder, ME, Giedroc, DP, and Leibowitz, JL. (2006). Putatative cis-acting stem-loops in the 5’untranslated region of the severe acute respiratory syndrome coronavirus can substitute for their MHV counterparts. J. Virol. 80:10600–10614. PMCID: PMC1641749 De Albuquerque, N, Baig, E, Xuezhong Ma, X, Zhang, J, He, J, Rowe, A, Habal, M, Liu M, Shale, I, Downey, GP, Gorczynski, R, Butany, J, Leibowitz, J, Weiss, SR, McGilvray, ID, Phillips, MJ, Fish, EN, and Levy, GA. (2006). Murine Hepatitis Virus Strain 1 (MHV-1) Produces a Clinically Relevant Model of SARS in A/J Mice. J. Virol. 80:10382–10394. PMCID: PMC1641767 Liu, P, Li, L, Millership, JJ, Kang, H, Leibowitz, JL, and Giedroc, DP. (2007). A U-turn motif-containing stem-loop in the coronavirus 5’ untranslated region plays a functional role in replication. RNA 13: 763-780. PMCID: PMC1852815 Kang, H, Bhardwaj, K, Li, Y, Palaninathan, S, Sacchettini, J, Linda Guarino, L, Leibowitz, JL, and Kao, CC. (2007). Biochemical and genetic analyses of the mouse hepatitis virus Nsp15 endoribonuclease. J Virol. 81:13587-13597. PMCID: PMC2168834 Li, L, Kang, H, Liu, P, Makkinje, N, Williamson, ST, Leibowitz, JL, Giedroc, DP. (2008). Structural lability in stem-loop 1 drives a 5' UTR-3' UTR interaction in coronavirus replication. J. Mol. Biol. 377:790-803. PMCID: PMC2652258 Liu, P, Li, L, Keane, SC, Yang, D, Leibowitz, JL, and Giedroc, DP. (2009). Mouse hepatitis virus stem-loop 2 adopts an uYNMG(U)a-like tetraloop structure that is highly functionally tolerant of base substitutions. J. Virol. 83:12084–12093. PMCID: PMC2786756 Grossoehme, NE, Li, L, Keane, SC, Liu, P, Dann III, CE, Leibowitz, JL, and Giedroc, DP. Coronavirus N protein N- terminal domain (NTD) specifically binds the transcriptional regulatory sequence (TRS) and melts TRS-cTRS RNA duplexes. (2009) J. Mol. Biol. 394:544-557. PMCID: PMC2783395 Leibowitz, JL, Srinivasa, R, Williamson, ST, Chua, MM, Liu, M, Wu, S, Kang, H, Ma, X-Z, Zhang, J, Itay Shalev, I, Smith, R, Phillips, MJ, Levy, GA, and Weiss,SR. (2010) Genetic determinants of mouse hepatitis virus strain 1 pneumovirulence. J. Virol. 84: 9278-9291. PMCID: PMC2937641 Yang, D, Liu, P, Giedroc, DP, and Leibowitz, JL. Mouse hepatitis virus stem-loop 4 functions as a spacer element required to drive subgenomic RNA synthesis. J. Virol. 85: 9199–9209, 2011. PMCID: PMC2786756. Keane, SC, Liu, P, Leibowitz, JL, and Giedroc, DP. Functional transcriptional regulatory sequence (TRS) RNA binding and helix destabilizing determinants of the murine hepatitis virus (MHV) nucleocapsid (N) protein. J. Biol. Chem. 287:7063–7073, 2012. PMID: 22241479 Bhardwaj, K, Liu, P, Leibowitz, JL, and Kao, CC. The coronavirus endoribonuclease nsp15 interacts with retinoblastoma tumor suppressor protein. J. Virol. 86: 4294-4304, 2012. PMCID: PMC3318636 Liu, P, Yang, D, Carter, K, Faryal, M, and Leibowitz, JL. Functional analysis of the stem loop S3 and S4 structures in the coronavirus 3'UTR. Virology 443:40-47, 2013. PMCID: PMC3700632 Kaufman, G, Liu, P, and Leibowitz, JL. Identification of novel functional regions within the spike glycoprotein of MHV- A59 based on a bioinformatics approach. Virus Res.189:177–188, 2014. McGruder, B and Leibowitz, JL. A review of genetic methods and models for analysis of coronavirus-induced severe pneumonitis. J. Gen. Virol., in press.

Program Director/Principal Investigator: LIGHTFOOT, J. Timothy

NAME POSITION TITLE Lightfoot, J. Timothy Omar Smith Endowed Professor eRA COMMONS USER NAME Director of the Sydney and JL Huffines Institute for jtlightf Sports Medicine and Human Performance EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Northeast Louisiana University, Monroe, LA BS 1981 Physical Education/Math Northeast Louisiana University, Monroe, LA MEd 1982 Exercise Physiology University of Tennessee, Knoxville, TN PhD 1986 Exercise Physiology Johns Hopkins University, Baltimore, MD Post-doc 1989 Physiology A. Positions and Honors Positions and Employment 1985 Research Consultant, The Bionetics Corporation, NASA, Kennedy Space Center; 1986-1989 Post-doctoral Research Fellow, Div. Physiology, Johns Hopkins University, Baltimore, MD; 1989-1993 Assistant Professor, Dept of Exercise Science, Florida Atlantic University, Boca Raton, FL; 1994-1996 Associate Professor & Dept Chair, Dept Exercise Science, Florida Atlantic University, Boca Raton, FL; 1996-2001 Associate Professor & Dept Chair, Dept of Kinesiology, University of North Carolina- Charlotte, Charlotte, NC; 2001-2005 Professor & Dept Chair, Dept of Kinesiology, University of North Carolina-Charlotte, Charlotte, NC; 2005-2010 Professor, Dept of Kinesiology, University of North Carolina-Charlotte, Charlotte, NC; 2010-current Omar Smith Endowed Professor & Director of the Huffines Inst. Sports Medicine and Human Performance, Dept. of Health and Kinesiology, Texas A&M University, College Station, TX. 2010-current Member, Faculty of Genetics (interdisciplinary faculty) Texas A&M University, College Station, TX. 2010-current Member, A&M Whole Systems Genomics Institute (interdisciplinary faculty) Texas A&M University, College Station, TX.

Other Experience and Professional Memberships 1983-curr Member, Southeast American College of Sports Medicine 1985-curr Member, American College of Sports Medicine 1991-cur Member, American Physiological Society 2003-06 American Physiological Society, Porter Physiology Minority Development Committee 2005 National Institutes of Health P50-Centers Of Research Translation Reviewer (ZAR1-MLB-G) 2005 National Institutes of Health – R03 Special Emphasis Study SectionReviewer (ZAR1-EHB-G) 2005 Compliance/Product Analyses US Army Medical Research Core 2006 U.S. Dept. of Defense/USARIEM Human Performance Optimization review panel (PRMRP) 2006-07 NIH P50-Centers Of Research Translation - Special Emphasis Reviewer (ZAR1-MLB-G) 2007 NIH, AMS 2008-01 Training Program Review Study Section 2008 NIH, Special Emphasis Panel/Scientific Review Group 2009/05 ZRR1 SEPA-6 2008-09 U.S. Dept. of Defense/USARIEM Human Performance Optimization review through the American Institute of Biological Services 2009 NIH, Special Emphasis Panel/Scientific Review Group ZAR1 EHBF(M2) 2009 NIH, Special Emphasis Panel/Scientific Review Group ZDK GRB-9(O1) 2010-12 Associate Editor, American College Sports Medicine’s Health and Fitness Journal 2010 Panelist, NIH NIAMS Roundtable “Mechanisms of Exercise Induced Health” (11/15/10) Program Director/Principal Investigator: LIGHTFOOT, J. Timothy

2011-15 Member, ACSM Science Integration & Leadership Committee 2013-curr Member, National Exercise Clinical Trials Network (NExTNet) B. Selected Peer-reviewed Publications (Selected from 60 peer-reviewed publications; *indicates student author) 1) Leamy, LJ, D Pomp, JT Lightfoot. Genetic variation in the pleiotropic association between physical activity and body weight in mice. Genetics Selection Evolution 41:41, 2009. PMID: 19772584 PMCID: PMCID: 2760520

2) *Moore-Harrison, T, Lightfoot, JT “Driven to be Inactive?: The Genetics of Physical Activity” Progress in Molecular Biology and Translational Science. 94: 271-290, 2010. PMID: 21036329, PMCID: 4183352

3) Bowen, RS*, DP Ferguson*, JT Lightfoot. Effects of Aromatase Inhibition on the Physical Activity Levels of Male Mice. Journal of Steroids and Hormonal Science S1:001, doi:10.4172/2157-7536.S1-001, 2011. PMCID: 3593090

4) Lightfoot, JT. Current understanding of the genetic basis for physical activity. J Nutrition 141: 526-530, 2011. PMID: 21270357 PMCID: PMC3040910

5) *Bowen, RS, MJ Turner, JT Lightfoot. Sex Hormone Effects on Physical Activity Levels: Why Doesn't Jane Run as Much as Dick? Sports Medicine 41(1): 73-86, 2011 PMID: 21142285 PMCID: 3050489

6) Leamy, LJ, D Pomp, JT Lightfoot. Epistatic interactions of genes influence within-individual variation of physical activity traits in mice. Genetica. 139(6): 813-821, 2011 PMID: 21667081, PMCID: 4181533

7) Lightfoot, JT. “Can You Be Born A Couch Potato? The Genomic Regulation of Physical Activity.” In Exercise Genomics (part of the Molecular and Translational Medicine Series)” Drs. S Roth and L Pescatello, eds. Humana/Springer (Publication date: April 2011).

8) *Knab, AM, *RS Bowen, AT Hamilton, JT Lightfoot. Pharmacological manipulation of the dopaminergic system affects wheel running activity in differentially active mice. Journal of Biological Regulators and Homeostatic Agents. 26(1): 119- 129, 2012. PMID: 22475103, PMCID: not assigned (NIHMS submission #: 631574)

9) Ferguson, DP*, EE Schmitt*, JT Lightfoot. Vivo-morpholinos induced transient knockdown of physical activity related proteins. PLoS ONE. 8(4): e61472. doi:10.1371/journal.pone.0061472 2013. PMID: 23630592, PMCID: 3632599

10) Lightfoot, JT. “Why Control Activity? Evolutionary selection pressures affecting the development of physical activity genetic and biologic regulation. BioMedical Research International, vol. 2013, Article ID 821678, 10 pages, 2013. doi:10.1155/2013/821678. PMID: 24455728, PMCID: 3884604

11) Dawes, M*, T Moore-Harrison*, AT Hamilton, T Ceaser*, KJ Kochan, PK Riggs, JT Lightfoot. Differential gene expression in high and low active inbred mice. BioMedical Research International. Vol. 2014, Article ID 361048, 9 pages, 2014. doi:10.1155/2014/361048. PMID: 24551844, PMCID: 3914289

12) Ferguson, DP*Ferguson, DP*, LJ Dangott, EE Schmitt*, HL Vellers*, JT Lightfoot. Differential skeletal muscle proteome of high and low active mice. J. Appl. Physiol. 116: 1057-1067, 2014 PMID: 24505100, PMCID: 4035790

13) Ferguson, DP*, LJ Dangott, JT Lightfoot. Lessons learned from vivo-morpholinos: How to avoid vivo-morpholino toxicity. Biotechniques. 56:251-256, 2014 PMID: 24806225, PMCID: 4182913

14) Bamman, MM, DM Cooper, FW Booth, ER Chin, PD Neufer, S Trappe, JT Lightfoot, WE Kraus, MJ Joyner. Exercise Biology and Medicine: Innovative Research to Improve Global Health. Mayo Clinic Proc. 89(2): 148-153, 2014. PMID: 24485128, PMCID: 3972063

15) deGeus, JCN, M Bartels, J Kaprio, JT Ligthfoot, M Thomis,. Genetics of regular exercise and sedentary behaviors. Twin Research and Human Genetics. 17(4): 262, 271, 2014 PMCID: not applicable Principal Investigator LINTS, Robyn

NAME POSITION TITLE Lints, Robyn Associate Professor of Biology at Texas A&M eRA COMMONS USER NAME University (TAMU) RLINTS EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of Auckland, New Zealand B.Sc. 1981-1984 Cell Biol., Biochemistry University of Auckland, New Zealand M.Sc. 1987-1989 Molecular biology University of Melbourne, Australia Ph.D 1989-1993 Molecular genetics Albert Einstein College of Medicine (AECOM), NY. Fellow 1996-2003 Developmental biology C. elegans Anatomy Center, AECOM, NY. Associate 2003-2005 Anatomy, Electron Micros

A. Positions and Honors. Positions and Employment 1987-1989 M.Sc.(Hons) graduate student, University of Auckland, New Zealand. Research: RFLP analysis of the genus Actinidia (kiwifruit). 1989-1993 Ph.D. graduate student, University of Melbourne, Australia. Research: Characterization of a transcription factor regulating Aspergillus nidulans growth. 1993-1996 Post-doctoral Fellow, Rutgers University, NJ. Research: Characterization of degenerin ion channel gene function in the vertebrate nervous system. 1996-2000 Post-doctoral Fellow, Albert Einstein College of Medicine, NY. Research: Genetic control of dopaminergic and serotonergic neuron development in C. elegans 2000-2003 Instructor of Molecular Genetics, Albert Einstein College of Medicine, NY. Research: Genetic control of dopaminergic and serotonergic neuron development in C. elegans 2003-2005 Associate of Neuroscience, Center for C. elegans Anatomy, Albert Einstein College of Medicine, NY. Research: Generation of a web-based anatomical atlas for the C. elegans male (http://www.wormatlas.org/handbook/contents.htm). 2005-2013 Assistant Professor, TAMU. Research: Optogenetic interrogation of sexually dimorphic circuits in C. elegans. 2013-present Associate Professor, TAMU. Research: Genetic and molecular dissection of neural circuit physiology using C. elegans as a model.

Other Experience and Professional Membership 2013 Society for Neuroscience, member 2003-2013 Genetics Society of America, member 2010-present TAMU Genetics and TAMU Neuroscience (TAMIN) graduate program faculty member. 2003-2005 Pittsburgh Supercomputing Center collaboration to development 3D models of sexually dimorphic neural tissues in C. elegans based on electron micrograph reconstructions. 2003-2005 Co-editor and author of the C. elegans Male Atlas on the wormatlas.org website. 2003-2007 Contributed chapters to the wormatlas.org hermaphrodite atlas and textbook: “C. elegans Altas” (2008). eds. David H. Hall and Z. Altun. Cold Spring Habor Laboratory Press, NY. 2014-present Collaboration with Jun Kameoka (TAMU Engineering) to develop microfluidic devices for visualizing mitochondria in C. elegans neurons. Honors 1993 Muscular Dystrophy Association of America Fellowship 2000 National Alliance for Schizophrenia and Depression (NARSAD), Young Investigators Award.

PHS 398/2590 (Rev. 09/04) Page 1 Biographical Sketch Format Page Principal Investigator LINTS, Robyn

B. Selected peer-reviewed publications (in chronological order).

Siehr M.S., Koo P.K., Sherlekar A.L., Bian X., Bunkers M.R., Miller R.M., Portman D.S. & Lints R*. (2011) Multiple doublesex-related genes specify critical cell fates in a C. elegans male neural circuit. PLoS One 6:e26811.

Koo P.K., Bian X, Sherlekar A.L., Bunkers M.R. & Lints R*. (2011) The robustness of Caenorhabditis elegans male mating behavior depends on the distributed properties of ray sensory neurons and their output through core and male-specific targets. J Neurosci 31:7497-510.

Liu Y., LeBeouf B., Guo X., Correa P.A., Gualberto D.G., Lints R. & Garcia L.R. (2011) A cholinergic- regulated circuit coordinates the maintenance and bi-stable states of a sensory-motor behavior during Caenorhabditis elegans male copulation. PLoS Genet 7:e1001326

Sherlekar AL, Janssen A, Siehr MS, Koo PK, Calfisch L, Boggess M, Lints R.* (2013) “The C. elegans male exercises directional control during mating through cholinergic regulation of the gender-shared command interneuron system” PLoS One 8: e60597.

Sherlekar AL, Lints R.* (2014). Nematode Tango Milonguero - The C. elegans male's search for the hermaphrodite vulva. Semin Cell Dev Biol. 33C:34-41. doi: 10.1016 (Invited Review)

*Corresponding author.

C. Research Support Institutional research support Robyn Lints, Ph.D (PI) 10/1/05-10/1/08 Texas A&M University Faculty Reinvestment Plan – R. Lints Start-Up Funds

NSF Grant (0818595) Robyn Lints, Ph.D (PI) 9/1/08-8/31/13 Title: Elucidating the genetic and neural basis of a C. elegans male motor behavior using stimulatory and inhibitory light-activated channels. Total Amount budgeted (direct + indirect): $556,890

PHS 398/2590 (Rev. 09/04) Page 2 Continuation Format Page Principal Investigator/Program Director (Last, First, Middle): LIU, Fei

NAME POSITION TITLE Liu, Fei Associate Professor LIUFEIHSC

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION (if YEAR(s) FIELD OF STUDY applicable) 4th Military Medical University, China MB 1989-1995 Medicine 4th Military Medical University, China MS 1995-1998 Immunology 4th Military Medical University, China Ph.D. 1999-2002 Immunology University of Dundee, Scotland, UK postdoctoral 2003 Developmental Biology training University of Aberdeen, Scotland, UK postdoctoral 2003-2005 Developmental Biology training University of Pennsylvania, USA postdoctoral 2005-2008 Developmental and training Cellular Biology

A. Positions and Honors

Employment Aug 1998–Aug 1999 Instructor, Department of Immunology, 4th Military Medical University, Xi'an, China Aug 2002–Jan 2003 Lecturer, Department of Immunology, 4th Military Medical University, Xi'an, China Oct 2008–Aug 2013 Assistant Professor, Institute for Regenerative Medicine at Scott & White, TAMHSC, Temple, TX Sep 2014–present Associate Professor, Institute for Regenerative Medicine at Scott & White, TAMHSC, Temple, TX Other Experience and Professional Memberships 2008-2009 Member, Society for Developmental Biology 2008-2009 Member, International Society for Stem Cell Research 2010-present Member, American/International Association for Dental Research 2011, 2012 Israel Science Foundation, ad hoc reviewer 2011-2014 Medical Research Council of United Kingdom, ad hoc reviewer 2012, 2014 NIH Peer Review Committee: NIDCR SPECIAL GRANTS REVIEW COMMITTEE (DSR)

B. Selected publications (from 41 papers)

1. Fei Liu, Yin Liu, Boquan Jin. Preparation and Characterization of Monoclonal Antibodies against GAM Protein, a Novel gp130 Associated Molecule. Hybridoma. 1999,12(4):371-378. PMID: 10571265. 2. Fei Liu, Boquan JIN, Yin LIU et al. The transcription co-repressor TLE1 Interacted with the intracellular

PHS 398/2590 (Rev. 09/04) Page Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle): LIU, Fei region of gp130 through its Q domain. Molecular and Cellular Biochemistry. 2002. 232(1-2): 163-167. PMID: 12030375 3. Fei Liu, Olaf van den Broek, Olivier Destrée and Stefan Hoppler. Distinct roles for Xenopus Tcf/Lef genes in mediating specific responses to Wnt/beta-catenin signalling in mesoderm development. Development, 2005. 132(24): 5375-5385. PMID: 16291789. 4. Thomas Andl, Elizabeth P. Murchison, Fei Liu, Yuhang Zhang, Monica Yunta-Gonzalez, John W. Tobias, Claudia D. Andl, John T. Seykora, Gregory J. Hannon, and Sarah E. Millar. The miRNA- Processing Enzyme Dicer Is Essential for the Morphogenesis and Maintenance of Hair Follicles. Current Biology, 2006. 16: 1041-1049. PMID: 16682203. PMCID: PMC2996092 5. Fei Liu, Shoba Thirumangalathu, Natalie M. Gallant, Cristi L. Stoick-Cooper, Steven H. Yang, Seshamma T. Reddy, Thomas Andl, Makoto M. Taketo, Andrzej A. Dlugosz, Randall T. Moon, Linda A. Barlow and Sarah E. Millar. Wnt/beta-catenin signaling initiates taste papilla development. Nature Genetics, 2007. 39(1):106-12. PMID: 17128274. PMCID: PMC3536498. 6. Fei Liu, Emily Y. Chu, Brenda Watt, Yuhang Zhang, Natalie M. Gallant, Thomas Andl, Steven H. Yang, Min-Min Lu, Stefano Piccolo, Ruth Schmidt-Ullrich, Makoto M. Taketo, Edward E. Morrisey, Andrzej A. Dlugosz, Sarah E. Millar. WNT/beta-catenin signaling directs multiple stages of tooth morphogenesis. Development Biology, 2008. 313(1):210-24. PMID: 18022614. Top cited article 2008-2010. 7. Afouda BA, Martin J, Liu F, Ciau-Uitz A, Patient R, Hoppler S. GATA transcription factors integrate Wnt signalling during heart development. Development. 2008 Oct;135(19):3185-90. PMID: 18715946. 8. Fei Liu, Thomas Andl, Yuhang Zhang, Alexander C. Wright, Monika Damek-Poprawa, Stefano Piccolo, Andras Nagy, Makoto M. Taketo, Thomas G. Diekwisch, Sunday Akintoye and Sarah E. Millar. beta- Catenin initiates tooth neogenesis in adult rodent incisors. Journal of Dental Research, 2010 Sep;89(9):909-14. PMID: 20530729. PMCID: PMC3148824. 9. Bo Hai, Zhenhua Yang, Sarah E. Millar, Yeon Sook Choi, Makoto Mark Taketo, Andras Nagy and Fei Liu. Wnt/β-catenin signaling regulates postnatal development and regeneration of the salivary gland. Stem cells and Development, 2010 19(11): 1793-1801. PMID: 20367250. Cover feature. 10. Bo Hai, Zhenhua Yang, Lei Shangguna, Yanqiu Zhao, Arthur Boyer and Fei Liu. Concurrent Transient Activation of Wnt/β-catenin Pathway Prevents Radiation Damage to Salivary Glands. International Journal of Radiation Oncology*Biology*Physics. (IJROBP). 2012 May 1;83(1):e109-16. PMID: 22342093. PMCID: PMC3340568. 11. Lei Shangguan, Xinyu Ti, Ulf Krause, Bo Hai, Yanqiu Zhao, Zhenhua Yang, and Fei Liu. Inhibition of TGF-β/Smad signaling by BAMBI blocks differentiation of human mesenchymal stem cells to carcinoma-associated fibroblasts and abolished their pro-tumor effects. Stem Cells, 2012 Dec;30(12):2810-9. doi: 10.1002/stem.1251. PMID: 23034983. 12. Zhenhua Yang, Bo Hai, Lizheng Qin, Xinyu Ti, Lei Shangguan, Yanqiu Zhao, Lindsey Wiggins, Ying Liu, Jian Q. Feng, Julia Yu Fong Chang, Fen Wang, Fei Liu. Cessation of epithelial Bmp signaling induces formation of cementum-like structures on tooth crowns by promoting EMT in a Wnt-dependent manner. Molecular and Cellular Biology, 2013. Dec;33(23):4732-44. doi: 10.1128/ MCB.00456-13. PMID: 24081330. PMCID: PMC3838012. 13. Bo Hai, Lizheng Qin, Zhenhua Yang, Qingguo Zhao, Lei Shangguan, Xinyu Ti, Yanqiu Zhao, Sangroh Kim, Dharanipathy Rangaraj, Fei Liu. Transient Activation of Hedgehog Pathway Rescued Radiation- induced Hyposalivation. Clinical Cancer Research, 2014 Jan 1;20(1):140-50. doi: 10.1158/1078- 0432.CCR-13-1434. PMID: 24150232. PMCID: PMC3951215. 14. Fei Liu & Songlin Wang. Invited Review. Molecular cues for development and regeneration of salivary glands. Histology and Histopathology, 2014 Mar; 29(3): 305-312. PMID: 24189993. 15. Qingguo Zhao, Fei Liu. Mesenchymal stem cells in progression and treatment of cancers. Invited Review. Frontiers in Biology, 2014 May, doi: 10.1007/s11515-014-1306-2

PHS 398/2590 (Rev. 09/04) Page Continuation Format Page Principal Investigator: LOOPSTRA, Carol A.

NAME POSITION TITLE Loopstra, Carol A. Associate Professor eRA COMMONS USER NAME

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Oregon State University B.Sc. 1979 Forest Management Oregon State University M.Sc. 1984 Forest Science North Carolina State University Ph.D 1992 Genetics and Forestry

A. Positions and Honors. 2001-present Associate Professor, Dept. of Ecosystem Science and Management, Texas A&M University, College Station, TX, USA 2002-2006 Associate Department Head for Graduate Programs, Dept. of Forest Science, Texas A&M University 1995-2001 Assistant Professor, Dept. of Forest Science, Texas A&M University 1995-present Member of the Faculty of Molecular and Plant Sciences, Texas A&M University 1995-present Member of the Faculty of Genetics, Texas A&M University 2000-present Member of the Faculty of Biotechnology, Texas A&M University 1993 - 1994 Research Officer, The University of Queensland, Brisbane, Australia* 1992 - 1993 Research Fellow, Griffith University, Brisbane, Australia* • These were the same postdoctoral position. Our university affiliation changed.

B. Selected peer-reviewed publications (in chronological order).

Neale DB, Wegrzyn JL, Stevens KA, Zimin A, Puiu D, Crepeau M, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, MartínezGarcía PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, Fuentes-Soriano S,Wu L,Gilbert D,Marçais G, Roberts M, Holt C,Yandell M, Davis JM, Smith K, Dean JFD, Lorenz W, Whetten RW Sederoff R, Wheeler N , McGuire PE, Main D, Loopstra CA , Mockaitis K, deJong P, Yorke JA , Salzberg SL, Langley CH. (2014) Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biology 15:R59. Wegrzyn JL, Liechty JD, Stevens KA, Wu L-S, Loopstra CA, Vasquez-Gross H, Dougherty WM, Lin BY, Zieve JJ, MartínezGarcía PJ, Holt C, Yandell M, Zimin A, Yorke JA, Grepeau M, Puiu D, Salzberg SL, de Jong, P, Mockaitis K, Main D, Langley CH, Neale DB. (2014) Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics 196:891-909. Eckert AJ, Wegrzyn JL, Liechty JD, Lee JM, Cumbie WP, Davis JM, Goldfarb B, Loopstra CA, Palle SR, Quesada T, Langley CH, Neale DB. (2013) The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae). Genetics 195: 1353-1372. Palle SR, Seeve CM, Eckert AJ, Wegrzyn JL, Neale DB, Loopstra CA. (2013) Association of loblolly pine xylem development gene expression with single nucleotide polymorphisms. Tree Physiology 33:763-774 Palle SR, Seeve CM, Eckert AJ, Cumbie WP, Goldfarb B, and Loopstra CA. (2011) Natural variation in expression of genes involved in xylem development in loblolly pine (Pinus taeda L.). Tree Genetics and Genomes 7: 193-206

PHS 398/2590 (Rev. 09/04) Page 1 Biographical Sketch Format Page Principal Investigator: LOOPSTRA, Carol A.

Kovach AS, Wegrzyn JL, Parra G , Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB (2010) The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics 11:420 doi:10.1186/1471-2164-11-420 Sathyan P, Newton RJ, and Loopstra CA (2005) Genes induced by WDS are differentially expressed in two populations of aleppo pine (Pinus halepensis). Tree Genetics and Genomes 1(4):166-173 Yang S-H and Loopstra CA (2005) Seasonal variation in gene expression for loblolly pines (Pinus taeda L.) from different geographical regions. Tree Physiology 25:1063-1073 Yang S-H, Wang H, Sathyan P, Stasolla C, and Loopstra CA (2005) Real-time RT-PCR analysis of loblolly pine (Pinus taeda L.) arabinogalatactan protein and arabinogalactan-protein-like genes. Physiologia Plantarum 124: 94-126

Yang S-H, van Zyl L, No E-G, and Loopstra CA (2004) Microarray analysis of genes preferentially expressed in differentiating xylem of loblolly pine (Pinus taeda). Plant Science 166:1185-1195 Zhang Y, Brown G, Whetten R, Loopstra CA, Neale D, and Sederoff RR. (2003) An arabinogalactan-protein associated with secondary cell wall formation in differentiating xylem of loblolly pine. Plant Molecular Biology – 52: 91-102 No E-G and Loopstra C.A. (2000) Hormonal and developmental regulation of two loblolly pine xylem arabinogalactan-proteins. Physiologia Plantarum – 110: 524-529. No E-G, Zhou Y, and Loopstra CA. (2000) Sequences upstream and downstream of two xylem-specific pine genes influence their expression. Plant Science 160: 77-86. Loopstra CA, Puryear JD, and No E-G. (2000) Purification and cloning of an arabinogalactan-protein from xylem of loblolly pine. Planta –210: 686-689 Loopstra C, Mouradov A, Vivian-Smith A, Glassick T, Gale B, Southerton S, Marshall H, and Teasdale R. (1998) Two Pinus radiata endo-b-1,4-glucanases are associated with rapidly growing reproductive structures. Plant Physiology 116: 959-967. Wang H and Loopstra C (1998) Cloning and characterization of a cellulose synthase cDNA (Accession No.AF081534) from xylem of hybrid poplar (Populus tremula X Populus alba). (PGR98-179) Plant Physiol. 118: 1101 Loopstra CA and Sederoff RR. (1995) Xylem-specific gene expression in loblolly pine. Plant Molecular Biology 27: 277-291. Loopstra CA, Weissinger AK and Sederoff RR (1992) Transient gene expression in differentiating pine wood using microprojectile bombardment. Can. J For. Res. 22: 993-996. Loopstra CA, Stomp A-M and Sederoff RR (1990) Agrobacterium mediated DNA transfer in sugar pine. Plant Molecular Biology. 15: 1-9. Stomp A-M, Loopstra CA, Chilton WS, Sederoff RR and Moore L. (1990) Agrobacterium tumefaciens in Pinus. Plant Physiology. 92: 1226-1232. Loopstra CA and Adams WT (1989) Patterns of variation in first year seedling traits within and among Douglas-fir breeding zones in southwest Oregon. Silvae genetica 38(5-6): 235-243. Adams WT, Neale DB and Loopstra CA (1988) Verifying controlled crosses in conifer tree-improvement programs. Silvae Genetica 37: 147-152. Alden J and Loopstra CA (1987) Genetic diversity and population structure of Picea glauca on an altitudinal gradient in interior Alaska. Can. J For. Res. 17: 1519-1526.

PHS 398/2590 (Rev. 09/04) Page 2 Continuation Format Page Principal Investigator/Program Director (Last, First, Middle): MAGILL Clint W.

NAME POSITION TITLE Magill, Clint . Professor eRA COMMONS USER NAME

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of Illinois B.Sc. 1963 Agricultural Science Cornell University Ph.D. 1968 Genetics Postdoctoral University of Minnesota 1967-69 Genetics Training

A. Positions and Honors Employment

1969-75 Assistant Professor, Dept. of Plant Sciences, Texas A&M University 1975-1989 Associate Professor, Dept. of Plant Sciences became Plant Pathology & Microbiology, TAMU 1989- Professor, Departent of Plant Pathology & Microbiology 1969- Member, Faculty of Genetics 1994- Member, Molecular and Environmental Plant Sciences (MEPS) 2005- Faculty, Masters in Biotechnology Program

Other Experience and Professional Memberships

Classroom Teaching (Current on an annual basis): Genetics 310, Principles of Heredity; Genetics 603 Introductory Graduate Genetics; BESC 481 and GENE 482, Undergraduate Seminars, Plant Pathology 610, Host Resistance Member, American Association for the Advancement of Science & American Phytoathology Society Editorial Advisory Board, Physiological and Molecular Plant Pathology

Honors 1986: TAMU-COALS Award for Excellence for Undergraduate Teaching 2008-2009 Speaker, TAMU Faculty Senate 2009: Named a Fellow of the American Association for the Advancement of Science

B. Selected peer-reviewed publications (Postdocs and Graduate Students as shown)

Magill, C.W. 2013 Bridging Classical and Molecular Genetics of Sorghum Disease Resistance, In Plant Genetics and Genomics: Crops and Models, Vol. 11 “Genomics of the Saccharinae” ed. Patterson, A.H., Ch. 15, pp347-367. Springer Little, C.R., Perumal, R., Tesso, T., Prom, L.K., Odvody, G.N., and Magill, C.W. 2012. Sorghum pathology and biotechnology - A fungal disease perspective: Part I. Grain mold, head smut, and ergot. The European Journal of Plant Science and Biotechnology 6: 10-30. Tesso, T., Perumal, R., Little, C.R., Adeyanju, A., Radwan, G., Prom, L.K., and Magill, C.W. 2012. Sorghum pathology and biotechnology - A fungal disease perspective: Part II. Anthracnose, stalk rot, and downy mildew. The European Journal of Plant Science and Biotechnology 6: 31-44. L. K. Prom,, R. Perumal,, SR Erattaimuthu,, CR Little, E-G No, J. E. Erpelding, W. L. Rooney, G. N. Odvody and C. W. Magill (2012) Genetic diversity and pathotype determination of Colletotrichum sublineolum isolates causing anthracnose in sorghum. European Journal of Plant Patholgy 133:671–685

PHS 398/2590 (Rev. 09/04) Page Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle): MAGILL Clint W.

Radwan, GL, Isakeit, T, Magill, CW, Perumal, R,.Prom, LK and Little, CR (2011) Screening exotic sorghum germplasm, hybrids and elite lines for resistance to a new virulent pathotype (P6) of Peronoslcerospr sorghi causing downy mildew. Plant Health Progress (online) doi:10.1094/PHP-2011-0323-01-RS Prom. LK, Perumal, R., Erattainmuthu, SR, Erpelding, JE, Montes, N, Odvody, GN., Greenwald, C. Jin Z., Frederiksen, R, and Magill, CW (2011) Virulence and Molecular Genotyping Studies of Sporisorium reilianum Isolates in Sorghum. Plant Disease 95:523-529. Prom, L. K., Perumal, R., Erpelding, J. E., Isakeit, T., and Montes, N., and Magill, C. W. 2009. A pictorial technique for mass screening of sorghum germplasm for anthracnose resistance. The Open Agric. J. 3:20-25 Katilé, SO, Perumal, R, Rooney, WL Prom, LK, Magill, C 2009 Expression of pathogenesis-related protein PR-10 in sorghum floral tissues in response to inocluation with Fusarium thapsinum and Curvularia lunata Mol. Plant Pathol. 11:93-103. Little, C.R., and Magill, C.W. 2009. The grain mold pathogen, Fusarium thapsinum, reduces caryopsis formation in Sorghum bicolor. Journal of Phytopathology 157: 518-519. Ramasamy, P, Menz, MA, Mehta, PJ, Katile, S, Gutierrez Rojas, LA, Klein, RR, Klein, PE, Prom, LK, Schlueter, JA, Rooney WL, & Magill, CW 2009. Molecular mapping of Cg1, a gene for resistance to anthracnose (Colletotrichum sublineolum) in sorghum. Euphytica 165:597-606. Perumal, R, Nimmakayala, P, Erattaimuthu, SR, No, E-G, Reddy,UK, Prom, LK, Odvody, GN, Luster, D. and Magill, CW. (2008) Simple sequence repeat markers useful for sorghum downy mildew (Peronosclerospora sorghi) and related species. BMC Genetics 9:77 http://www.biomedcentral.com/1471-2156/9/77 Liu, J., Stipanovic, R.D., Bell, A.A., Puckhaber, L.S., and Magill, C.W. (2008) Stereospecfific coupling of hemigossypol to form (+)-gossypol in moco cotton. Phytochemistry 69:3038-3042. - Perumal,, R., Krishnaramanujan, R., Menz, M.A., Katilé, S., Dahlberg, J., Magill, C.W., and Rooney, W.R. (2007) Genetic Diversity among Sorghum Races and Working Groups Based on AFLPs and SSRs. Crop Sci 47:1375-1383. Ramasamy, P., Frederiksen, R. A., Prom, L. K., and C. W. Magill (2007) “Head Smut” in Thakur, R. P., Reddy, B. V. S. and K Mathur (eds.) Screening Techniques for Sorghum Diseases. Information Bulletin No. 76. ICRISAT, Patancheru 502 324, Andhra Pradesh, India Sabry, A.B., Jeffers, D.,Vasal, S.K., Frederiksen, R., and Magill, C.W. (2006) A region of maize chromosome 2 affects response to downy mildew pathogens. Theor. Appl. Genet. 113:321-330. Perumal, R. Isakeit, T., Menz, M., Katilé, S., No, E-G, Magill, C.W. (2006) Characterization and genetic distance analysis of isolates of Peronosclerospora sorghi using AFLP fingerprinting. Mycological Res. 110:471-478. He, B., Magill, C. & Starr, J. (2005) Laser capture microdissection and real-time PCR for measuring mRNA in giant cells induced by Melodogyne javanica. Journal of Nematology 37: 308-31. Bolek, Y., El Zik, K., Pepper, A.E., Bell, A.A., Magill, C.W., Thaxton, P.M., and Reddy, O.U.K. 2005. Mapping of verticillium wilt resistance genes in cotton. Plant Science 168: 1581-1590. Benedict, C.R., Martin, G., Liu, J., Puckhaber, L. and Magill C. W. 2004. Terpenoid aldehyde formation and lysigenous gland storage sites in cotton: Variant with mature glands but suppressed levels of terpenoid aldehydes Phytochemistry 65:1351-1359. Little, C. R. and Magill, C. W. 2004. Elicitation of defense response genes in Sorghum bicolor (L.) Moench in response to infection by Fusarium thapsinum and Curvularia lunata at anthesis. Mol. & Physiol. Plant Patholgy 63: 271 - 279. Martin, G., Liu, J., Benedict, C., Stipanovic, R., Magill, C. 2003. Reduced levels of cadinane sesquiterpenoids in cotton plants expressing antisense (+)-d-cadinene synthase. Phytochemistry 62:31-38. Liu, J., Benedict, C, Bell, AA, Stipanovic, RD, Magill, CW, 2002. Cloning and Expression of Desoxyhemigossypol-6-O- Methyltransferase from Cotton (Gossypium barbadense) Journal of Agricultural & Food Chemistry 50: 3165-3172 Cui, Y., Bell, A. A., Puckhaber, L., Joost, O., and Magill, C. 2000. Induction of defense genes in wilt-resistant and susceptible cotton cultivars by Verticillium and Fusarium. Physiol. & Mol. Plant Pathology 56:25-31. Naidoo, G., R. A. Frederiksen, J. H. Torres-Montalvo, and C. W. Magill (1999) Maize and sorghum isolates of Sporisorium reilianum differ in electrophoretic karyotype MMPOL. (http://www.bspp.org.uk/mppol/1999/0419Naidoo) Boora, Khazan S., Richard A. Frederiksen and Clint W. Magill (1999) A molecular marker that segregates with sorghum leaf blight resistance in one cross is maternally inherited in another. Molecular and General Genetics 261:317-322.

PHS 398/2590 (Rev. 09/04) Page Continuation Format Page Principal Investigator/Program Director (Last, First, Middle): MATEOS, Mariana

NAME POSITION TITLE Mateos, Mariana Associate Professor eRA COMMONS USER NAME

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Biochemical Engineer in ITESM-Campus Guaymas, Sonora, México B.Sc. (Hons) 1991-1995 Aquatic Resources Rutgers University Ph.D. 1996-2002 Ecology and Evolution University of Arizona Postdoc. 2002-2005 Ecology and Evolution

A. Positions and Honors

Employment 1995 Coordinator’s Assistant, Conservation International, Mexico 1996-99 Graduate Research Assistant, Rutgers University 1999-02 Monterey Bay Aquarium Research Institute Graduate Research Assistant 2005-06 Assistant Professor, Dept. Biology, University of Texas at El Paso 2006-14 Assistant Professor, Dept. Wildlife and Fisheries Sciences, Texas A&M University 2014-P Associate Professor, Dept. Wildlife and Fisheries Sciences, Texas A&M University Member, Faculty of Genetics Member, IRB Ecology and Evolutionary Biology

Other Experience and Professional Memberships

2008 Panelist NSF-“Population and Evolutionary Processes” 2012 Co-Chair, Session at the Entomological Society of America’s Annual Meeting 2013 Panelist NSF-“Evolutionary Processes”

Honors and Awards

1996-99 Fulbright-García Robles Fellowship for Doctoral studies 2014-15 Award from CONACyT (Consejo Nacional de Ciencia y Tecnología) for sabbatical visit hosted by Dr. Esperanza Martínez-Romero, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM) 2014-17 Level II Distinction of the National Researcher System of Mexico (Sistema Nacional de Investigadores)

B. Selected peer-reviewed publications (*Graduate students in my lab, ** Undergraduate students in my lab, †Graduate students who interned in my lab, CCorresponding author, ¶Contributed equally) http://www.researcherid.com/rid/B-5235-2008 http://scholar.google.com/citations?user=5crpC3sAAAAJ

Santamaria*, C.A., M. MateosC, and L.A HurtadoC. 2014. Diversification at the narrow sea-land interface in the Caribbean: phylogeography of endemic supralittoral Ligia isopods. Frontiers in Ecology and Evolution 2: 42. doi: 10.3389/fevo.2014.00042

PHS 398/2590 (Rev. 09/04) Page Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle): MATEOS, Mariana HurtadoC, L.A., E.J. Lee*, M. Mateos, and S. Taiti. 2014. Global diversification at the harsh sea-land interface: Mitochondrial phylogeny of the supralittoral isopod genus Tylos (Tylidae, Oniscidea). PLoS ONE 8: e94081. doi: 10.1371/journal.pone.0094081 Santamaria*, C.A., M. Mateos, S. Taiti, T.J. DeWitt, and L.A. HurtadoC. 2013. A complex evolutionary history in a remote archipelago: phylogeography and morphometrics of the Hawaiian endemic Ligia isopods. PLoS ONE 8: e85199. doi:10.1371/journal.pone.0085199 Xie*, J., S. Butler**, G. Sanchez**, and M. MateosC. 2013. Male killing Spiroplasma protects Drosophila melanogaster against two parasitoid wasps. Heredity http://www.nature.com/hdy/journal/vaop/ncurrent/full/hdy2013118a.html [paper featured in The Heredity Podcast http://www.nature.com/multimedia/podcast/hdy/hdypodcast_1311.mp3] EberlC, R., M. Mateos, R.K. Grosberg, C.A. Santamaria*, and L.A. HurtadoC. 2013. Phylogeography of the supralittoral isopod Ligia occidentalis around the Point Conception marine biogeographic boundary. Journal of Biogeography 40: 2361-2372. HurtadoC, L.A., E.J. Lee*, and M. Mateos. 2013. Contrasting phylogeography of sandy vs. rocky supralittoral isopods in the megadiverse and geologically dynamic Gulf of California and adjacent areas. PLoS ONE 8:e67827 Silva* N.O., L.L. Guenther**, J. Xie*, and M. MateosC. 2012. Infection densities of three Spiroplasma strains in the host Drosophila melanogaster. Symbiosis 57: 83–93. Martinez*, H., J. Toledo, P. Liedo, and M. MateosC. 2012. Survey of heritable endosymbionts in southern Mexico populations of the fruit fly species Anastrepha striata and A. ludens. Current Microbiology 65: 711–718. Mateos¶C, M., L.A. Hurtado¶C, C.A. Santamaria*, V. Leignel, and D. Guinot. 2012. Molecular systematics of the deep-sea hydrothermal vent endemic brachyuran family Bythograeidae: a comparison of three Bayesian Species tree methods. PLoS ONE 7: e32066. ToblerC, M., M. Palacios†, L. Chapman, I. Mitrofanov, D. Bierbach, M. Plath, L. Arias-Rodriguez, F. J. García de León, and M. Mateos. 2011. Replicated phenotypic differentiation in livebearing fish inhabiting sulfidic springs. Evolution 65: 2213–2228. Xie*, J., B. Tiner**, I. Vilchez†, and M. MateosC. 2011. Reproductive fitness of Spiroplasma-infected Drosophila flies surviving a parasitoid wasp attack. Evolutionary Ecology 25: 1065–1079. CulumberC, Z., H. Fisher, M. Tobler, M. Mateos, P. Barber, M. Sorenson, and G. Rosenthal. 2011. Replicated hybrid zones of Xiphophorus swordtails along an elevational gradient. Molecular Ecology 20: 342–356. Xie*, J., I. Vilchez†, and M. MateosC. 2010. Spiroplasma bacteria enhance survival of Drosophila hydei attacked by the parasitic wasp Leptopilina heterotoma. PLoS ONE 5: e12149. HurtadoC, L.A., M. Mateos, and C.A. Santamaria*. 2010. Phylogeography of Ligia isopods from Central California to Central Mexico. PLoS ONE 5: e11633. O’NeillC, M.J., B.R. Lawton, M. Mateos, D.M. Liscinsky, G.C. Ferreri, T. Hrbek, R.W. Meredith, D.N. Reznick, and R.J. O’Neill. 2007. Ancient and continuing Darwinian selection on Insulin-like Growth Factor II in Placental fishes. Proceedings of the National Academy of Sciences, USA: 104: 12404- 12409. MateosC, M., S.J. Castrezana, B.J. Nankivell, A.M. Estes, T.A. Markow, and N.A. Moran. 2006. Heritable endosymbionts of Drosophila. Genetics: 174: 363–376. WeiderC, L.J., J.J. Elser, T.J. Crease, M. Mateos, T.A. Markow, and J.B. Cotner. 2005. Functional ecological significance of ribosomal(r)DNA variation: Impacts on the evolutionary ecology of organisms. Annual Review of Ecology Evolution and Systematics 36: 219–242.

PHS 398/2590 (Rev. 09/04) Page Continuation Format Page Principal Investigator MCKNIGHT, Thomas D.

NAME POSITION TITLE McKnight, Thomas D. Professor & Head of Biology at Texas A&M eRA COMMONS USER NAME University (TAMU)

A. Positions and Honors. Positions and Employment 1982-1985 Postdoctoral Associate, Atlantic Richfield Plant Cell Research Institute, Dublin CA 1985-1991 Assistant Professor, Department of Biology, Texas A&M University 1985- Member of Interdepartmental Faculties of Genetics and Plant Physiology 1991-2002 Associate Professor, Department of Biology, Texas A&M University 2002 - Professor, Department of Biology, Texas A&M University 2003 - 2014 Associate Head, Department of Biology, Texas A&M University 2003 - 2007 Director, Introductory Biology Program, Texas A&M University 2008 Acting Department Head, Department of Biology, Texas A&M University 2013 Interim Department Head, Department of Biology, Texas A&M University 2014 - Department Head, Department of Biology, Texas A&M University

B. Selected peer-reviewed publications (in chronological order).

SELECTED PUBLICATIONS (from 48 total): Góngora-Castillo, E., Childs, K.L., Fedewa, G., Hamilton, J.P., Liscombe, D.K., Magallanes-Lundback, M., Mandadi, K.K., Nims, E., Runguphan, W., Vaillancourt, B., Varbanova-Herde, M., Dellapenna, D., McKnight, T.D., O'Connor, S., Buell, C.R. 2012. Development of transcriptomic resources for interrogating the biosynthesis of monoterpene indole alkaloids in medicinal plant species. PLoS One. 7(12):e52506. doi: 10.1371/journal.pone.0052506. Robinson, W.D., Park, J., Tran, H.T., Del Vecchio, H.A., Ying, S., Zins, J.L., Patel, K., McKnight, T.D., Plaxton, W.C. 2012. The secreted purple acid phosphatase isozymes AtPAP12 and AtPAP26 play a pivotal role in extracellular phosphate-scavenging by Arabidopsis thaliana. J. Exp. Bot. 63; 6531-6542. Mandadi,K.K., Misra, A., Ren, S., and McKnight, T.D. 2009. BT2, a BTB protein, mediates multiple responses to nutrients stresses, and hormones in Arabidopsis. Plant Physiol. 150; 1930-1939. Shakirov E.V., McKnight, T.D., and Shippen, D.E. 2009. POT1-independent single-strand telomeric DNA-binding activities in Brassicaceae. Plant J. 58; 1004-1015. Ren, S., Boedeker, A., Rathore, K., and McKnight, T.D. 2007. Regulation of telomerase in Arabidopsis by BT2, an apparent target of the TAC1 transcription factor. Plant Cell 19; 23-31. Lu, H., Gorman, E., and McKnight, T.D. 2005. Molecular Characterization of two anthranilate synthase alpha subunit genes in Camptotheca acuminata. Planta 221; 352-360. Ren, S., Johnston,J.S., Shippen, D. E., and McKnight, T.D. 2004. TELOMERASE ACTIVATOR1 induces telomerase activity and potentiates responses to auxin in Arabidopsis. Plant Cell 16; 2910- 2922.

PHS 398/2590 (Rev. 09/04) Page 1 Biographical Sketch Format Page Principal Investigator MCKNIGHT, Thomas D. McKnight, T.D. and Shippen, D.E. 2004. Historical Perspective: Plant Telomere Biology. Plant Cell 16; 794-803. McKnight, T.D., Riha, K., and Shippen, D.E. 2002. Telomeres, telomerase, and stability of the plant genome. Plant Mol. Biol. 48; 331-337. Riha, K., McKnight,T.D., Griffing, L.R., and Shippen, D.E. 2001. Living with genome instability: plant responses to telomere dysfunction. Science 291; 1797-1800. Fitzgerald, M.S., Shakirov, E.V., Hood, E.E., McKnight, T.D., and Shippen, D.E. 2001. Different modes of de novo telomere formation by plant telomerases. Plant J. 26; 77-88. Riha, K., McKnight, T.D., Fajkus, J., Vyskot, B., and Shippen, D.E. 2000. Analysis of the G-overhang structures on plant telomeres: evidence for two distinct telomere architectures. Plant J. 23; 633- 641. Hanson, R.E., Islam-Faridi, M.N., Crane, C.F., Zwick, M.S., Czeschin, D.G., Wendel, J.F., McKnight, T.D., Price, H.J., and Stelly, D.M. 2000. Ty1-copia retrotransposon behavior in a polyploid and its putative diploid ancestors. Chromosome Res. 8; 73-76. Fitzgerald, M.S., Riha, K., Gao, F., Ren, S., McKnight, T.D., and Shippen, D.E. 1999. Disruption of the telomerase catalytic subunit gene from Arabidopsis inactivates telomerase and leads to a slow loss of telomeric DNA. Proc. Natl. Acad. Sci. USA.. 96;14813-14818. Patel, K.S., Lockless, S.W., Thomas, B.E., and McKnight, T.D. 1999. Secreted purple acid phosphatase from Arabidopsis thaliana. In Phosphorous in Plant Biology; Regulatory Roles in Molecular, Cellular, Organismic and Ecosystem Processes. J.P. Lynch and J. Deikman, eds. ASPP, Rockville, MD. Ji, Y., De Donato, M., Crane, C.F., Raska, W.A., Islam-Faridi, M.N., McKnight, T.D., Price, H. J., and Stelly, D.M. 1999. New ribosomal RNA gene locations in Gossypium hirsutum mapped by meiotic FISH. Chromosoma 108; 200-207. Lu, H. and McKnight, T.D. 1999. Tissue-specific expression of the $-subunit of tryptophan synthase in Camptotheca acuminata, an indole alkaloid-producing plant. Plant Physiol. 120;43-51. Hanson, R.E., Zhao, X.-P., Islam-Faridi, M.N. Paterson, A.H., Zwick, M.S., Crane, C.F., McKnight, T.D., Stelly, D.M., and Price, H.J. 1998. Evolution of interspersed repetitive elements in Gossypium (Malvaceae). Am. J. Bot. 85;1364-1368. Shippen, D.E. and McKnight, T.D. 1998. Telomeres, telomerase, and plant development. Trends in Plant Sciences. 3;126-130. (Invited Review) McKnight, T.D., Fitzgerald, M.S., and Shippen, D.E. 1997. Plant telomeres and telomerase. Biochemistry (Moscow). 62;;1224-1231. (Invited Review) Vincent, R.M., López-Meyer, M., McKnight, T.D. and Nessler, C.L. 1997. Sustained harvest of camptothecin from the leaves of Camptotheca acuminata. J. Natural Products.60;618-619. Zwick, M.S., Hanson, R.E., McKnight, T.D., Islam-Faridi, MN., Stelly, D.M., Wing, R.A., and Price, H.J. 1997. A rapid procedure for the isolation of Cot-1 DNA from plants. Genome 40;138-142. Ji, Y., Raska, D.A., McKnight, T.D., Islam-Faridi, M.N., Crane, C.F., Zwick, M.S., Hanson, R.E., Price, H.J., and Stelly, D.M. 1997. Use of meiotic FISH for identification of a new monosome in Gossypium hirsutum L. Genome 40;34-40. Fitzgerald, M.S., McKnight, T.D., and Shippen, D.E. 1996. Characterization and developmental patterns of telomerase expression in plants. Proc. Natl. Acad. Sci. USA. 93;14422-14427. Hanson, R.E., Islam-Faridi, M.N., Percival, E.A., Crane, C.F., Ji, Y., McKnight, T.D., Stelly, D.M., and Price, H.J. 1996. Distribution of 5S and 18S-28S rDNA loci in a tetraploid cotton (Gossypium hirsutum L.) and its putative diploid ancestors. Chromosoma 105;55-61.

PHS 398/2590 (Rev. 09/04) Page 2 Continuation Format Page

Program Director/Principal Investigator (Last, First, Middle): MENET, Jerome S

NAME POSITION TITLE Menet, Jerome S Assistant Professor eRA COMMONS USER NAME (credential, e.g., agency login) MenetPI EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) Science & Technology University, Lille, France B.S. 1998 Cell Biology & Physiology Louis Pasteur University, Strasbourg, France Master 1999 Neuroscience Louis Pasteur University, Strasbourg, France Ph.D. 2003 Neuroscience Brandeis University, MA Post-doc 2003-2013 Molecular Biology

A. Personal statement The goal of the proposed research is to investigate the contribution of the three-dimensional organization of the genome in the coordination of rhythmic gene expression by the circadian clock. Specifically, we plan to characterize long-range chromatin interactions in mouse tissues collected at different time of day, and examine whether dynamic changes in chromatin interactions underlie rhythmic gene expression. To this end, we will use several techniques including the Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET), which has been successfully set up in our lab. I have the motivation, expertise and leadership necessary to successfully carry out the proposed work. I have worked in the field of circadian biology for 16 years and, as a postdoctoral fellow at Brandeis University, I more particularly investigated the molecular basis of circadian rhythms in insects and mammals. Over the last 5 years, I initiated independent projects as a HHMI Research Specialist and examined the role of the molecular clock in the generation of circadian rhythms at the genome-wide level in the mouse. I set up a wide-range of molecular and biochemical techniques that include next-generation sequencing (RNA-Seq, ChIP-Seq, Nascent-Seq and MNase-Seq) and produced several high-profile peer- reviewed publications. I recently started my own lab in the Department of Biology and the Center for Biological Clock Research at Texas A&M University to continue my work on the molecular basis of circadian rhythms in the mouse. In particular, we are expanding our recent discovery that the molecular clock promotes rhythmic chromatin remodeling (Menet et al., 2014), a finding that laid the groundwork for the proposed research. I have trained a graduate student, Alexandra Trott, who will work on this specific project during her Ph.D. thesis. In summary, I have a demonstrated record of productive research projects in the field of molecular circadian rhythms, and my expertise and experience have prepared me well to lead the proposed project.

B. Positions and Honors. Positions and Employment 1998-1999 Master student, Louis Pasteur University, Strasbourg, France 1999-2003 Ph.D. student, Louis Pasteur University, Strasbourg, France 2002-2003 Lecturer, Louis Pasteur University, Strasbourg, France 2003-2009 Post-doctoral Fellow, Michael Rosbash laboratory, Brandeis University, Waltham, MA 2009-2013 HHMI Research Specialist, Michael Rosbash laboratory, Brandeis University, Waltham, MA 2013- Assistant Professor, Department of Biology, Texas A&M University, TX

Other Experience and Professional Memberships 2008- Member of the Society for Research on Biological Rhythms 2013- Member of the Center for Biological Clocks Research, Texas A&M University, TX PHS 398/2590 (Rev. 11/07) Page 1 Biographical Sketch Format Page 2013- Faculty of Genetics, Texas A&M University, TX 2014- Faculty of Neuroscience, Texas A&M Institute for Neuroscience, Texas A&M University, TX

Grant Review 2014 Ad hoc reviewer, National Science Foundation, Division of Molecular and Cellular Biosciences

Journal Review 2014- Ad hoc Reviewer for PLoS One; Biochim. Biophys. Acta; Nucleic Acids Res

Honors and Awards 1999-2002 Ph.D. fellowship from the French Ministry of National Education and Research 2004-2005 Long-term EMBO post-doctoral fellowship 2008 Young Investigator Award, French-speaking Society of Chronobiology 2009 Talk selected for the Hot Topic symposium of the 11th congress of the EBRS 2011 Hot Topic presentation at the Chronobiology Gordon Research Conference 2013 Chair of the Chronobiology Gordon Research Seminar 2013 Hot topic presentation at the Chronobiology Gordon Research Conference

C. Selected Peer-reviewed Publications (of 20 total) 1. Stoleru D, Nawathean P, de la Paz Fernandez M, Menet JS, Ceriani MF, Rosbash M (2007) The Drosophila circadian network: a brain clock for all seasons. Cell 129(1):207-19. 2. Revel FG, Herwig A, Garidou ML, Dardente H, Menet JS, Masson-Pévet M, Simonneaux V, Saboureau M, Pévet P (2007) The circadian clock stops ticking during deep hibernation in the European hamster. Proc Natl Acad Sci U S A 104(34):13816-13820. PMC1959465. 3. Kadener S, Menet JS, Schoer R, Rosbash M (2008) Circadian Transcription Contributes to Core Period Determination in Drosophila. PLoS Biol 6(5):e119. PMC2386838. 4. Kadener S, Menet JS, Sugino K, Horwich MD, Nawathean P, Vagin VV, Zamore PD, Nelson S, Rosbash M. (2009) A role for microRNAs in the Drosophila circadian clock. Genes Dev 23(18):2179-91. PMC2751990. 5. Menet JS, Abruzzi KA, Desrochers J, Rodriguez J, Rosbash M (2010) Dynamic PER repression in the Drosophila circadian clock: from on- to off-DNA. Genes Dev 24(4):358-67. PMC2816735. 6. Menet JS, Rosbash M (2011) When brain clocks lose track of time: cause or consequence of neuropsychiatric disorders. Curr Opin Neurobiol 21(6) 849-57. PMC3252427. 7. Abruzzi KC, Rodriguez J, Menet JS, Desrochers J, Zadina A, Luo W, Tkachev S, Rosbash M. (2011) Drosophila CLOCK target gene characterization: implications for circadian tissue-specific gene expression. Genes Dev 25(22):2374-86. PMC3222903. 8. Rodriguez J, Menet JS, Rosbash M. (2012) Nascent-Seq indicates widespread cotranscriptional RNA editing in Drosophila. Mol Cell 47(1):27:37. PMC3409466. 9. Khodor YL, Menet JS, Tolan M, Rosbash M. (2012) Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse. RNA 18(12):2174-86. PMC3504670. 10. Menet JS, Rodriguez J, Abruzzi KC, Rosbash M. (2012) Nascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation. eLife 1:e00011. PMC3492862. 11. Rodriguez J, Tang CH, Khodor YL, Vodala S, Menet JS, Rosbash M. (2013) Nascent-Seq analysis of Drosophila cycling gene expression. Proc Natl Acad Sci U S A. 110(4):E275-84. PMC3557077. 12. Menet JS, Pescatore S, Rosbash M. CLK:BMAL1 is a pioneer-like transcription factor. (2014) Genes Dev 28(1):8-13. PMC3894415.

D. Research Support 2013-2016 Texas A&M startup funds

2014 Center for Biological Clock Research Seed Fund ($14,000)

PHS 398/2590 (Rev. 11/07) Page 2 Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle): MILLER, Jr., J. Creighton

NAME POSITION TITLE Miller, Jr., J. Creighton Professor eRA COMMONS USER NAME jcmillerjr EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Louisiana State University B.S. 1965 General Studies Louisiana State University M.S. 1967 Horticulture Horticulture (Plant Michigan State University Ph.D. 1972 Breeding)

A. Positions and Honors

Employment

1965-67 Research Assistant, Louisiana State University 1967-68 Research Assistant, University of Wisconsin 1968-72 Research Assistant, Michigan State University 1972-75 Assistant Professor, Texas Agricultural Experiment Station, Lubbock 1975-77 Assistant Professor, Texas A&M University 1977-82 Associate Professor, Texas A&M University 1980-83 Interim Head, Horticultural Sciences Department 1981 - Graduate Faculty of Genetics 1982 - Professor, Texas A&M University 1984 - 2008 Graduate Faculty of Molecular and Environmental Plant Sciences 2010 - Graduate Faculty of Biotechnology

Other Experience and Professional Memberships

1992 American Society for Horticultural Science, Southern Region, President 1976 American Society for Horticultural Science 1998-99 The Potato Association of America, President 1970 American Association for the Advancement of Science

Honors

1987 American Society for Horticultural Science, Fellow 1997 Horticulture Graduate Council, Faculty Distinguished Service Award 2002 Southern Region, American Society for Horticultural Science, L.M. Ware Distinguished Teaching Award 2003 Honorary Life Member, Potato Association of America 2005 Association of Former Students Distinguished Teaching Award 2009 Outstanding Researcher Award, American Society for Horticultural Science 2009 Research Patent Award, TAMU System Office of Technology Commercialization

B. Selected peer-reviewed publications (Postdocs and Graduate Students as shown)

Reddivari, L., A.L. Hale, and J.C. Miller, Jr. (2007). Genotype and location influence antioxidant activity, phenolic content, carotneiod content, and phenolic composition in specialty potatoes. J. Agric. Food Chem. 55:8073-8079. PHS 398/2590 (Rev. 09/04) Page Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle): MILLER, Jr., J. Creighton

Reddivari, L., J. Vanamala, S. Chintharlapalli, S.H. Safe, and J.C. Miller, Jr. (2007). Anthocyanin fraction from potato extracts is cytotoxic to prostate cancer cells through activation of caspase-dependent and caspase- indepenent pathways. Carcinogenesis. 28:2227-2235. (doi 10.1093/carcin/bgm117).

Hale, A.L., L. Reddivari, N.M. Nzaramba, J.B. Bamberg, and J.C. Miller, Jr. (2008). Interspecific variability for antioxidant activity and phenolic content among Solanum species. Amer. J. Potato Res. 85:332-241.

Nzaramba, M.N., L. Reddivari, J.B. Bamberg, and J.C. Miller, Jr. (2009). Antiproliferative activity and cytoxicity of Solanum jamesii tuber extracts on human colon and prostrate cancer cells in Vitro. J. Agric. Food Chem. 57:8308-8315.

Bona, C.M., J.H. Gould, J.C. Miller Jr., D. Stelly, and E.S. Louzada (2009). Citrus asymmetric somatic hybrids produced via fusion of gamma-irradiated and iodoacetamide-treated protoplasts. Pesq. Agropec. Bras., Brasilia, 44: 454-462.

Bona, C.M., D. Stelly, J.C. Miller Jr., and E.S. Louzada (2009). ‘Fusion of protoplasts with irradiated microprotoplasts as a tool for radiation hybrid panel in citrus’ Pesq. Agropec. Bras., Brasilia. 44(12):1616-1623.

Brown, C. R., K.G. Haynes, M. Moore, M.J. Pavek, D.C. Hane, S.L. Love, R.G. Novy, and J.C. Miller, Jr. (2010). Stability and broad-sense heritability of mineral content in potato: Iron. Amer. J. Potato Res. 87:390-396.

Reddivari, L., J. Vanamala, S.H. Safe, and J.C. Miller, Jr. (2010). The bioactive compounds α - chaconine and gallic acid in potato extracts decrease survival and induce apoptosis in LNCaP and PC3 prostate cancer cells. Nutr. Cancer. 62(5): 601-610.

Blessington, T., M.N. Nzaramba, D.C. Scheuring, A.L. Hale, L. Reddivari, and J.C. Miller, Jr. (2010). Cooking methods and storage treatments of potato: Effects on carotenoids, antioxidant activity, and phenolics. Amer. J. Potato Res. 87:479-491. (Outstanding Paper Award 2010, Potato Association of America).

Jansky, S. and J.C. Miller, Jr. (2010). Evaluation of Verticillium wilt resistance in Russet Norkotah and six strain selections. Amer. J. Potato Res. 87:492-496.

Brown, C. R., K.G. Haynes, M. Moore, M.J. Pavek, D.C. Hane, S.L. Love, R.G. Novy, and J.C. Miller, Jr. (2011). Stability and broad-sense heritability of mineral content in potato: Zinc. Amer. J. Potato Res. 88:238-244.

Butler, C.D., B. Gonzalez, M.L. Keremane, R.F. Lee, R.G. Novy, J.C. Miller, and J.T. Trumble (2011). Behavioral responses of adult potato psyllid, Bactericera cockerelli (Hemiptera: Triozidae), to potato germplasm and transmission of Candidatus Liberibacter psyllaurous. Crop Prot. 30:1233-1238.

deBona, C.M., D.C. deCarvalho, D.M. Stelly, J.C. Miller, Jr, and E.S. Louzada (2011). Symmetric and asymmetric somatic hybridization in citrus: A review. Citrus Res Technol, Cordeiropolis. 32:139-153.

Bamberg, J.and J.C. Miller, Jr. (2012). Comparisons of ga1 with other reputed gibberellin mutants in potato. Amer. J. Potato Res. 89:142-149.

Brown, C.R., K.G. Haynes, M. Moore, M.J. Pavek, D.C. Hane, S.L. Love, R.G. Novy, and J.C. Miller, Jr. (2012). Stability and broad-sense heritability of mineral content in potato: Calcium and Magnesium. Amer. J. Potato Res. 89:255-261.

Nzaramba, M.N, D.C. Scheuring, J.W. Koym, and J.C. Miller, Jr. (2013). Relationships among antioxidant activity, phenolics and specific gravity in potato (Solanum tuberosum L.) cultivars grown in different environments. Amer. J. Potato Res. 90:541–550.

PHS 398/2590 (Rev. 09/04) Page Continuation Format Page

Principal Investigator/Program Director (Last, First, Middle): MIRANDA, Rajesh C.

NAME POSITION TITLE Rajesh C. Miranda, Ph.D. Professor eRA COMMONS USER NAME rmiranda EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) St. Xavier’s College, Bombay, India B.A. 1982 Psychology Bombay University, Bombay, India M.A. 1984 Clinical Psychology University of Rochester, Rochester, N.Y. M.A. 1987 Biopsychology University of Rochester, Rochester, N.Y. M.S. 1988 Neurobiology University of Rochester, Rochester, N.Y. Ph.D. 1989 Biopsychology/Neurobiol. Columbia University, Col. Physicians & Surgeons, NY Post-Doctoral 1989-1994 Neurobiology

A. Personal Statement: My primary research interest is in maternal-fetal health, with a focus on fetal brain development, stem cell programming and the biology of microRNAs. In 2007, we were the first research group to identify microRNAs as a target for teratogens and drugs of abuse like alcohol (PMCID: 2915840). Since then, we have focused on identifying additional teratogen-sensitive miRNAs associated with the maturation of fetal neural stem cells, as well as miRNAs associated with neural adaptation to degeneration. My laboratory is also currently using a variety of high-throughput screening approaches to identify vascular circulating microRNA biomarkers for ethanol consumption and for fetal ethanol exposure (as part of a consortium, U24 AA014811). I expect that our research on microRNAs and their mRNA targets will uncover novel mechanisms of fetal brain adaptation and plasticity that are amenable to therapeutic intervention.

B. Positions and Honors 1983-1984 St. Xavier’s College, Bombay India, University Grants Commission teaching assistant 1983 Psychaid, Bombay, India, Clinical assistant, psychological testing 1984-1989 University of Rochester, Depts. of Psychology and Neuroscience: Teaching assistant. 1989-1992 Columbia University College of Physicians and Surgeons, Center for Reproductive Sciences: Post- doctoral research Scientist 1990-1994 Columbia University College of Physicians and Surgeons, Instructor, Medical Neuroanatomy 1992-1994 Columbia University, Center for Reproductive Sciences: Associate Research Scientist. 1995-2000 Texas A&M University, Dept. Human Anatomy and Medical Neurobiology, Assistant Professor. 2000-2009 Texas A&M, Health Science Center, Dept. Neurosci & Expt. Therapeutics, Associate Professor 2009- Texas A&M Health Science Center, Professor 2005- Texas A&M University, Department of Psychology, Adjunct Professor 1995-present Member of the Faculties of Neuroscience, Reproductive Biology and Toxicology at TAMU 1999-present Member, Center for Environmental and Rural Health, Texas A&M University 2002-2003 Ad-hoc reviewer, NIH, ALTX-3 and NAL study section 2004-2007 Member, NIH, NAL (Neurotoxicology and Alcohol) study section 2006-2009 Ad. Hoc. Member, NIH AA-1, ZAA1-BB98, NCF, MNG & AA-4 study sections 2009-2012 Member, NIH AA-4 study section. 2012- 2015 Chair, AA-4 study section 2009-2011 Treasurer, vice president Fetal Alcohol Spectrum Disorders Study Group (FASDSG) 2011-2012 President, Fetal Alcohol Spectrum Disorders Study Group 2012- Member of the Steering Committee on FASD prevention at the Texas PHS Office for Prevention of Developmental Disabilities

PHS 398/2590 (Rev. 09/04) Page Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle):

Relevant Publications: 1. Balaraman S, Lunde ER, Sawant OB, Cudd TA, Washburn SE, Miranda RC (2014) Maternal And Neonatal Plasma MicroRNA Biomarkers For Fetal Alcohol Exposure In An Ovine Model. Alcoholism: Clinical And Experimental Research:In Press. PMCID in progress. 2. Bake S, Tingling J, Miranda RC (2012) Ethanol exposure during pregnancy persistently attenuates cranially-directed blood flow in the developing fetus: Evidence from ultrasound imaging in a murine second trimester equivalent model. Alcohol Clin Exp Res. May;36(5):748-58. PMCID: PMC3297711 3. Balaraman S, Winzer-Serhan UH, Miranda RC (2012) Opposing actions of ethanol and nicotine on microRNAs are mediated by nicotinic acetylcholine receptors in fetal cerebral cortical-derived neural progenitor cells. Alcohol Clin Exp Res. Oct;36(10):1669-77. PMCID: PMC3390449 4. Sathyan P, Golden, HB, Miranda RC (2007) Competing interactions between microRNAs determine neural progenitor survival and proliferation following ethanol exposure: Evidence from an ex vivo model of the fetal cerebral cortical neuroepithelium. Journal of Neuroscience Aug 8;27(32):8546-57. PMCID: PMC2915840 5. Santillano DR, Kumar LK, Prock TL, Tingling J, Miranda RC (2005) Ethanol induces cell-cycle activity and reduces stem cell heterogeneity in cerebral cortical neuroepithelial precursors. Biomed Central: Neuroscience 6:59. PMCID: PMC1249578 6. Selvamani A, Sathyan P, Miranda RC, Sohrabji F (2012) An antagomir to microRNA Let7f promotes neuroprotection in an ischemic stroke model. PLoS ONE 7(2):e32662. PMCID: PMC3290559. 7. Miranda, RC (2012) MicroRNAs and fetal brain development: implications for ethanol teratology during the second trimester period of neurogenesis. Front Genet. 3: 77. PMCID: PMC3353139. 8. Sudheendran N, Bake S, Miranda RC, Larin KV (2013) Comparative assessments of the effects of Alcohol Exposure on Fetal Brain Development Using Optical Coherence Tomography and Ultrasound Imaging. Journal of Biomedical Optics 18(2):20506. PMCID: PMC3563965. 9. Selvamani A, Williams M, Miranda RC, Sohrabji F (2014) Circulating miRNA profiles provide a biomarker for severity of stroke outcomes associated with age and sex in a rat model. Clin Sci:In Press.

D. Other Support: AA13440 (P.I.: Rajesh C. Miranda) 03/01/2002-08/31/2014 NIAAA Fetal Alcohol exposure and neurodevelopment I serve as PI for this project. AA13440 investigates (1) the role of alcohol exposure on the control of receptor-neural stem cell maturation. (2) The involvement of miRNAs as critical mediators of ethanol’s effects on stem cell maturation.

1R01NS074895 (Sohrabji, PI) 9/01/2011- 05/30/2016 NIH Neuroprotection in the Aging Female Brain I serve as a co-investigator on this project. The overall goal of this application is determine the interaction of estrogen and IGF-1 in the context of stroke and neuroprotection in middle age females, using an animal model

U01 AA014835-09 (Chambers, PI) 2012-2017 NIH Early Identification of Affected Children and Risk Factors for FASD in Ukraine I serve as a co-investigator on this proposal. My role will be to screen for plasma miRNA biomarkers for alcohol exposure in mothers and children in an FASD cohort in the Ukraine. This proposal will correlate the expression of miRNA biomarkers with other epigenetic markers and anatomical markers of fetal alcohol exposure.

PHS 398/2590 (Rev. 09/04) Page Continuation Format Page Principal Investigator MULLET, John E.

NAME POSITION TITLE Mullet, John E. Professor eRA COMMONS USER NAME RLINTS EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Colgate University, Hampton, New York B.Sc. 1972-1976 Biology University of Illinois, Champaign Ph.D. 1976-1980 Cell Biology

A. Positions and Honors. Positions and Employment 1999-2005 Director, Institute for Plant Genomics and Biotechnology, Texas A&M University 1993-1999 Director, Crop Biotechnology Center, Texas A&M University 1991-prsesent Professor, Department of Biochemistry and Biophysics, Texas A&M University 1986-1991 Associate Professor, Department of Biochemistry and Biophysics, Texas A&M University 1983-1986 Assistant Professor, Department of Biochemistry & Biophysics, Texas A&M University 1980-1983 NIH Postdoctoral Fellow, Rockefeller University 1978-1980 NATO research at the CNRS, France, 1980; Japan, 1978

B. Selected peer-reviewed publications (in chronological order). PUBLICATIONS (Total 180):

Borrell, AK, Mullet, JE, George-Jaeggli, B, Oosterom, EJV, Hammer, GL, Klein, PE, Jordan, DR (2014) Drought adaptation of stay-green sorghum is associated with canopy development, leaf anatomy, root growth, and water uptake. Journal of Experimental Botany (doi:10.1093/jsb/eru232)

Mullet, J.E., Morishige, D.T., McCormick, R., Truong, S., Hilley, J, McKinley, B., Anderson, R., Olson, S., and Rooney, W. (2014) Energy Sorghum – A Genetic Model for the Design of C4 Grass Bioenergy Crops. Journal of Experimental Botany (doi:10.1093/jsb/eru229)).

Yang, S., Murphy, R.L., Morshige, D.T., Klein, P.E., Rooney, W.L., and Mullet, J.E. (2014) Sorghum Phytochrome B Inhibits Flowering in Long Days by Activating Expression of SbPRR37 and SbGHD7, Repressors of SbEHD1, SbCN8 and SbCN12. PloS One (submitted)

Yang, S., Weers, B.W., Morshige, D.T., Mullet, J.E. (2014) CONSTANS is a Photoperiod Regulated Activator of Flowering in Sorghum. BMC Plant Biology (In press).

Rebecca L. Murphy, Daryl T. Morishige, Jeff A. Brady, William L. Rooney, Shanshan Yang, Patricia

E. Klein, John E. Mullet (2014) Ghd7 (Ma6) Represses Sorghum Flowering in Long Days: Ghd7 Alleles Enhance Biomass Accumulation and Grain Production. The Plant Genome (In press, doe:

PHS 398/2590 (Rev. 09/04) Page 1 Biographical Sketch Format Page Principal Investigator MULLET, John E. 10.3835/plantgenome2013.11.0040).

Evans, J.E., McCormick, R.F., Morishige, D., Olson, S.N., Weers, B.D., Hilley, J., Klein, P., Rooney, W., Mullet, J.E. (2013) Extensive Variation in the Density and Distribution of DNA Polymorphism in Sorghum Genomes. PLOS One 8:e79192 .

Morishige, D.T., Klein, P.E., Hilley, J.L., Sahraeian, S.M.E., Sharma, A., and Mullet, J.E. (2013) Digital Genotyping of Sorghum – A Diverse Species with a Repeat-Rice Genome. BMC Genomics 14: 448-467.

Olson, Sara, Kimberley Ritter, Jim Medley, Ted Wilson, William Rooney, and John E. Mullet (2013) Energy Sorghum Hybrids: Functional Dynamics of High Nitrogen Use Efficiency. Biomass and Bioenergy 56: 307-316.

Kapanigowda, M.H., Payne, W.A., Rooney, W.L., and J.E. Mullet (2012) Transpirational efficiency in sorghum [Sorghum bicolor (L.) Moench) for increased water-use efficiency and drought tolerance. Journal of Arid Land Studies 22, No 1.

Olson, S.N., Ritter, K., Rooney, W., Kemanian, A., McCarl, B.A., Zhang, Y., Hall, S., Packer, D., and Mullet, J. (2012) High Biomass Yield Energy Sorghum: Developing a Genetic Model for C4 Grass Bioenergy Plants. Biofuels, Bioproducts and Biorefining 6: 640-655 (DOI: 10:1002/bbb)

Murphy, B., Klein, R., Morishige, D., Brady, J.A., Rooney, W. L., Miller, F.R., Dugas, D.D., Klein, P., Mullet, J.E. (2011) Coincident Clock and Light Regulation of Pseudo Response Regulator Protein 37 PRR37 Controls Photoperiodic Flowering in Sorghum. PNAS 108: 16469-16474

Borrell, A., Jordan, D., George-Jaeggli. B., Mace, E., Hamlet, S., Hammer, G., Mclean, G., Van Oosterom, E., Hunt, C., Klein, P., Mullet. J.E. (2010) Fine Mapping Candidate Genes for ‘Stay- Green’ in Sorghum; Simplicity Beyond Complexity? Summer Crops Research Conference.

Murray, S.C., Sharma, A., Rooney, W.L., Klein, P., Mullet, J.E., Mitchell, S.E., Kresovich, S. (2008) Genetic Improvement of Sorghum as a Biofuel Feedstock: I. QTL for Stem Sugar and Grain Nonstructural Carbohydrates. Crop Science 48: 2165-2179.

Murray, S.C., Rooney, W.L., Mitchell, S.E., Sharma, A., Klein, T., Mullet, J.E., Kresovich, S. (2008) Genetic Improvement of Sorghum as a Biofuel Feedstock: II. QTL for Stem and Leaf Structural Carbohydrates. Crop Science 48: 2180-2193

Klein, R.R., Mullet, J.E., Jordan, D.R., Miller, F.R., Rooney, W.L., Menz, M.M., Franks, C.D., Klein, P.E. (2008) The Effect of Tropical Sorghum Conversion and Inbred Development on Genome Diversity as Revealed by High-Resolution Genotyping. Plant Genome 48: S12-26.

Rooney, W.L., Blumenthal, J., Bean, B., Mullet, J.E. (2007) Designing sorghum as a dedicated bioenergy feedstock. Biofuels, Bioproducts and Biorefining 1:147-157.

Yim, Y.-S., Moak, P., Shachez-Villeda, H., Musket, T.A., Close, P., Klein, P.E., Mullet, J.E., McCullen, M.D., Fang, A., Schaeffer, M.L., Gardiner, J.M., Coe, E.H., Davis, G. L. (2007) A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps. BMC Genomics 8:47-56.

PHS 398/2590 (Rev. 09/04) Page 2 Continuation Format Page Program Director/Principal Investigator: MURPHY, William J.

NAME POSITION TITLE Murphy, William J. Professor eRA COMMONS USER NAME

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Illinois State University, Normal, Illinois BS 1992 Biological Sciences The University of Tulsa, Tulsa, Oklahoma PhD 1997 Biological Sciences Laboratory of Genomic Diversity, National Postdoc 1997-2003 Comparative Genomics Cancer Institute, NIH, Frederick, Maryland

A. Positions and Honors Positions and Employment 2013-present Professor, Dept. of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 2004-2013 Associate Professor (tenured in 2008), Dept. of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 2008-present Research Associate, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 2005-present Faculty of Genetics, Texas A&M University, College Station, TX 2006-present Faculty of Ecology and Evolutionary Biology, Texas A&M University, College Station, TX 2003-2004 Senior Scientist, SAIC-Frederick, Inc., Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD Honors 1997-1999 NIH IRTA Postdoctoral Fellowship 2001-2002 National Institutes of Health Loan Repayment Program Recipient 2007 Pfizer Animal Health Award for Research Excellence 2009 JoAnn Treat Research Excellence Award, Texas A&M Research Foundation 2010 Texas A&M University Association of Former Students Distinguished Achievement Award in Research 2013 American Veterinary Medical Foundation/Winn Feline Foundation Excellence in Research Award Other Experience 2009-present Mammal co-chair, G10K Community of Sciences 2007-present Associate Editor, Journal of Mammalian Evolution 2008-present Associate Editor, Journal of Heredity 2008 Editor, Phylogenomics: Methods in Molecular Biology, Humana Press

B. Selected peer-reviewed publications (from 94 journal articles and book chapters)

Montague, M., Li, G., Gandolfi, B., Khan, R., Aken, B., Searle, S., Minx, P., Hillier, L., Kolboldt, D., Davis, B.W., Driscoll, C.A., Marques-Bonet, T., Thomas, G., Hahn, M., Menotti-Raymond, M., O’Brien, S.J., Wilson, R.K., Lyons, L.A., Murphy, W.J., and W. C. Warren. 2014. Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and Program Director/Principal Investigator: MURPHY, William J.

domestication. Proceedings of the National Academy of Sciences USA. (In press) Alfoldi, J., Soh, Y.W.S., Pyntikova, T., Brown, L.G., Graves, T., Minx, P.J., Fulton, R.S., Kremitzki, C., Koutseva, N., Mueller, J.L., Rozen, S., Hughes, J.F., Owens, E., Womack, J.E., Murphy, W.J., Cao Q., de Jong, P., Warren, W.C., Wilson, R.K., Skaletsky, H., and D.C. Page. 2014. Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes. Cell (In press) Li, G., Davis, B.W., Raudsepp, T., Pearks Wilkerson, A.J., Mason, V.C., Ferguson-Smith, M.A., O’Brien, P., Waters, P., and W.J. Murphy. 2013. Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution. Genome Research 23: 1486-1495. PMID: 23788650. Hughes, G., Li, G., Murphy, W.J., Higgins, D., and E.C. Teeling. 2013. Using Illumina next generation sequencing technologies to sequence multigene families in de novo species. Molecular Ecology Resources, 13(3): 510-21. PMID: 23480365. Meredith, R. W., Janečka, J.E., Gatesy, J., Ryder, O. A., Fisher, C.A., Teeling, E.C., Goodbla, A., Eizirik, E., Simão, T. L. L., Stadler, T., Rabosky, D. L., Honeycutt, R. L., Flynn, J. J., Ingram, C. M., Steiner, C., Williams, T. L., Robinson, T. J., Burk-Herrick, A., Westerman, M., Ayoub, N. A., Springer, M. S., and W. J. Murphy. 2011. Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on mammal diversification. Science 334: 521-525. PMID: 21940861 Mason, V.C., Li, G., Helgen, K. M., and W. J. Murphy. 2011. Efficient cross-species capture hybridization and next-generation DNA sequencing from non-invasively sampled museum specimens. Genome Research 21: 1695-1704. PMID: 21880778 Li, G., Janečka, J. E., and W. J. Murphy. 2011. Accelerated evolution of CES7, a gene encoding a novel major urinary protein in the cat family. Molecular Biology and Evolution 28: 911-920. PMID: 20138224 Davis, B.W., Li, G., and W.J. Murphy. 2010. Reconciling the evolutionary radiation of the big cats (Panthera) using a Y chromosome supermatrix and a critical reanalysis of mitochondrial DNA. Molecular Phylogenetics and Evolution. 56: 64-76. PMID: 21940861 Davis, B. W., Raudsepp, T., Pearks Wilkerson, A. J., Agarwala, R., Schäffer, A. A., Houck, M., Chowdhary, B. P., and W. J. Murphy. 2009. A high-resolution cat radiation hybrid and integrated FISH mapping resource for phylogenomic studies across Felidae. Genomics. 93: 299-304. PMID: 18951970 Johnson, W. E., Eizirik, E., Pecon-Slattery, J., Murphy, W. J., Antunes, A., Teeling, E. C., and S. J. O’Brien. 2006. The late Miocene radiation of modern Felidae: a genetic assessment. Science 311: 73-77. PMID: 16400146 Murphy, W. J., Pearks Wilkerson, A. J., Raudsepp, T., Agarwala, R., Schäffer, A. A., Stanyon, R., and B. P. Chowdhary. 2006. Novel gene acquisition on carnivore Y chromosomes. PLoS Genetics 2: e43. PMID: 16596168. Murphy, W. J., Larkin, D., Everts van-der Wind, A., Bourque, G., Tesler, G., Auvil, L., Beever, J. E., Chowdhary, B. P., Galibert, F., Gatzke, L., Hitte, C., Meyers, S. N., Ostrander, E. A., Pape, G., Parker, H. G., Raudsepp, T., Rogatcheva, M. B., Schook, L. B., Skow, L. C., Welge, M., Womack, J. E., O'Brien, S. J., Pevzner, P. A., H. A. Lewin. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309: 613-617. PMID: 16040707 Murphy, W. J., Shan, S., Pecon-Slattery, J., Chen, Z. Q., and S. J. O'Brien. 1999. Extensive conservation of sex chromosome organization between cat and human revealed by parallel radiation hybrid mapping. Genome Research 9: 1223-1230. PMID: 10613845.

Principal Investigator: MURRAY, Seth C.

NAME POSITION TITLE Murray, Seth C. Associate Professor eRA COMMONS USER NAME

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Michigan State University B.Sc. 2001 Crop and Soil Sciences Cornell University Ph.D. 2008 Plant Breeding & Genetics

A. Positions and Honors. Professional Appointments: 2014-present Associate Professor, Texas A&M University, College Station 2008-2014 Assistant Professor, Texas A&M University, College Station

Synergistic Activities: 2013 – present Associate Editor, Crop Science 2009 – present Associate Editor (Maize), Journal of Plant Registrations 2012 Program Chair, American Seed Trade Association Corn and Sorghum Meeting 2009 – present Executive Committee (Web Editor), National Association of Plant Breeders and Plant Breeding Coordinating Committee • Grant review panels: USDA-DOE, NSF-PGRP (1 year each)

• Run an applied public corn breeding program focused on improving aflatoxin resistance, yield, stress resistance, and exotic introgression across the State of Texas. Developing and releasing new germplasm, inbred lines, populations and hybrid combinations.

Awards: 2014 Crop Science Society of America, Young Crop Scientist Award 2013 National Association of Plant Breeders Early Career Award 2007 The Barbara McClintock Graduate Student Award, Cornell College of Ag. & Life Sci. 1998 Eagle Scout, Boy Scouts of America

B. Selected peer-reviewed publications (in chronological order).

Total refereed – 32, conference abstracts – 83, book chapters – 4, extension publications – 5; graduate students listed in italics; * corresponding author; 1. Mahan, A. L. S.C. Murray*, L.W. Rooney, and M.P. Scott. 2014. Quality Protein Maize Germplasm Characterized for Amino Acid Profiles and Endosperm Opacity. Crop Science. 54: 863-872. 2. Murray, S.C.*, P. Eckhoff, L. Wood, and A.H. Paterson. 2013. Toward Rapid Genetic Advancement in Agricultural Species via Cycling of Gametes in Vitro. Nature Biotechnology 31, 877–880.

PHS 398/2590 (Rev. 09/04) Page 1 Biographical Sketch Format Page Principal Investigator: MURRAY, Seth C. 3. Barerro, I.D.F., S.C. Murray*, D. Pietsch, S. Labar. 2013. A multi-environment trial analysis of commercial maize shows a slight grain yield improvement in Texas commercial maize. Field Crops Research 149:167-176. 4. Meeks M., S.C. Murray*, S. Hague, and D. Hays. 2013. Measuring maize seedling drought response in search of tolerant germplasm. Agronomy 3:135-147. 5. Mahan, A.L. S.C. Murray*, L.W. Rooney, and K.M. Crosby. 2013. Combining Ability for Total Phenols and Secondary Traits in a Diverse Set of Colored (Red, Blue, and Purple) Maize. Crop Science. 53:1248-1255. 6. De La Fuente, G.N, S.C. Murray*, T.Isakeit, Y.-S. Park, Y. Yan, M. Warburton and M.V. Kolomiets. 2013. Characterization of genetic diversity and linkage disequilibrium of ZmLOX4 and ZmLOX5 Loci in maize. PLoS ONE 8(1): e53973. 7. Washburn, J.D., S.C. Murray, B.L. Burson, R.R. Klein, R.W. Jessup*. 2012. Targeted mapping of QTL regions for rhizomatousness in Chr 1 and analysis of overwintering in a Sorghum bicolor x S. propinquum population. Molecular Breeding 31:153-162. 8. Meeks M., S.C. Murray*, S. Hague, D. Hays, and A. Ibrahim. 2012. Genetic variation for maize epicuticular wax response to drought stress at flowering. Journal of Agronomy and Crop Science. 198: 161-172. 9. Murray, S.C.* 2012. Differentiation of seed, sugar, and biomass-producing genotypes in Saccharinae species. In A.H. Paterson (ed.) Genetics and Genomics of the Saccharinae. Springer. p. 479-502. 10. Mayfield, K.L., S.C. Murray*, W.L. Rooney, T. Isakeit, and G.A. Odvody. 2011. Confirmation of QTL reducing aflatoxin in maize testcrosses. Crop Science 51:2489-2498. 11. Brummer, E.C., W.T. Barber, S. Collier, T.S. Cox, R. Johnson, S.C. Murray*, R.T. Olsen, R.C. Pratt, and A.M. Thro. 2011. Plant breeding for harmony between agriculture and the environment. Frontiers of Ecology and the Environment 9:561-568. 12. Glover , J. D.*, J. P. Reganold, L. W. Bell, J. Borevitz, E. Buckler, C. M. Cox, T. S. Cox, T. E. Crews, S. W. Culman, T. Day-un, L. R. DeHaan, D. Eriksson, H. Fengyi, B. Gill, J. Holland, B. Hulke, A. Ibrahim, S. Jones, S.C. Murray, E. Ploschuk, E. Sacks, S. Snapp, D. Van Tassel, L. Wade, D. Wyse, and Y. Xu. 2010. Increasing food and ecosystem security on marginal lands through perennial grain breeding. Science 328:1638-1639. 13. Murray, S.C., W.L. Rooney, M.T. Hamblin, S.E. Mitchell, and S. Kresovich*. 2009. Sweet sorghum diversity and association mapping for brix and height. The Plant Genome. 2:48-62. 14. Murray, S.C., W.L. Rooney, S.E. Mitchell, A. Sharma, P.E. Klein, J.E. Mullet, and S. Kresovich*. 2008. Genetic improvement of sorghum as a biofuel feedstock II: quantitative loci for stem and leaf structural carbohydrates. Crop Science 48:2180-2193. 15. Wisser, R.J., S.C. Murray, J.M. Kolkman, H. Ceballos, and R.J. Nelson*. 2008. Selection mapping of loci for quantitative disease resistance in a diverse maize population. Genetics 180:583-599.

C. Research Support PI/co-PI of 25 projects totaling $7,198,439, of which $1,001,601 are/were for Murray; 19 were external (not from Texas AgriLife or TAMU).

PHS 398/2590 (Rev. 09/04) Page 2 Continuation Format Page Principal Investigator/Program Director (Last, first, middle): PANIN, Vladislav M.

Panin, Vladislav M. Associate Professor eRA COMMONS USER NAME (credential, e.g., agency login) PANINV EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)

INSTITUTION AND LOCATION DEGREE YEAR(s) FIELD OF STUDY (if applicable) Moscow State University, Moscow (USSR) B.S., M.S. 1981-1987 Biophysics Moscow State University, Moscow (USSR) Ph. D. 1987-1990 Biophysics Waksman Institute, Rutgers University, Postdoc 1995-2001 Developmental Biology Piscataway, NJ & Glycobiology

A. Positions and Honors

Positions and Employment 1990-1992 Junior Research Scientist, Engelghardt Institute of Molecular Biology, Drosophila Molecular Genetics Laboratory, The Russian Academy of Sciences, Moscow, Russia 1992-1995 Research Scientist, Senior Research Scientist, Laboratory of Neurogenetics and Developmental Biology, Institute of Gene Biology, The Russian Academy of Sciences, Moscow, Russia 1994 Visiting Scientist, Laboratory of Mammalian Genetics and Neurobiology, Institut Pasteur, Paris, France 1995-2001 Postdoctoral Research Associate, Research Associate, Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey, USA 2002-2008 Assistant Professor, Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, USA 2008-2013 Chair, Graduate Recruitment and Admission Committee, Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 2009-2012 Member, Faculty of Genetics Executive Committee, Texas A&M University, College Station, TX 2013-2014 Faculty Development Leave: Visiting Professor, Richard Benton’s laboratory, Center for Integrative Genomics, University of Lausanne, Switzerland 2003-present Member, Faculty of Genetics, Texas A&M University, College Station, TX 2006-present Participating Investigator, the Consortium for Functional Glycomics (CFG). CFG is a large research initiative supported by NIH to define the paradigms of carbohydrate functions, http://www.functionalglycomics.org. 2008-present Member, Faculty of Neuroscience, Texas A&M Institute for Neuroscience, College Station, TX 2008-present Associate Professor, Department of Biochemistry & Biophysics, Texas A&M University 2013-present Member, Graduate Program Committee, TAMU Institute for Neuroscience

Other Professional Experience and Memberships 1993 Participant, Summer School on Bioinformatics, International Center for Genetic Engineering & Biotechnology, Trieste, Italy 1995 Invited Lecturer, Moscow State University, Moscow, Russia 1997-present Member, The Genetics Society of America 2000-present Member, The Society for Glycobiology 2009-present Member, The Society for Neuroscience 2010-present Board of Directors, The Society for Glycobiology 2013-present Editorial Board Member, Journal of Biological Chemistry

PHS 398/2590 (Rev. 05/01) Page ___1___ Biographical Sketch Format Page Principal Investigator/Program Director (Last, first, middle): Panin, Vladislav M. 2013 -present Editorial Board Member, Glycobiology 2013-present Editorial Board Member, Glycoconjugate Journal

Honors and Fellowships 1987 Diploma SummaCum Laude, Moscow State University, Moscow, Russia 1994 Honor Fellowship for Outstanding Young Scientists from the President of Russia Boris Yeltsin, Moscow, Russia 1994 Fellowship from the International Science Foundation (est. by George Soros), New York, NY 1998 Charles and Johanna Busch Fellowship, Waksman Institute, NJ 2003 Basil O’Connor Starter Scholar Research Award, March of Dimes Foundation, NY

C. Selected peer-reviewed publications (in reverse chronological order, postdocs, graduate and undergraduate students as shown) 1. Scott, H and Panin, VM (2014) The role of protein N-glycosylation in neural transmission. Glycobiology, 24:407-417 2. Panin VM and Wells L (2014) Protein O-mannosylation in metazoan organisms. Curr Protoc Prot Sci 75: Unit 12.12. 3. Islam, R., Nakamura, M., Scott, H., Repnikova, E., Carnahan, M., Pandey, D., Caster, C., Khan, S., Zimmermann, T., Zoran, M.J., Panin, V.M. (2013) The role of Drosophila cytidine monophosphate-sialic acid synthetase in the nervous system. J Neurosci 33:12306-12315. [PMID: 23884937, PMCID: PMC3721841] 4. Nakamura, M., Pandey, D., Panin, V.M. (2012) Genetic interactions between Drosophila sialyltransferase and β1,4-N- acetylgalactosaminyltransferase-A genes indicate their involvement in the same pathway. G3: Genes Genomes Genetics, 2(6): 653-656 [PMID: 22690374 PMCID: PMC3362294] 5. Repnikova, E., Koles, K., Nakamura, M., Pitts, J., Li, H., Ambavane, A., Zoran, M.J., Panin, V.M. (2010) Sialyltransferase regulates nervous system function in Drosophila. J Neurosci. 30(18):6466-76. [PMID: 20445073, PMCID: PMC3354699] 6. Nakamura, N., Lyalin, D., and Panin, V.M (2010) Protein O-mannosylation in animal development and physiology: from human disorders to Drosophila phenotypes. Semin. Cell. Dev. Biol. 21(6):622-30 [PMID: 20362685, PMC2917527, NIHMS220225] 7. Nakamura, N., Stalnaker, S., Lyalin, D., Lavrova, O., Wells, L., Panin, V. (2010) Drosophila Dystroglycan is a target of O-mannosyltransferase activity of two protein O-mannosyltransferases, Rotated Abdomen and Twisted. Glycobiology. 20:381-94 [PMID: 19969597, PMC2912551] 8. Koles, K., Repnikova, E., Pavlova, G., Korochkin, L.I., Panin, V.M. (2009) Sialylation in protostomes: a perspective from Drosophila genetics and biochemistry. Glycoconj J. 26(3):313-24 [PMID: 18568399]. 9. Koles, K., Lim, J.-M, Aoki, K., Porterfield, M., Tiemeyer, M., Wells, L., and Panin, V.M. (2007) Identification of N- glycosylated glycoproteins from the central nervous system of Drosophila melanogaster. Glycobiology. 17(12):1388- 1403 [PMID: 17893096] 10. Luo, Y., Koles, K., Vorndam, W., Haltiwanger, R.S., Panin V.M. (2006) Protein O-fucosyltransferase 2 adds O-fucose to thrombospondin type 1 repeats. J. Biol. Chem. 281(14): 9393-9 [PMID: 16464857] 11. Lyalin, D. A., Koles, K., Roosendaal, S. D., Repnikova, E. A., Van Wechel, L., and Panin, V. M. (2006) The twisted gene encodes Drosophila protein O-mannosyltransferase 2 and genetically interacts with the rotated abdomen gene encoding Drosophila protein O-mannosyltransferase 1. Genetics. 172(1): 343-53 [PMID: 16219785, PMC1456162] 12. Koles, K., Irvine, K.D., Panin V.M. (2004) Functional characterization of Drosophila Sialyltransferase. J Biol Chem. 279: 4346-57 [PMID: 14612445] 13. Lei, L., Xu, A., Panin V.M, Irvine, K.D. (2003) An O-fucose site in the ligand binding domain inhibits Notch activation. Development.130: 6411-21 [PMID: 14627724] 14. Correia, T., Papayannopoulos, V., Panin V., Woronoff, P., Jiang, J., Vogt, T.F., Irvine, K.D. (2003) Molecular genetic analysis of the glycosyltransferase Fringe in Drosophila. Proc Natl Acad Sci USA.100: 6404-9 15. Panin, V. M., Shao, L., Lei, L., Moloney, D. J., Irvine, K. D., and Haltiwanger, R. S. (2002) Notch ligands are substrates for protein O-fucosyltransferase-1 and Fringe. J. Biol. Chem. 277: 29945-52 [PMID: 12036964] 16. Moloney, D. J., Panin, V. M., Johnston, S. H., Chen, J., Shao, L., Wilson, R., Wang, Y., Stanley, P., Irvine, K. D., Haltiwanger, R. S., and Vogt, T. F. (2000) Fringe is a glycosyltransferase that modifies Notch. Nature. 406: 369-375. 17. Papayannopoulos, V., Tomlinson, A., Panin, V. M., Rauskolb, C., and Irvine, K. D. (1998) Dorsal-ventral signaling in the Drosophila eye. Science 281: 2031-2034 18. Panin, VM, Papayannopoulos, V, Wilson, R, and Irvine, KD(1997) Fringe modulates Notch-ligand interactions. Nature. 387: 908-913

Page ___2___ Biographical Sketch Format Page Principal Investigator PARK, William D.

NAME POSITION TITLE Park, William D. Professor eRA COMMONS USER NAME

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of South Carolina B.Sc. 1973 Chemistry University of University of Florida Ph.D. 1977 Biochemistry University of Minnesota Postdoc. 1978-1980 Genetics and Cell Biology

A. Positions and Honors. Positions and Employment 1980 - 1983 Assistant Professor, Horticulture, Purdue University 1984 - 1990 Associate Professor, Biochemistry and Biophysics, TAMU 1991- Present Professor, Biochemistry and Biophysics, TAMU

Honors 2014: Invited to participate in the symposium “Dietary fiber: Optimizing accuracy of data for Labeling, Databases and Research” to be held at the Institute for Food Technologist annual meeting in June 2014. 2012: Our work on deficiencies in the CODEX compliant total dietary fiber assay AOAC 2009.01/AACCI 3245.01 was cited by the originator of the assay, Barry McCleary, in a formal request to both AOAC and AACCI to revise the official assay protocols for dietary fiber that are used when making nutrient composition claims on food products. 2011: Based on the success of our long term collaboration, MARS Inc. donated an additional $45,000 to upgrade starch analytical capabilities of the Department of Biochemistry and Biophysics. 2010: Faculty Recognition Award from the Biochemistry Graduate Association. 2010: Based on the success of our long term collaboration, MARS Inc. donated $94,000 to upgrade starch analytical capability of the Department of Biochemistry and Biophysics. 2009: Our lab was officially recognized as a key component of the MARS Global Food Platform. 2007: MARS Inc. recognized our “outstanding research and significant contributions on rice knowledge”. This award was presented in person jointly by the Vice President of Research and Development for MARS FOOD USA, and his counterparts from Europe and Australia. 2007: Faculty Recognition Award from the Biochemistry Graduate Association 2007: Invited to speak at MARS’ Science Advisory Council Meeting in Amsterdam and to attend the Executive Session to set directions for the use of molecular methods to enhance nutrition in MARS human and pet food programs 2006. Invited to speak at MARS’ Plant Breeding Multidisciplinary Research Unit meeting at MARS corporate headquarters and to attend the “closed” Executive Session to set directions for the MARS’ cocoa program

PHS 398/2590 (Rev. 09/04) Page 1 Biographical Sketch Format Page Principal Investigator PARK, William D.

B. Selected peer-reviewed publications (in chronological order).

Dobo M, N Ayres, G Walker, WD Park (2010) Polymorphism in the GBSS Gene Affects Amylose Content in US and European Rice Germplasm. J Cereal Science 52: 450-456

Vitalini MW, RM de Paula, WD Park, D Bell-Pedersen (2006) The rhythms of life: Circadian output pathways in Neurospora. J. Biological Rhythms 21: 434-444.

Fjellstrom, R, CA Conaway-Bormans, AM McClung, W Park (2004) Development of DNA Markers Suitable for Marker Assisted Selection of Three Pi- Genes Conferring Resistance to Multiple Pyricularia grisea pathotypes. Crop Science. 44: 1790-179,

McClung AM, CJ Bergman, RG Fjellstrom, CA Bormans, WD Park, MA Marchetti (2003) Registration of Bolivar Rice. Crop Science 44: 353-354,

McClung AM, RG Fjellstrom, CJ Bergman, CA Bormans, WD Park, MA Marchetti (2003) Registration of Saber Rice. Crop Science 44: 248-249.

Larkin PD, WD Park (2003) Association of waxy gene single nucleotide polymorphisms with starch characteristics in rice (Oryza sativa L.) Molec. Breeding 12: 335-339.

Bormans C, A McClung, A Marchetti, C Johnson, W Park (2003) Molecular markers linked to the blast resistance gene Pi-z in rice for use in marker-assisted selection. Theor. Appl. Genet. 107: 1014-1020

Larkin, PD, MA McClung, NM Ayres, WD Park (2003) The effect of the Wx locus (Granule Bound Starch Synthase) on pasting curve characteristics in specialty rice. Euphytica 131: 243-253

PHS 398/2590 (Rev. 09/04) Page 2 Continuation Format Page Program Director/Principal Investigator: PAYNE, Susan

BIOGRAPHICAL SKETCH

NAME POSITION TITLE Payne, Susan Associate Professor Veterinary Pathobiology eRA COMMONS USER NAME (credential, e.g., agency login) spayne EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) Southeastern MA Univ., N. Dartmouth MA B.S. 1978 Marine Science Louisiana State University, Baton Rouge LA Ph.D. 1983 Microbiology Louisiana State University, Baton Rouge LA 1983-1988 Molecular Virology

A. Positions and Honors

Employment 1983-1988 Postdoctoral Research Associate, Dept. of Biochemistry, LSU, Baton Rouge, LA 1988-1996 Assistant Professor of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 1990-1996 Assistant Professor of General Medical Sciences, Case Western Reserve University, Cleveland, OH 1996-1999 Assistant Professor of Biology, The University of Texas at Arlington 1999-2001 Associate Professor of Biology, The University of Texas at Arlington 2001- Associate Professor, Veterinary Pathobiology, Texas A&M University 2002- Member, Intercollegiate Faculty of Genetics, Texas A&M University 2007- Member Graduate Faculty, TAMU, Health Science Center Graduate School of Biomedical Sciences

Other Experience and Professional Memberships

1996-2001 Radiation Safety Committee Member, The University of Texas at Arlington. 2001 Chair, Radiation Safety Committee, The University of Texas at Arlington. 2000-2001 Associate Chair of Biology, The University of Texas at Arlington. 2006-2009 Institutional Biosafety Committee, Texas A&M University. 2007-2008 Interim Biosafety Officer (09/1/07-01/30/08), Texas A&M University.

American Society for Microbiology (ASM) American Society for Virology (ASV) American Association for the Advancement of Science (AAAS)

B. Selected Peer-reviewed Publications (Postdocs and Graduate Students as shown)

Payne, S, Delnatte, P, Guo, J, Heatley, JJ, Tizard, I. and DA Smith (2012) Birds and Bornaviruses. Animal Health Research Reviews 13:145-156.

Mirhosseini, N, Gray, PL, Tizard, I, and S. Payne (2012) Complete genome sequence of avian bornavirus genotype 1 from a macaw with proventricular dilatation disease. Journal of Virology 86:7023.

Guo, J, Covaleda, L, Heatley, J, Baroch, J, Tizard, I, and S. Payne. (2011) Widespread avian bornavirus infection in mute swans in the northeast United States. Veterinary Medicine: Research and Reports. 3:49-52.

Payne, S, Covaleda, L, Jianhua, G, Swafford, S, Baroch, J, Ferro, PJ, Lupiani, B, Heatley, J, and I Tizard. (2011) Detection and Characterization of a Distinct Bornavirus Lineage from Healthy Canada Geese (Branta canadensis). Journal of Virology 85:12053-12056.

Mirhosseini, N, Gray, PL, Hoppes, S, Tizard, I, Shivaprasad, HL and SL Payne (2011) Proventricular dilatation disease in cockatiels (Nymphicus hollandicus) following infection with a genotype 2 avian bornavirus. Journal of Avian Medicine and Surgery. 25: 199-204. Gray PL, Suchodolski P, Wigle W, Mirhosseini N, Villanueva I, Hoppes S, Payne S, Briese, T, Reddy, S and I Tizard. (2010) Use of avian Bornavirus isolates to induce proventricular dilatation disease in conures. Emerging Infectious Diseases 16:473-479. PMID: 20202423 Covaleda, L, Gno B-T, Fuller, FJ and SL Payne (2010) Identification of cellular proteins interacting with equine infectious anemia virus S2 protein. Virus Research 151:235-239. DOI: 10.1016/j.viruses.2010.04.007. PMCID: PMC2897910 NIHMSID: NIHMS206371 Covaleda, L, Fuller, FJ, Payne, SL (2010) EIAV S2 protein enhances pro-inflammatory cytokine and chemokine responses in infected macrophages. Virology 397:217-223.PMCID: PMC2813941; NIHMS159828. Fagerness, A.J., Flaherty, M.T., Perry, S.T., Jia, B., Payne, S.L., Fuller, F.J. (2006) The S2 accessory gene of equine infectious anemia virus is essential for expression of disease in ponies. Virology 349:22-30. PMID: 16503341. Ball, JM, Swaggerty, CL, Pei, X-F, Lim, W-S, Xu, X, Cox, VC, Payne, SL (2005) SU proteins from virulent and avirulent EIAV demonstrate distinct biological properties. Virology 333:132-144. PMID: 15708599. Lim, W.-S, Payne, SL, Edwards, JF, Kim, I and JM Ball (2005) Differential Effects of Virulent and Avirulent Equine Infectious Anemia Virus on Macrophage Cytokine Expression. Virology 332:295-306. PMID: 15661161 Payne, SL, Pei, XF, Jia, B, Fagerness, A, Fuller, F (2004). Influence of long terminal repeat and env on the virulence phenotype of equine infectious anemia virus. Journal of Virology 78:2478-2485. PMID:14963146 Lim, W-S, Edwards, JF, Boyd, NK, Payne, SL, and Ball JM (2003) Simultaneous quantitation of equine cytokine mRNAs using a multi-probe ribonuclease protection assay. Veterinary Immunology and Immunopathology 91:45-51. PMID:12507849 Payne, SL, La Celle, K, Pei, X, Qi, X, Shao, H, Steagall, W, Perry, S and F. Fuller (1999) Long terminal repeat sequences of equine infectious anaemia virus are a major determinant of cell tropism. Journal of General Virology. 80:755-759. PMID:10092016 Payne, SL, Qi, XM, Dwyer, A, and F Fuller (1998) Disease induction by virus derived from molecular clones of equine infectious anemia virus. Journal of Virology. 72:483-487. PMID:9420249 Shao, H, Robek, MD, Threadgill, DT, Mankowski, LS, Cameron, CE, Fuller, FJ, and SL Payne (1997) Characterisation and mutational studies of equine infectious anemia virus dUTPase. Biochimica et Biophysica Acta. 1339:181-191. PMID:9187238 Steagall, WK, Robek, MD, Perry, ST, Fuller, FJ and S. Payne (1995) Incorporation of uracil into viral DNA correlates with reduced replication of equine infectious anemia virus in macrophages. Virology. 210:302-313. PMID:7542416 Payne, SL, Rausch, J, Rushlow, K, Montelaro, RC, Issel, C, Flaherty, M, Perry, S, Sellon, D, and F Fuller (1994) Characterization of infectious molecular clones of equine infections anemia virus. Journal of General Virology 75:425- 429. PMID:8113766 Threadgill, DS. Steagall, WK, Flaherty, MT, Fuller, FJ, Perry, ST, Rushlow, KE, LeGrice, SFJ and SL Payne (1993) Characterization of equine infectious anemia virus deoxyuridine triphosphatase: Growth properties of a dUTPase deficient mutant. Journal of Virology 67:2592-2600. PMID: 8386267

Principal Investigator/Program Director (Last, First, Middle): PERERSON, David O. BIOGRAPHICAL SKETCH Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Peterson, David O. Professor and Associate Department Head eRA COMMONS USER NAME

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION (if YEAR(s) FIELD OF STUDY applicable) Pomona College, Claremont, CA B.S. 1968-1972 Chemistry Harvard University, Cambridge, MA Ph.D. 1972-1978 Chemistry UCSF, San Francisco, CA Postdoc 1978-1981 Molecular Biology

A. Positions and Honors

Employment

1981 - 1987 Assistant Professor, Biochemistry and Biophysics, TAMU 1982 - present Graduate Faculty of Genetics, TAMU 1987 - 1996 Associate Professor, Biochemistry and Biophysics, TAMU 1993 - 1998 Associate Head for Graduate Programs, Biochemistry and Biophysics, TAMU 1996 - present Professor, Biochemistry and Biophysics, TAMU 2002 Visiting Professor, Institute of Molecular Biology, University of Oregon 2007 - present Associate Head for Undergraduate Programs, Biochemistry and Biophysics, TAMU Honors

1972 Phi Beta Kappa 1978-1981 Helen Hay Whitney Postdoctoral Fellowship 1999, 2009 TAMU Association of Former Students Distinguished Achievement Award in Teaching (College Level) 2008, 2010 TAMU Wells Fargo Honors Student Faculty Mentor Award 2014 Margaret Annette Peters Advising Award

B. Selected peer-reviewed publications

Knippa, K. and D.O. Peterson. 2013. Fidelity of RNA Polymerase II Transcription: Role of Rbp9 in Error Detection and Proofreading. Biochemistry 52:7807-7817.

Nesser, N.K., D.O. Peterson, and D.K. Hawley. 2006. RNA polymerase II subunit Rpb9 is important for transcriptional fidelity in vivo. Proc. Natl. Acad. Sci. USA 103:3268-3273.

Chen, X., B. Zhang, P.M. Harmon, W. Schaffner, D.O. Peterson, and D.P. Giedroc. 2004. A novel cysteine cluster in human metal-responsive transcription factor 1 is required for heavy metal-induced transcriptional activation in vivo. J. Biol. Chem. 279:4515-4522. PHS 398/2590 (Rev. 09/04) Page Biographical Sketch Format Page Principal Investigator: POLYMENIS, Michael

NAME POSITION TITLE Polymenis, Michael Associate Professor eRA COMMONS USER NAME

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of Patras, Greece Pharm. D. 1988 Pharmacy Tufts University Ph.D. 1994 Biochemistry Harvard Medical School Postdoc. 1994-1999 Cancer Center

A. Positions and Honors.

PROFESSIONAL APPOINTMENTS 1999 - 2005 Assistant Professor, Biochemistry and Biophysics, TAMU 2005 - present Associate Professor , Biochemistry and Biophysics, TAMU

AWARDS, HONORS, EDITORIAL, REVIEW AND ADVISORY BOARD APPOINTMENTS Grant Review The Czech Academy of Sciences – mail reviewer (2007) National Science Foundation – mail reviewer (2007) National Science Foundation – Cell Regulation Panel (2009) NIH Director’s Pioneer Award (NDPA) outcome evaluations – mail reviewer (2010) National Science Foundation – SBIR –Phase I, Platforms and Diagnostics Panel (2013) The Netherlands Organization for Scientific Research –mail reviewer (2013) National Science Foundation – SBIR –Phase II, Platforms and Diagnostics Panel (2014)

Editorial PLoS One (2009-present) PLoS Genetics (guest) (2013) Microbial Cell (2014-present)

Other Session Chair, International Conference on Yeast Genetics & Molecular Biology (2013) ASM-NSF/LINK award (2013)

B. Selected peer-reviewed publications (in chronological order).

(SINCE 2005, out of 35 total): 1. Park, J., Wu, J., Polymenis, M., A. Han. Microchemostat array with small-volume fraction replenishment for steady-state microbial culture. (2013). Lab Chip. 13:4217-24. 2. Truong, S.K., McCormick, R.F., and M. Polymenis. Genetic determinants of cell size at birth and their impact on cell cycle progression in Saccharomyces cerevisiae. (2013). G3 (Bethesda). 3:1525-1530.

PHS 398/2590 (Rev. 09/04) Page 1 Biographical Sketch Format Page Principal Investigator: POLYMENIS, Michael

3. Hoose, S.A., Trinh, J.T., Leitch, M.C., Kelly, M.M., McCormick, R.F., Spyrou, C.L., Smith, R. 3rd, and M. Polymenis. Saccharomyces cerevisiae deletion strains with complex DNA content profiles. (2013). FEMS Microbiol Lett. 345: 72-6. 4. M. Polymenis and Kennedy, B.K. Chronological and replicative lifespan in yeast: Do they meet in the middle? (2012). Cell Cycle 11:3531. 5. M. Polymenis and Kennedy, B.K. High-tech yeast ageing. (2012). Nature 486:37-38. 6. Hoose, S.A., Duran, C., Malik, I., Eslamfam, S., Shasserre, S.C., Downing, S.S., Hoover, E.M., Dowd, K.E., Smith III, R., and M. Polymenis. Systematic analysis of cell cycle effects of common drugs leads to the discovery of a suppressive interaction between gemfibrozil and fluoxetine. (2012). PLoS One 7: e36503. 7. Hoose, S.A., Rawlings, J.A., Kelly, M.M., Leitch, M.C, Ababneh, Q.O., Robles, J.P., Taylor, D., Hoover, E.M., Hailu, B., McEnery, K.A., Downing, S.S., Kaushal, D., Chen, Y., Rife, A., Brahmbhatt, K.A., Smith III, R., and M. Polymenis. A systematic analysis of cell cycle regulators in yeast reveals that most factors act independently of cell size to control initiation of division. (2012). PLoS Genetics 8:e1002590. 8. Henry, K.A., Blank, H.M., Hoose, S.A., and M. Polymenis. The unfolded protein response is not necessary for the G1/S transition, but it is required for chromosome maintenance in Saccharomyces cerevisiae. (2010). PLoS One 5:e12732. 9. Blank, H.M., S. Gajjar, A. Belyanin and M. Polymenis. Sulfur metabolism actively promotes initiation of cell division in yeast. (2009). PLoS One 4:e8018. 10. Blank, H.M., C. Li, J.E. Mueller, L.M. Bogomolnaya, M. Bryk and M. Polymenis. An increase in mitochondrial DNA promotes nuclear DNA replication in yeast. (2008). PLoS Genetics 4:e1000047. 11. Pathak, R., H.M. Blank, J. Guo, S. Ellis and M. Polymenis. The Dcr2 phosphatase targets Sic1 to promote initiation of cell division. (2007). Biochem Biophys Res Comm 361:700-4. 12. Guo, J. and M. Polymenis. Dcr2p targets Ire1p and down-regulates the unfolded protein response in S. cerevisiae. (2006). Embo Rep. 7:1124-7. 13. Bogomolnaya, L.M., Pathak, R., J. Guo, and M. Polymenis. Roles of the RAM signaling network in cell cycle progression in Saccharomyces cerevisiae. (2006). Curr Genet. 49:384-92. 14. Blank, H.M., J.M. Totten, and M. Polymenis. CDK control of membrane-bound organelle homeostasis. (2006) Cell Cycle. 5:486-8. 15. Han, B.-K., L.M. Bogomolnaya, J.M. Totten, H.M. Blank, L.J. Dangott and M. Polymenis. Bem1p, a scaffold signaling protein, mediates cyclin-dependent control of vacuolar biogenesis in Saccharomyces cerevisiae. (2005). Genes Dev. 19:2606-2618. Pathak, R., L.M. Bogomolnaya, J. Guo, and M. Polymenis. A novel function for Kem1p that

C. Research Support

Current Support 9/14-8/15 Genomics Initiative - TAMU (Role: PI) “Targets of translational control that link protein synthesis with initiation of division”

Completed Support (since 2006) 9/08-8/13 National Science Foundation (MCB-0818248; Role: PI) “Control of Initiation of Cell Division by the Unfolded Protein Response” 10/12-3/13 National Science Foundation (IIP-1265349; Role: PI) “An effective and rapid platform to identify factors that delay aging of cells and organisms”

PHS 398/2590 (Rev. 09/04) Page 2 Continuation Format Page BIOGRAPHICAL SKETCH Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Qin, Hongmin Assistant Professor of Cell Biology

eRA COMMONS USER NAME HONGMINQ EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Shandong University, China B.S. 1989-1993 Microbiology Shandong University, China M.S. 1993-1996 Microbiology The Institute of Microbiology, Chinese Academy Ph. D. 1996-1999 Plant Molecular Biology of Sciences, China Postdoctoral Yale University 1999-2005 Cell Biology Training

A. Personal Statement

This proposal tests the time-of-flight model for Intraflagellar Transport (IFT) regulation, where the IFT particles can tell how long they have been inside the flagellum. My group will investigate the biochemistry of IFT complexes when retrograde motion is slowed down with mutants and inhibitors, and express G protein mutants that are predicted to alter catalytic efficiency for quantitative TIRF imagine. Being in the field over 12 years, I have accumulated the necessary expertise and reagents to address the questions asked in the proposal.

B. Positions and Honors. Positions and Employment Assistant Professor, Texas A&M University, 2006-present

Honors 2002- 2004 Polycystic Kidney Disease Foundation Postdoctoral Fellowship 1999 “DiAo” Predoctoral Fellowship, Chinese Academy of Sciences, China 1993-1996 “SunShine” Predoctoral Fellowship, China

C. Selected peer-reviewed publications (Selective from 25 publications) 1. Richey E, Qin H. Isolation of Intraflagellar Transport Particle Proteins from Chlamydomonas reinhardtii. Methods in Enzymology (Cilia) 2013;524:1-17. 2. Richey E, Qin H. Dissecting the sequential assembly and localization of Intraflagellar Transport Particle complex B in Chlamydomonas. PLoS One. 2012;7(8):e43118. PMCID: PMC3416778 3. Behal RH, Miller MS, Qin H, Lucker B, Jones A, Cole DG. Subunit Interactions and Organization of the Chlamydomonas reinhardtii Intraflagellar Transport Complex A. J Biol Chem. 2012;287(15):11689-703. PMCID: PMC3320918 4. Silva DA, Huang X, Behal RH, Cole DG, Qin H. The RABL5 homolog IFT22 regulates the cellular pool size and the amount of IFT particles partitioned to the flagellar compartment in Chlamydomonas reinhardtii. Cytoskeleton (Hoboken). 2012;69(1):33-48. 5. Williamson S, Silva D, Richey E, Qin H. Probing the role of IFT particle complex A and B in flagellar entry and exit of IFT dynein in Chlamydomonas. Protoplasma, 2012;249(3): 851-856 6. Fan Z-C, Behal R H, Geimer S, Wang Z, Williamson SM, Zhang H, Cole DG, Qin H. Chlamydomonas IFT70/CrDYF-1 is a core component of IFT particle complex B and is required for flagellar assembly. Mol Biol Cell, 2010;21, 2696–2706. PMCID: PMC2912355 7. Wang Z, Fan Z-C, Williamson S, Qin H. Intraflagellar transport (IFT) protein IFT25 is a phosphoprotein component of the IFT complex B and physically interacts with IFT27 in Chlamydomonas. PLoS ONE, 2009;4(5):e5384. PMID: 19412537 8. Qin H*, Wang Z*, Diener D, Rosenbaum J. Intraflagellar transport protein 27 is a small G protein involved in cell-cycle control. Curr Biol, 2007;(3):193-202. * equal contribution PMID:17276912 9. Hou Y, Qin H, Follit JA, Pazour GJ, Rosenbaum JL, Witman GB. Functional analysis of an individual IFT protein: IFT46 is required for transport of outer dynein arms into flagella. J Cell Biol, 2007;76(5):653-665. PMID: 17312020 10. Bae YK, Qin H, Knobel KM, Hu J, Rosenbaum JL, Barr MM. General and cell-type specific mechanisms target TRPP2/PKD-2 to cilia. Development, 2006;33(19):3859-3870. PMID:16943275 11. Marshall WF, Qin H, Rodrigo Brenni M, Rosenbaum JL. Flagellar length control system: testing a simple model based on intraflagellar transport and turnover. Mol Biol Cell, 2005;16(1):270-278. PMCID:PMC539171 12. Ou G* Qin H* Rosenbaum JL, Scholey JM. The PKD protein qilin undergoes intraflagellar transport. Curr Biol, 2005;15(11):R410-411. * equal contribution PMID:15936258 13. Qin H*, Burnette DT*, Bae YK, Forscher P, Barr MM, Rosenbaum JL. Intraflagellar transport is required for the vectorial movement of TRPV channels in the ciliary membrane. Curr Biol, 2005;15(18):1695-1699. * equal contribution PMID:16169494 14. Qin H, Diener DR, Geimer S, Cole DG, Rosenbaum JL. Intraflagellar transport (IFT) cargo: IFT transports flagellar precursors to the tip and turnover products to the cell body. J Cell Biol, 2004;164(2):255-266. PMID:14718520 15. Qin H, Rosenbaum JL, Barr MM. An autosomal recessive polycystic kidney disease gene homolog is involved in intraflagellar transport in C. elegans ciliated sensory neurons. Curr Biol, 2001;11(6):457-461. PMID:11301258 C. Research Support Ongoing Research Support NSF MCB-0923835 Qin (PI) 02/01/2010 - 02/28/2013, no cost extension Small GTPase regulators of Intraflagellar Transport (IFT) The goal of this study is to understand the regulatory role of small GTPases in IFT. Role: PI

Completed Research Support in the Past Three Years Polycystic Kidney Diseases Foundation 173G08a Qin (PI) 03/01/2008 - 02/28/2011 Identification of Effectors for IFT27, an Intraflagellar Transport Particle Protein Functioning in the Cell cycle Role: PI

American Heart Association 09SDG2280325 Qin (PI) 07/01/2009 - 06/30/2013 Small GTPase regulators of Intraflagellar Transport (IFT) The grant was relinquished on April 1st, 2010 before the funds for the same proposal from the NSF was released. Role: PI

BIOGRAPHICAL SKETCH NAME POSITION TITLE Raudsepp, Terje Associate Professor (tenured) eRA COMMONS USER NAME traudsepp EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION (if YEAR(s) FIELD OF STUDY applicable) Tartu University, Estonia MSc 1982 Genetics & Cytology The Swedish University of Agricultural Sciences, PhD 1999 Molecular Genetics Uppsala, Sweden

A. Personal Statement I have had extensive research experience (20 years, 98 peer reviewed publications, 11 book chapters) in the areas of mammalian genomics, cytogenetics, studies on mammalian sex chromosomes, and the genomics of reproduction. I have received funding from federal and private agencies, published in high impact journals, such as Science, PNAS, Genome Research, PLoS Genetics, and Theriogenology and trained 3 post-docs, 18 graduate students, and 22 undergraduates. B. Positions and Honors Positions and Employment 2011– Associate Professor, Associate Director of Texas A&M Molecular Cytogenetic present Service Laboratory, Department of Veterinary Integrative BioSciences (VIBS), Texas A & M University, College Station, TX 77 843, USA 2005–2011 Assistant Professor, Associate Director of Texas A&M Molecular Cytogenetic Service Laboratory, Department of Veterinary Integrative BioSciences (VIBS), Texas A & M University, College Station, TX 77 843, USA 2001–2005 Assistant Research Scientist, Department of Veterinary Anatomy & Public Health, Texas A & M University, College Station, TX 77 843, USA 1999–2001 Assistant Research Professor, Dept. of Animal Breeding and Genetics, The Royal Veterinary & Agricultural University, Copenhagen, Denmark 1999 Guest Scientist, Dept. of Animal Breeding and Genetics, The Royal Veterinary & Agricultural University, Copenhagen, Denmark (Recipient of NorFA scholarship for three months) 1995–1999 Dept. of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden (Recipient of the Swedish Institute’s International scholarship for two years) 1994–1995 Research Associate, Laboratory of Molecular Genetics, Institute of Chemical & Biophysics, Estonian Academy of Sciences, Tallinn, Estonia. 1982–1994 Jr. Res. Associate, Dept. of Animal Genetics, Institute of Experimental Biology, Estonian Academy of Sciences, Tallinn, Estonia. Other Experience and Professional Memberships • Ad hoc external reviewer for Estonian Science Foundation, National Science Foundation, AKC Canine Health Foundation, CONACYT and FONDECYT Programs. • Member of International Society of Animal Genetics (ISAG); Texas Genetics Society (TGS), American Association of Clinical Cytogenetics, American Genetic Association and Horse Genome Haplotype Committee. • Member of the editorial board: The Journal of Fertility Biomarkers; Scholarena Journal of Genetics; BMC Genomics Honors/Awards • Winner of the Nature Genetics AND Nature Best Poster Award among over 519 posters from around the world: Human Genome Meeting, March 22-24,1996, Heidelberg, Germany. • The Swedish Institute (Stockholm Sweden) Scholarship Award, 1995-1997. • The Nordic Academy of Training Researchers, NorFA Scholarship Award, Feb. 1999 - Apr. 1999. • Cold Spring Harbor Laboratory (USA) Travel Award, March 2003. • 2010-2011 Montague Center for Teaching Excellence Scholar.

C. Selected peer-reviewed publications out of 100 (¥ corresponding author) 1. Raudsepp, T., Santani, A., Wallner, B., Kata, S.R., Ren, C., Zhang, H.-B., Womack, J.E., Skow, L.C., Chowdhary, B.P. 2004. A detailed physical map of the horse Y chromosome. PNAS, 101, 9321-9326. 2. Raudsepp, T., Lee, E.-J., Kata, S.R., Brinkmeyer, C., Mickelson, J.R., Skow, L.C., Womack, J.E., Chowdhary, B.P. 2004. Exceptional conservation of horse-human gene order on X chromosome revealed by high-resolution radiation hybrid mapping. PNAS 101, 2386-2391. 3. Wade CM, Giulotto E, …., Raudsepp T. et al. 2009. Genome sequence, comparative analysis and population genetics of the domestic horse (Equus caballus). SCIENCE 326 (5954): 865-867. 4. Das, P.J., Chowdhary, B.P., Raudsepp, T¥. 2009. Characterization of the bovine pseudoautosomal region (PAR) and comparison with sheep, goat and other mammalian PARs. Cytogenet. Genome Res., 126, 139-147. 5. Paria, N*, Raudsepp, T* ¥., Wilkerson, A.J., O’Brien, P.C.M., Ferguson-Smith, M.A., Love, C.C., Arnold, C., Rakestraw, P., Murphy, W.J., Chowdhary, B.P ¥. 2011. A gene catalogue of the euchromatic male specific region of the horse Y chromosome: Comparison with human and other mammals. PLoS One 6 :e21374; Epub 2011 Jul 25.* - the authors have equal contribution. 6. Raudsepp T¥, Das PJ, Avila F, Chowdhary BP. 2012. The Pseudoautosomal Region and Sex Chromosome Aneuploidies in Domestic Species. Sex Dev 6:72-83. Received JOURNAL COVER. 7. Raudsepp, T¥, McCue, M.M. *, Das, P.J. *, Dobson, L., Vishnoi, M., Fritz, K.L., Schaefer, R., Rendahl, A.K., Derr, J.N., Love, C.C., Varner, D.D., Chowdhary, B.P. 2012. Genome-Wide Association Study Implicates Testis-Sperm Specific FKBP6 as a Susceptibility Locus for Impaired Acrosome Reaction in Stallions. PLoS GENETICS, Dec;8(12):e1003139. Epub 2012 Dec 20. 8. Avila, F., Das, P.J., Kutzler, M., Owens, E., Perelman, P., Jiri Rubes, Miroslav Hornak, Warren E. Johnson and Raudsepp,T.¥ 2012. Development and application of camelid molecular cytogenetic tools. The Journal of Heredity, 2012 Oct 29. [Epub ahead of print]). 9. Das,P.J., McCarthy, F., Vishnoi, M., Paria, N., Gresham, C., Li, G., Kachroo, P., Sudderth, K.A., Teague, S., Love, C.C., Varner, D.D., Chowdhary, B.P., Raudsepp.T. ¥ 2013. Stallion sperm transcriptome comprises functionally coherent coding and regulatory RNAs as revealed by microarray analysis and RNA-seq. PLoS ONE 2013;8(2):e56535. doi: 10.1371/journal.pone.0056535. Epub 2013 Feb 11. 10. Das, P.J., Mishra, D., Ghosh, S., Avila, F., Johnson, G.A., Chowdhary, B.P., Raudsepp, T¥. 2013. Comparative organization and gene expression profiles of the porcine pseudoautosomal region (PAR). Cytogenet. Genome Res. Published online DOI: 10.1159/000351310. 11. Wang, F., Ekiert. D.E., Ahmad, I., Li, W., Zhang, Y., Bazirgan, O., Torkamani, A., Raudsepp, T., Waithaka, M, Criscitiello, M.F., Wilson, I.A., Schultz, P.G., Vaughn V. Smider, V.V. 2013. Reshaping antibody diversity. Cell 153, 1379–1393. Received journal COVER. 12. Gang Li, Brian W. Davis, Terje Raudsepp, Alison J. Pearks Wilkerson, Victor C. Mason, Malcolm Ferguson-Smith, Patricia C. O’Brien, Paul Waters and William J. Murphy. 2013. Comparative Analysis of Mammalian Y Chromosomes Illuminates Ancestral Structure and Lineage-Specific Evolution. Genome Res. published online June 20, 2013, doi:10.1101/gr.154286.112. 13. Ghosh S, Qu Z, Das PJ, , Fang E, Juras R, Cothran EG, McDonell S, Kenney DG, Lear TL, Adelson D, Chowdhary BP, Raudsepp T¥. 2014. Copy number variation in the horse genome. PLoS GENETICS, accepted August 26, 2014. 14. Raudsepp, T¥. 2014. Cytogenetics and Infertility. In: Llama and Alpaca Care: Medicine, Surgery, Reproduction, Nutrition and Herd Health. Chis Cebra, David E. Andreson, Ahmed Tibary, Robert J. Van Saun and LaRue W. Johnson (Editors). 1st ed. Philadelphia: W.B. Saunders, an imprint of Elsevier Inc., Part III, Chapter 21, 243-249. D. Research Support (current) 1. USDA-AFRI (Chowdhary PI) 2012-2015. Sequencing and functional analysis of the horse Y chromosome, role co-PI. 2. American Quarter Horse Foundation (AQHF), Discovery of Genomic Copy Number Variants in Equine Cryptorchidism, 2012- 2014, role PI. 3. Link Endowment Fund, Equine Genome Analysis 2013-2014,Group proposal. 4. Morris Animal Foundation (MAF); D14LA-005, 2014-2017, Improving the Alpaca Genome Sequence Assembly to Allow Efficient Discovery of the Underlying Genetic Causes of Diseases, Disorders and Traits, role PI.

2 Program Director/Principal Investigator (Last, First, Middle): RIGGS, Penny K.

NAME POSITION TITLE Riggs, Penny K. Associate Professor of Functional Genomics eRA COMMONS USER NAME (credential, e.g., agency login) pk-riggs EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) Purdue University, West Lafayette, IN B.S. 8/87 Biology Purdue University, West Lafayette, IN M.S. 5/91 Animal Cytogenetics Texas A&M University, College Station, TX Ph.D 5/96 Molecular Genetics NASA Johnson Space Center / Univ. of Houston, TX Postdoc 9/96-10/97 Radiation Biophysics Univ of Texas M.D. Anderson Cancer Center, TX Postdoc 11/97-5/02 Carcinogenesis

A. Positions and Honors Employment 1996 – 1997 Texas Aerospace Postdoctoral Fellow, Dept of Pharmacological and Pharmaceutical Sciences, University of Houston, Institute of Space Systems Operations (ISSO) and Medical Operations Branch, NASA L.B. Johnson Space Center. 1997 Visiting Scientist, National Institute of Radiological Sciences, HIMAC, Chiba, Japan 1997 – 2002 Postdoctoral Fellow, University of Texas M.D. Anderson Cancer Center, Department of Carcinogenesis, Science Park – Research Division, Smithville, TX. 2002 – 2006 Instructor, Department of Carcinogenesis, University of Texas M.D. Anderson Cancer Center, Science Park – Research Division. 2002 – 2006 Associate Director, Functional Genomics Facility Core (2002-2005), Analyst, Biostatistics and Informatics Core (2003-2005), & Co-Director, Molecular Biology Facility Core (2005- 2006), NIEHS Center for Research on Environmental Disease (CRED), Smithville, TX. 2006 – 2012 Assistant Professor, Department of Animal Science, Texas A&M University 2007 – Adjunct Faculty, Department of Veterinary Integrative Biosciences, Texas A&M University 2007 – Member, Faculty of Genetics, Texas A&M University, College Station, TX. 2007 – Steering committee, Alliance for Bioinformatics, Computational Biology and Systems Biology, Texas A&M University 2012 – Associate Professor, Department of Animal Science, Texas A&M University. 2013 – 2015 Texas A&M Council of Principal Investigators (Executive Committee 2013-15)

Other Experience and Professional Memberships 1988 – member, American Genetic Association 1991 – member, Gamma Sigma Delta 1992 – member, American Association for the Advancement of Science 1992 – member, Texas Genetics Society (Board of Directors 2006-2009, President 2013-14) 1997 – member, American Association for Cancer Research 2007 – member, American Society of Animal Science (Public Policy Comm 2013-16) 2007 – member, International Society of Animal Genetics 2007 – member, USDA NIFA Multistate Regional Project NC1131: Molecular Mechanisms Regulating Skeletal Muscle Growth and Differentiation (Secretary 2008-09, Chair 2009-10, Project Renewal writing team 2009) 2007 – member, USDA National Animal Genome Program, NRSP8 (Bovine workshop chair 2009) 2011 – 2014 USDA NIFA Review Panel 2014 National Science Foundation, Panelist

PHS 398/2590 (Rev. 06/09) Page Biographical Sketch Format Page Program Director/Principal Investigator (Last, First, Middle): RIGGS, Penny K. Honors 2001 American Association for Cancer Research Brigid G. Leventhal Scholar award. 2009– Selected participant – National Academies Keck Futures Initiative (Synthetic Biology) 2009 Vice-Chancellor’s Award in Excellence – McGregor Genomics Team Research Award 2013 Faculty Award for Merit in Research, Gamma Sigma Delta (TAMU chapter)

C. Peer-reviewed Publications (past 2 years) Shen J., E. A. Abel, P. K. Riggs, J. Repass, S. C. Hensley, L. Schroeder, A. Temple, A. Chau, S. A. McClellan, O. Rho, K. Kiguchi, M. D. Ward, O. J. Semmes, M. D. Person, J. M. Angel, and J. DiGiovanni. 2012 Proteomic and pathway analyses reveal a network of inflammatory genes associated with differences in skin tumor promotion susceptibility in DBA/2 and C57BL/6 mice. Carcinogenesis 33:2208–2219. Allen C., B. Alves, X. Li, L. Tedeschi, H. Zhou, J. Paschal, P.K. Riggs, U. Brag-Neto., D. Keisler, G. Williams, M. Amstalden. 2012. Gene expression in the arcuate nucleus of heifers is affected by controlled intake of high- and low-concentrate diets. J. Anim. Sci. 90:2222–2232. Brannan J.L., P.J. Holman, P.M. Olafson, J.H. Pruett, and P.K. Riggs. 2012 Extraction of high quality RNA from bovine and cervine hide biopsies for ectoparasite-host studies. J. Parasitol. 99:19-23. Stafuzza, N. B., A. J. Greco, J. R. Grant, C. A. Abbey, C. A. Gill, T. Raudsepp, L. C. Skow, J. E. Womack, P. K. Riggs and M. E. J. Amaral. 2012. A high resolution radiation hybrid map of the river buffalo major histocompatibility complex (MHC) and comparison with BoLA. Anim. Genet. 44:369-376. Chitko-McKown C.G., S.K.Chapes, L.C. Miller, P.K. Riggs, M.T. Ortega, B.T. Green, and R.D. McKown. 2013 Development and characterization of two porcine monocyte-derived macrophage lines. Results Immunol. 3:26-32. PMCID: PMC3631004 Riley D.G., T.H. Welsh Jr, L.L. Hulsman, C.A. Gill, A.D. Herring, P.K. Riggs, J.E. Sawyer, J.O. Sanders. 2013. Whole genome association of SNP with newborn calf cannon bone length. Livestock Sci. 155:186-196. Brinkmeyer-Langford C., A. Rodrigues., K.J. Kochan, R. Haney, F. Rassu, A. Steelman. C. Young., M. Meagher, P.K. Riggs, and J. Welsh. 2014. Consequences of perinatal BPA exposure in a mouse model of multiple sclerosis. Autoimmunity 47:57-66. Stafuzza N.B., K.J. Kochan, P.K. Riggs, and M.E.J. Amaral. 2013. Single nucleotide variations in the buffalo kappa-casein gene (CSN3). Buffalo Bulletin 32:675-679. Dawes M., T. Moore-Harrison, A.T. Hamilton, T. Ceaser, K.J. Kochan, P.K. Riggs, and J.T. Lightfoot. 2014. Differential gene expression in high- and low-active inbred mice. BioMed Res. Intl. 2014:361048. Hanna, L.L.H., D.J. Garrick, C.A. Gill, A.D. Herring, P.K. Riggs, R.K. Miller, J.O. Sanders, D.G. Riley. 2014. Genome-wide association study of temperament and tenderness using different Bayesian approaches in a Nellore-Angus crossbred population. Livestock Sci. 161:17-27. Thorson J.F., L.D. Prezotto, R.C. Cardoso, S. M. Sharpton, John F. Edwards, T.H. Welsh, Jr., P.K. Riggs, A. Caraty, M Amstalden, G.L. Williams. 2014. Hypothalamic distribution, adenohypophyseal receptor expression and ligand functionality of RF-amide-related peptide 3 in the mare during the breeding and non- breeding seasons Biol. Reprod. 90:28, 1-9. DOI 10.1095/biolreprod.113.112185 Ing, N.H., L. Berghman, D. Abi-Ghanem, K. Abbas, A. Kaushik, P.K. Riggs, J.B. Puschett. 2014. Marinobufagenin regulates permeability and gene expression of brain endothelial cells. Am. J. Physiol. Regul. Integr. Comp. Physiol. 306: R918-R924. Angel, J.M., E.L. Abel, P.K. Riggs, S.A. McClellan, and J. DiGiovanni. 2014 Fine mapping reveals that promotion susceptibility locus 1 (Psl1) is a compound locus with multiple genes that modify susceptibility to skin tumor development. G3: Genes|Genomes|Genetics. 4:1071-9. doi:10.1534/g3.113.009688 PMCID: PMC4065250 Riley, D.G., C.A. Gill, A.D. Herring, P.K. Riggs, J.E. Sawyer, D.K. Lunt, and J.O. Sanders. 2014. Genetic evaluation of aspects of temperament in Nelore-Angus calves. J. Anim. Sci. 92:3223-3230. Ing, N.H., D.W. Forrest, P.K. Riggs, S. Loux, C.C. Love, S.P. Brinsko, D.D. Varner, T.H. Welsh Jr. 2014. Dexamethasone acutely down-regulates genes involved in steroidogenesis in stallion testes. J. Steroid Biochem. Mol. Biol. 143:451-459. Brannan, J.L., P.K. Riggs, P.U. Olafson, I. Ivanov, P.J. Holman. 2014. Expression of bovine genes associated with local and systemic immune response to infestation with the Lone Star tick, Amblyomma americanum. Ticks and Tick-borne Diseases. 5:676-688. PMID: 25108787

PHS 398/2590 (Rev. 06/09) Page 2 Biographical Sketch Format Page Principal Investigator RILEY, Bruce B.

NAME POSITION TITLE Riley, Bruce B. Professor eRA COMMONS USER NAME

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of Colorado-Boulder B.Sc. 1982 Biology University of Wisconsin-Madison Ph.D. 1990 Mol. And Dev. Biology University of Wisconsin-Madison Postdoc. 1989-1992 Chick Development

Personal Statement I have worked in the field of zebrafish developmental genetics for over 20 years, with 19 years as a PI running my own lab. Research in my lab has focused primarily on development of the zebrafish inner ear, with a number of seminal contributions to the field: We were the first group to demonstrate that Fgf is the primary factor responsible of otic placode induction; we were amongst the first to directly test the role of Delta-Notch signaling in patterning hair cells and support cells; we demonstrated that Atoh1 acts akin to proneural genes, establishing the entire pro-sensory equivalence group rather than simply promoting hair cell differentiation; we were the first to demonstrate that Sox2 potentiates the pro-sensory activity of Atoh1; and we showed that Sox2 is essential for hair cell regeneration (to our knowledge the first such gene identified in the inner ear).

A. Positions and Honors. Positions and Employment 2007-present Professor, Biology Department, Texas A&M University. 2000-2007 Associate professor, Biology Department, Texas A&M University. 1995-2000 Assistant professor, Biology Department, Texas A&M University. 1992-1995 Postdoctoral research with David Grunwald, University of Utah. 1990-1992 Postdoctoral research with John Fallon and Brad Olwin, University of Wisconsin- Madison. 1985-1990 Graduate research with Steve Barclay, University of Wisconsin-Madison.

Honors 1982 B.A. with distinction, University of Colorado 1992-1994 Postdoctoral Fellowship, NIH, University of Utah 1994-1996 Postdoctoral Fellowship, ACS, University of Utah 1996-1998 Texas Advanced Research Program awardee 1997-1999 March of Dimes awardee, 1997-1999. 1998-present NIH awardee

PHS 398/2590 (Rev. 09/04) Page 1 Biographical Sketch Format Page Principal Investigator RILEY, Bruce B.

B. Selected peer-reviewed publications (in chronological order).

Edlund, R. K., Ohyama, T., Kantarci, H., Riley, B. B. and Groves, A. K. (2014). Foxi transcription facotrs promote pharyngeal arch development by regulating formation of FGF signaling centers. Dev. Biol. 390, 1-13. Maulding, K, Padanad, M. S., Dong, J. and Riley, B. B. (2014). Mesodermal Fgf10b cooperates with other Fibroblast Growth Factors during induction of otic and epibranchial placodes in zebrafish. Dev. Dyn. 243, 1275-1285. Bhat, N., Kwon, H. J. and Riley, B. B. (2013). A gene network that coordinates preplacodal competence and neural crest specification in zebrafish. Dev. Biol. 373, 107-117. Vemaraju, S., Kantarci, H., Padanda, M. S. and Riley, B. B. (2012). A spatial and temporal gradient of Fgf differentially regulates distinct stages of neural development in the zebrafish inner ear. PLoS Genetics 8(11), e1003068. Padanad, M. S., Bhat, N., Guo, B. and Riley, B. B. (2012). Conditions that influence how cells respond to Fgf during otic placode induction. Dev. Biol. 364, 1-10. Bhat, N. and Riley, B. B. (2011). Integrin-a5 coordinates assembly of posterior cranial placodes in zebrafish and enhances Fgf-dependent regulation of otic/epibranchial cells. PLoS ONE 6(12), e27778. Sweet, E. M., Vemaraju, S. and Riley, B. B. (2011). Sox2 and Fgf interact with Atoh1 to promote sensory competence throughout the zebrafish inner ear. Dev. Biol. 358, 113-121. Padanad, M. S. and Riley, B. B. (2011). Pax2/8 proteins coordinate sequential induction of otic and epibranchial placodes through differential regulation of foxi1, sox3 and fgf24. Dev. Biol. 351, 90- 98. Kwon, H. J., Bhat, N., Sweet, E. M., Cornell, R. A. and Riley, B. B. (2010). Identification of early requirements for preplacodal ectoderm and sensory organ development. PLoS Genetics 6 (9), e1001133. PMC2944784 Millimaki, B. B., Sweet, E. M. and Riley, B. B. (2010). Sox2 is required for maintenance and regeneration, but not initial development, of hair cells in the zebrafish inner ear. Dev. Biol. 338, 262-269. PMCID: PMC2815045. Kwon, H.-J. and Riley, B. B. (2009). Mesendodermal signals required for otic induction: Bmp-antagonists cooperate with Fgf and can facilitate formation of ectopic otic tissue. Dev. Dynam. 238, 1582-1594. PMCID: PMC2835543. Millimaki, B. B., Sweet, E. M., Dhason, M. S. and Riley, B. B. (2007). Zebrafish atoh1 genes: Classic proneural activity in the inner ear and regulation by Fgf and Notch. Development 134, 295-305. Kwak, S. J., Vemaraju, S., Moorman, S. J., Zeddies, D., Popper, A. N., and Riley, B. B. (2006). Zebrafish pax5 regulates development of the utricular macula and vestibular function. Dev. Dynam. 235, 3026-3038. Mackereth, M. D., Kwak, S.-J., Fritz, A. and Riley, B. B. (2005). Zebrafish pax8 is required for otic placode induction and plays a redundant role with Pax2 genes in the maintenance of the otic placode. Development 132, 371-382. Phillips, B. T., Storch, E. M., Lekven, A. C. and Riley, B. B. (2004). A direct role for Fgf but not Wnt in otic placode induction. Development 131, 923-931. Phillips, B. T., Bolding, K. and Riley, B. B. (2001). Zebrafish fgf3 and fgf8 encode redundant functions required for otic placode induction. Dev. Biol. 235, 351-365. Riley, B. B., Chiang, M.-Y., Farmer, L., and Heck, R. (1999). The deltaA gene of zebrafish mediates lateral inhibition of hair cells in the inner ear and is regulated by pax2.1. Development 126, 5669- 5678. Riley, B. B., Zhu, C., Janetopoulos, C., and Aufderheide, K. J. (1997). A critical period of ear development controlled by distinct populations of ciliated cells in the zebrafish. Dev. Biol.191, 191-201. Riley, B. B. and Grunwald, D. J. (1996). A mutation in zebrafish affecting a localized cellular function required for normal ear development. Dev. Biol. 179, 427-435.

PHS 398/2590 (Rev. 09/04) Page 2 Continuation Format Page Principal Investigator/Program Director (Last, First, Middle): RILEY, David, G.

NAME POSITION TITLE Riley, David, G. Associate Professor eRA COMMONS USER NAME

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Texas A&M University, College Station B.Sc. 1980-1984 Agricultural Economics M.S. 1995-1997 Animal Breeding Ph.D. 1997-2000 Genetics

A. Positions and Honors

Employment

1984-1985 United States Army, Fort Sill, OK 1985-1995 Manager, DeKalb Swine Breeders, Plains, KS 2000-2009 Research Geneticist, USDA Agricultural Research Service, Subtropical Agricultural Research Station, Brooksville, FL 2009-present Associate Professor, Department of Animal Science, Texas A&M University Member, Faculty of Genetics

Other Experience and Professional Memberships

American Society of Animal Science

Honors

2011 Brahman Friend of the Year, American Brahman Breeders Association

B. Selected peer-reviewed publications (Graduate Students as shown)

Riley, D. G., C. C. Chase, Jr., A. C. Hammond, R. L. West, D. D. Johnson, T. A. Olson, and S. W. Coleman. 2003. Estimated genetic parameters for palatability traits of steaks from Brahman cattle. J. Anim. Sci. 81:54-60.

Riley, D. G., C. C. Chase, Jr., T. A. Olson, S. W. Coleman, and A. C. Hammond. 2004. Genetic and nongenetic influences on vigor at birth and preweaning mortality of purebred and high percentage Brahman calves. J. Anim. Sci. 82:1581–1588.

Casas, E., S. N. White, D. G. Riley, T. P. L. Smith, R. A. Brenneman, T. A. Olson, D. D. Johnson, S. W. Coleman, G. L. Bennett, and C. C. Chase, Jr. 2005. Assessment of single nucleotide polymorphisms in genes residing on chromosomes 14 and 29 for association with carcass composition traits in Bos indicus cattle. J. Anim. Sci. 83:13–15.

White, S. N., E. Casas, T. L. Wheeler, S. D. Shackelford, M. Koohmaraie, D. G. Riley, C. C. Chase, Jr., D. D. Johnson, J. W. Keele, and T. P. L. Smith. 2005. A new SNP in CAPN1 extends the current tenderness marker test to include cattle of Bos indicus, Bos taurus, and crossbred descent. J. Anim. Sci. 83:2001–2008.

Riley, D. G., S. W. Coleman, C. C. Chase, Jr., T. A. Olson, and A. C. Hammond. 2007. Genetic parameters for weight, hip height, and the ratio of weight to hip height from random regression analyses of Brahman feedlot cattle. J. Anim. Sci. 85:42–52.

PHS 398/2590 (Rev. 09/04) Page Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle): RILEY, David, G.

Riley, D. G., and J. A. Van Wyk. 2009. Genetic parameters for FAMACHA© score and related traits for host resistance/resilience and production at differing severities of worm challenge in a Merino flock in South Africa. Vet. Parasitol. 164:44–52.

Riley, D. G., C. C. Chase, Jr., S. W. Coleman, T. A. Olson, and R. D. Randel. 2010. Evaluation of tropically adapted straightbred and crossbred beef cattle: Heifer age and size at first conception and characteristics of their first calves. J. Anim. Sci. 88:3173–3182.

Luna-Nevárez, P., G. Rincón, J. F. Medrano, D. G. Riley, C. C. Chase, Jr., S. W. Coleman, D. M. VanLeeuwen, K. L. DeAtley, A. Islas-Trejo, G. A. Silver, and M. G. Thomas. 2011. Single nucleotide polymorphisms in the growth hormone insulin-like growth factor axis in straightbred and crossbred Angus, Brahman, and Romosinuano heifers: Population genetic analyses and association of genotypes with reproductive phenotypes. J. Anim. Sci. 89:926–934.

Riley, D. G., and J. A. Van Wyk. 2011. The effects of penalization of FAMACHA® scores of lambs treated for internal parasites on the estimation of genetic parameters and prediction of breeding values. Small Rum. Res. 99:122–129.

Riley, D. G., C. C. Chase, Jr., S. W. Coleman, and T. A. Olson. 2012. Genetic assessment of rectal temperature and coat score in Brahman, Angus, and Romosinuano crossbred and straightbred cows and calves under subtropical summer conditions. Livest. Sci. 148:109–118.

Riley, D. G., T. H. Welsh, Jr., C. A. Gill, L.L. Hulsman, A. D. Herring, P. K. Riggs, J. E. Sawyer, and J. O. Sanders. 2013. Whole genome association of SNP with newborn calf cannon bone length. Livest. Sci. 155:186–196.

Hulsman Hanna, L. L., D. J. Garrick, C. A. Gill, A. D. Herring, P. K. Riggs, R. K. Miller, J. O. Sanders, and D. G. Riley. 2014. Genome-wide association study of temperament and tenderness using different Bayesian approaches in a Nellore-Angus crossbred population. Livest. Sci. 161:17–27.

Hulsman Hanna, L. L., J. O. Sanders, D. G. Riley, C. A. Abbey, and C. A. Gill. 2014. Identification of a major locus interacting with MC1R and modifying black coat color in an F2 Nellore-Angus population. Genet. Sel. Evol. 46:4.

Hulsman Hanna, L. L., and D. G. Riley. 2014. Mapping genomic markers to closest feature using the R package Map2NCBI. Livest. Sci. 162:59–65.

Riley, D. G., C. C. Chase, Jr., S. W. Coleman, and T. A. Olson. 2014. Evaluation of the Criollo breed Romosinuano as purebred and crossbred cows with Brahman and Angus in Florida: I. Reproduction and parturition. J. Anim. Sci. 92:1902–1910.

Riley, D. G., C. C. Chase, Jr., S. W. Coleman, and T. A. Olson. 2014. Evaluation of the Criollo breed Romosinuano as purebred and crossbred cows with Brahman and Angus in Florida: II. Maternal influence on calf traits, cow weight, and measures of maternal efficiency. J. Anim. Sci. 92:1911–1919.

Schmidt, S. E., D. A. Neuendorff, D. G. Riley, R. C. Vann, S. T. Willard, T. H. Welsh, Jr., and R. D. Randel. 2014. Genetic parameters of three methods of temperament evaluation of Brahman calves. J. Anim. Sci. 92:3082–3087.

Riley, D. G., C. A. Gill, A. D. Herring, P. K. Riggs, J. E. Sawyer, D. K. Lunt, and J. O. Sanders. 2014. Genetic evaluation of aspects of temperament in Nellore-Angus calves. J. Anim. Sci. doi:10.2527/jas.2014-7797. In Press.

Riley, D. G., C. A. Gill, A. D. Herring, P. K. Riggs, J. E. Sawyer, and J. O. Sanders. 2014. Alternative parameterizations of relatedness in whole genome association analysis of pre-weaning traits of Nelore-Angus calves. Genet. Mol. Biol. In Press.

PHS 398/2590 (Rev. 09/04) Page Continuation Format Page Program Director/Principal Investigator: ROSENTHAL, Gil G.

NAME POSITION TITLE Rosenthal, Gil G. Professor eRA COMMONS USER NAME Department of Biology ROSENTHALG Texas A&M University EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable)

Harvard University AB 1993 Biology University of Texas, Austin PhD 2000 Zoology University of California, San Diego Postdoc 2000-02 Evolutionary genetics

A. Personal Statement

I have spent my career studying sexual selection and hybridization in swordtail fish. The core set of techniques developed in my lab involves sophisticated measures of morphological and behavioral phenotypes associated with sexual selection. I have been working in central Mexico since 1993 and have established good working relationships with Mexican colleagues and regulatory agencies. With three PhD students graduated (James B. Johnson, PhD 2013; Zach Culumber, CONACyT postdoctoral researcher at Universidad Autónoma del Estado de Hidalgo; Heidi Fisher, NRSA trainee in Hopi Hoekstra’s lab at Harvard, assistant professor at College of William & Mary starting August 2013) and three former postdocs with faculty jobs (Seth Coleman – Gonzaga University; Michael Tobler – Oklahoma State University; Bob Wong – Monash University), I have an established track record of mentoring trainees. I have two NSF- funded projects nearing completion, which have laid the methodological foundation for this proposal. One project involves characterizing female mating preferences in two naturally-hybridizing species, while the other focuses on developing software for presentation of realistic and biologically rigorous computer animations to animals in behavioral assays. The data we are generating on quantifying variation in visual performance will be directly applicable to the proposed work.

B. Positions and honors Positions and Employment

1993 Research assistant, Smithsonian Tropical Research Institute, Gamboa, Panama. 1993-94, ‘96-98 NSF predoctoral fellow, University of Texas at Austin. 1994 Assistant researcher, Texas Natural History Collection, Texas Memorial Museum. 1994-1995 Teaching assistant, University of Texas at Austin. 1995-1996 University fellow, University of Texas at Austin. 1998-2000 Graduate research assistant, University of Texas at Austin. 2000-2002 National Eye Institute postdoctoral fellow, University of California, San Diego. 2002-date Assistant Professor, Department of Biology and Marine Program, Boston University. 2003 Visiting Professor, Interuniversity Institute, Eilat, Israel. 2002-2006 Assistant Professor, Department of Biology, Boston University. 2006-2009 Assistant Professor, Department of Biology, Texas A&M University 2006-date Faculties of Neuroscience, Genetics, Reproductive Biology, and Marine Biology, Texas A&M University 2005-date Director, Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 2009-2013 Associate Professor, Department of Biology, Texas A&M University 2011-date Chair, Faculty of Ecology & Evolutionary Biology, Texas A&M University 2013-date Professor, Department of Biology, Texas A&M University

Program Director/Principal Investigator: ROSENTHAL, Gil G. Other Experience and Professional Memberships

1993-date Member, Animal Behavior Society 1994-date Member, Society for the Study of Evolution 1994-date Member, American Society of Naturalists 1994-date Member, American Society of Ichthyologists and Herpetologists 1995-date Member, International Society for Behavioral Ecology 1998-date Member, Sociedad de Ictiología Mexicana, A. C. 2006-2008 Public Affairs Chair, Animal Behavior Society 2010-date Associate Editor, Behavioral Ecology

Honors

1989 National Scholar, Harvard University. 1992 NSF RTG Undergraduate Fellowship, University of California at Davis. 1993 University Fellowship, University of Texas at Austin. 1993 University of California Special Regents’ Fellowship (declined). 1993 National Science Foundation Predoctoral Fellowship. 1995 Texas chapter American Fisheries Society Scholarship. 1995 Sigma Xi Grant-in-Aid of Research. 1997 National Science Foundation Doctoral Dissertation Improvement Grant. 1999 American Livebearer Association research award. 2000 Outstanding Doctoral Dissertation Award, University of Texas at Austin. 2000 National Research Service Award, NIH. 2003 Lipper Fellowship.

C. Selected peer-reviewed publications (from 72 publications)

Most relevant to the current application

Cui R, Schumer M, Kruesi K, Walter R, Andolfatto P, Rosenthal G. 2013. Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes. Evolution, in press. Schumer M, Cui R, Boussau B, Walter R, Rosenthal G, Andolfatto P. 2012. An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences. Evolution 67:1155- 1168. Z.W. Culumber, D.B. Shepard, S.W. Coleman, G.G. Rosenthal and M. Tobler, 2012. Physiological adaptation along environmental gradients and replicated hybrid zone structure in swordtails (Teleostei: Xiphophorus). J. Evol. Biol. Z.W. Culumber, H. S. Fisher, M. Tobler, M. Mateos, P.H. Barber, M. D. Sorenson and G.G. Rosenthal 2011. Replicated hybrid zones of Xiphophorus swordtails along an elevational gradient. Mol. Ecol. 20: 342-356.

Additional recent publications of importance to the field (in chronological order) M. Tobler, Z.W. Culumber, M. Plath, K.O. Winemiller, and G.G. Rosenthal 2011. An indigenous religious ritual selects for resistance to a toxicant in a livebearing fish. Biol. Lett. 7:229-232. M.N. Verzijden, Z.W. Culumber, and G.G. Rosenthal 2012. Opposite effects of learning cause asymmetric mate preferences in hybridizing species. Behav. Ecol. 23: 1133-1139. M.N. Verzijden and G. G. Rosenthal 2011. Effects of sensory modality on learned mate preferences in female swordtails. Anim. Behav. 82: 557-562. P.M. Willis, M.J. Ryan, and G. G. Rosenthal 2011. Encounter rates with conspecific males influence female mate choice in a naturally hybridizing fish. Behav. Ecol. 22: 1234-1240.

Principal Investigator/Program Director (Last, First, Middle): Sachs, Matthew S. BIOGRAPHICAL SKETCH Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Matthew S. Sachs eRA COMMONS USER NAME Professor SACHSM EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION (if YEAR(s) FIELD OF STUDY applicable) Cornell University, Ithaca, NY A.B. 1979 Biochemistry Massachusetts Institute of Technology, Ph.D. 1986 Biology Cambridge, MA Stanford University, Stanford, CA Postdoc. 1986-1990 Biological Sciences

A. Personal Statement My research focuses on two key areas of biology: understanding post-transcriptional control mechanisms, and understanding fungal biology at the whole genome-level. With respect to post-transcriptional control, I have probed the functions of upstream open reading frames (uORFs), important in controlling gene expression. My laboratory discovered that the nascent arginine attenuator peptide (AAP), encoded by an evolutionarily conserved uORF in fungal mRNA for an arginine biosynthetic enzyme, stalls ribosomes in response to arginine, reducing gene expression. As a result of these efforts, AAP is currently the best understood eukaryotic ribosome arrest peptide, and is a paradigm for understanding how arrest peptides, like antibiotics, interfere with protein synthesis. We discovered that AAP-mediated stalling leads to mRNA degradation through the NMD pathway. This work provided the first conclusive link between ribosome occupancy of a uORF termination codon and mRNA stability. My expertise in translation was instrumental in uncovering an unexpected role for nonoptimal codon usage in regulating the synthesis rate of a core component of the circadian clock, necessary for circadian rhythmicity. With respect to genome work, I coauthored The Neurospora Compendium: Chromosomal Loci (Academic Press, 2001), which encyclopedically described, gene-by-gene, what was known about the biochemistry, cell biology and genetics of N. crassa from the Nobel- Prize winning studies of Beadle and Tatum through the millennium. This remains a standard reference for Neurospora. I was co-PI on the project to sequence the N. crassa genome. This was the first public genome of a filamentous fungus, and it opened the floodgates for fungal genome sequencing, and provided the necessary platforms for fungal genome analyses. I am a co-PI on the NIH-P01 that knocked-out, and made publicly available, nearly every predicted N. crassa gene, and using my laboratory’s transcriptome studies established experimentally verified gene models for annotation. The resources generated by the P01 have revolutionized basic research in N. crassa, as well as having a major impact on understanding the biology of fungal pathogens .By combining my expertise in translation and genome biology, along with my record of success in administering grants, we are now in a unique position to successfully attack mechanisms of ribosome arrest, and to obtain a comprehensive genome-wide view of how upstream translation of uORFs and related sequences impacts eukaryotic gene expression.

B. Positions and Honors

1990-1995 Assistant Professor, Oregon Graduate Institute of Science and Technology, Beaverton, OR 1995-2001 Associate Professor, Oregon Graduate Institute of Science and Technology, Beaverton, OR PHS 398/2590 (Rev. 09/04) Page Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle): Sachs, Matthew S.

1995-2001 Adjunct Associate Professor, Department of Molecular Microbiology and Immunology, Oregon Health & Science University (OHSU), Portland, OR 2001-2006 Associate Professor, OGI School of Science & Engineering, OHSU; Joint Associate Professor, Department of Molecular Microbiology and Immunology,OHSU 2007 Professor, OGI School of Science & Engineering, OHSU, Department of Molecular Microbiology and Immunology, OHSU 2007-present Professor, Department of Biology, Texas A&M University, College Station, TX 2011 Association of Former Students of Texas A&M University Distinguished Achievement Award, College of Science – Teaching 2011 Student Recognition Award for Teaching Excellence 2013 American Association for the Advancement of Science Fellow 2014 American Academy of Microbiology Fellow

C. Selected Peer-Reviewed Publications (out of 55)

Ivanov, I., Loughran, G., Sachs, M.S., and Atkins, J.F. (2010). Initiation context modulates autoregulation of eukaryotic translation initiation factor 1 (eIF1). Proc Natl Acad Sci USA. 42,18056-180580 [PMID 20921384] Spevak, C.C., Ivanov, I., and Sachs, M.S. (2010). Sequence requirements for ribosome stalling by the arginine attenuator peptide. J Biol Chem. 285, 40933-40942 [PMCID 3003393]. Loughran, G., Sachs, M.S., Atkins, J.F., and Ivanov, I.P. (2011). Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5. Nucleic Acids Res 40, 2898-2906. [PMID: 22156057]. Wu, C., Wei, J., Lin, P.J., Tu, L., Deutsch, C., Johnson, A.E., and Sachs, M.S. (2012). Arginine changes the conformation of the arginine attenuator peptide relative to the ribosome tunnel. J Mol Biol 416, 518-533. [PMID: 22244852] Wei, J., Wu, C., and Sachs, M.S. (2012). The arginine attenuator peptide interferes with the ribosome peptidyl transferase center. Mol Cell Biol 32, 2396-2406. [PMID: 22508989] Zhai, B., Wu, C., Wang, L., Sachs, M.S., and Lin, X. (2012). The antidepressant sertraline provides a promising therapeutic option for neurotropic Cryptococcal infections. Antimicrob Agents Chemother 56, 3758-3766. [PMID: 22508310] Zhou, M., Guo, J., Cha, J., Chae, M., Chen, S., Barral, J.M., Sachs, M.S., and Liu, Y. (2013). Non-optimal codon usage affects expression, structure and function of clock protein FRQ. Nature 495, 111-115. Dreyfuss, J.M., Zucker, J.D., Hood, H.M., Ocasio, L.R., Sachs, M.S., and Galagan, J.E. (2013). Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PLoS Comput Biol 9, e1003126. Martínez, A.K., Gordon, E., Sengupta, A., Shirole, N., Klepacki, D., Martinez-Garriga, B., Brown, L.M., Benedik, M.J., Yanofsky, C., Vazquez-Laslop, N., Sachs, M.S., Cruz-Vera, L.R. (2014). Interactions of the TnaC nascent peptide with rRNA in the exit tunnel enable the ribosome to respond to free tryptophan. Nucleic Acids Res 42, 1245-1256. [PMID 3902921]. Wu, C., and Sachs, M.S. (2014). Preparation of a Saccharomyces cerevisiae cell-free extract for in vitro translation. Methods Enzymol 539, 17-28. Wu, C., Yang, F., Smith, K.M., Peterson, M., Dekhang, R., Zhang, Y., Zucker, J., Bredeweg, E.L., Mallappa, C., Zhou, X., Lyubetskaya, A., Townsend, J.P., Galagan, J.E., Freitag, M., Dunlap, J.C., Bell-Pedersen, D., and Sachs, M.S. (2014). Genome-wide characterization of light-regulated genes in Neurospora crassa. G3 4, 1731-1745.

PHS 398/2590 (Rev. 09/04) Page Continuation Format Page Program Director/Principal Investigator: SAMUEL, James E. BIOGRAPHICAL SKETCH Provide the following information for the Senior/key personnel and other significant contributors in the order listed on Form Page 2. Follow this format for each person. DO NOT EXCEED FOUR PAGES. NAME POSITION TITLE Samuel, James E. Professor and Chair eRA COMMONS USER NAME (credential, e.g., agency login) SAMUELJ EDUCATION/TRAININGSAMUELJ (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) Miami University B.A. 1976 Zoology & Chemistry Washington State University M.S. 1983 Biology Washington State University Ph.D. 1986 Microbiology Uniformed Services University Post-Doc 1987-1990

B. POSITIONS AND HONORS 1991-1994 Director, Molecular Biology, MicroCarb Inc., Gaithersburg, MD 1994-2000 Assistant Professor, Dept. of Med. Micro. College of Medicine, TAMUSHSC 2000-2005 Associate Professor, Dept. of Med. Micro. , College of Medicine, TAMUSHSC 2005-Present Professor, Dept. of Med. Micro. , College of Medicine, TAMUSHSC 2006-2010 Associate Dept. Chair, Dept. of Micro. & Mol. Pathogenesis, TAMUSHSC 2010-present Dept. Chair, Dept. of Microbial Pathogenesis & Immunology, TAMUSHSC

C. SELECTED (15) PUBLICATIONS: LAST 5 YEARS (From list of ~105) Briggs, H., N. Pul, R. Seshadri, M.J. Wilson, C. Tersteeg, K.E. Russell-Lodrique, M. Andoh, A.J. Baumler, and J.E. Samuel. A limited role for iron regulated genes in Coxiella burnetii pathogenesis. 2008. Infect. Immun. 76:2189-2201. PMCID: 2346684.

Mertens, K., L. Lantsheer, D.G. Ennis, and J.E. Samuel. Constituitive SOS expression and damage-inducible AddAB- mediated recombinational repair systems for Coxiella burnetii as potential adaptations for survival within macrophages. 2008. Mol. Microbiol.69: 1411-1426.

P.A. Beare, N. Unsworth, M. Andoh, D.E. Voth, A. Omsland, S.D. Gilk, K.P. Williams, B.W. Sobral, J.J. Kupko, S. Porcella, J.E. Samuel and R.A. Heinzen. Comparative genomics reveal extensive transposon-mediated genomic plasticity and diversity among potential effector proteins within the genus Coxiella. 2009. Infect. Immun. 77:642-656. PMCID: 2632050.

Chen C., Bouman T.J., Beare P.A., Mertens K., Zhang G.Q., Russell-Lodrigue K.E., Hogaboam J.P., Peters B., Felgner P.L., Brown W.C., Heinzen R.A., Hendrix L.R., Samuel J.E. Candidate antigens for Q fever serodiagnosis revealed by immunoscreening of a Coxiella burnetii protein microarray. 2009. Clin. Microbiol. Infect. 15:2:156-157. PMCID: 2916703.

Voth, D.E., D. Howe, P.A. Beare, J.P. Vogel, N. Unsworth, J.E. Samuel, R.A. Heinzen. The Coxiella burnetii ankyrin repeat domain-containing protein family is heterogeneous with C-terminal truncations that influence Tot/Icm-mediated secretion. 2009. J. Bacteriol. 191:4232-4242. PMCID: 2698476.

Russell-Lodrigue, K.E., M. Andoh, M.W.J. Poels, H.R. Shive, B.R. Weeks, G.Q. Zhang, C. Tersteeg, T. Masegi, A. Hotta, T. Yamaguchi, H. Fukushi, K. Hirai, D.N. McMurray, and J.E. Samuel.. Coxiella burnetii isolates cause genogroup-specific virulence in mouse and guinea pig models of acute Q fever. 2009. Infect. Immun.77:5640-5650. PMCID: 2786457.Chen C, S Banga, K Mertens, MM Weber, I Gorbaslieva, Yun-Hao Tan, Zhao-Qing

Luo, and JE Samuel. Large-scale identification and translocation of Type IV secretion substrates by Coxiella burnetii. 2010. Proc. Nat. Acad. Sci. USA.107:21755-21760. PMCID: 3003115.

Narasaki, C.T., K. Mertens, and J.E. Samuel. 2011. Characterization of the GDP-d-mannose biosynthetic pathway in Coxiella burnetii: the initial steps for GDP-β-D-virenose. PLoS One. 2011;6(10):e25514. Epub 2011 Oct 31 PMID: 22065988

Program Director/Principal Investigator: SAMUEL, James E.

Hill, J. and J.E. Samuel. Coxiella burnetii acid phosphatase: Inhibiting the release of reactive oxygen intermediates in polymorphonuclear leukocytes. 2011. Infect. Immun. 79:414-420. PMCID: 3019863

Omsland, A. P.A. Beare, J. Hill, D.C. Cockrell, D. Howe, B. Hansen, J.E. Samuel and R.A. Heinzen. Isolation from animal tissue and genetic transformation of Coxiella burnetii are facilitated by an improved axenic growth medium. 2011. Appl. Environ. Microbiol. 77:3720-3725. PMID 2148315.

Vigil, A., C. Chen, A. Jain, R. Nakajima-Sasaki, A. Jasinskas, J. Pablo, L.R. Hendrix, J.E. Samuel, P.L. Felgner. Profiling the humoral immune response of acute and chronic Q fever by protein microarray. 2011. Mol. Cell. Proteomics PMID: 21817167.

Zhang, Y. G. Zhang, L.R. Hendrix, V.L. Tesh, and J.E. Samuel. Coxiella burnetii induces apoptosis during early stage infection via a caspase-independent pathway in human monocytic THP-1 cells. 2012. PLoS One ;7(1): e30841. Epub 2012 Jan 27 PMID: 22303462. van Schaik, E.J., C. Chen, K. Mertens, M. Weber, and J.E. Samuel. Molecular pathogenesis of the obligate intracellular bacterium Coxiella burnetii. 2013. Nat. Microbiol. Rev.561-573. PMID:22711628.

Pearson T., Hornstra H.M., Sahl J.W., Schaack S., Schupp J.M., Beckstrom-Sternberg S.M., O'Neill M.W., Priestley R.A., Champion M.D., Beckstrom-Sternberg J.S., Kersh G.J., Samuel J.E., Massung R.F., Keim P. When outgroups fail; Phylogenomics of rooting the emerging pathogen, Coxiella burnetii. 2013. Syst Biol. Jun 4. PMID:23736103.

Weber, M.M., C. Chen, K. Rowin, K. Mertens, G. Galvan, H. Zhi, C. M. Dealing, V. A. Roman, S. Banga, Y. Tan, Zhao- Qing Luo, and J. E. Samuel. Identification of Coxiella burnetii type IV secretion substrates required for intracellular replication and Coxiella-containing vacuole formation. 2013. J. Bacteriol. PMID:23813730.

Criscitello, M.F., M.B Dickman, J.E. Samuel, and P. de Figeiredo. Tripping on acid: trans-kingdom perspectives on biological acids in immunity and pathogenesis. 2013. PlosPathog. (7):e1003402. Epub 2013 Jul 18. PMID23874196.

C. RESEARCH SUPPORT. U54 AI057156 NIH/NAIAD (Walker, D.H., PI) 3/1/2009-2/27/2015 (NCE) SOUTHWEST RCE: VACCINE DEVELOPMENT AGAINST Q FEVER (J.E. Samuel, Major Project) The goal of this project is to develop heterologous expression of Coxiella burnetii LPS dominant antigens (O-side chain) and evaluate its ability to confer protective immunity in combination with dominant T cell antigen-containing proteins.

R01AI090142-01A1 NIH/NIAID (Samuel, J.E. PI) 8/20/2012-7/31/2016 IDENTIFICATION AND ROLE OF TYPE 4 EFFECTOR PROTEINS IN COXIELLA BURNETII. The goal of this project is to identify a wide group of type 4 secretion system effector proteins using Legionella pneumophila as a heterologous expression system. Candidates will be verified in C. burnetii using novel genetic methods. Effector functions will be monitored using in vitro and in vivo mutations defining mechanisms at the cellular level.

HDTRA1-13-1-0003 (Samuel, J.E., PI) DOD/DTRA 10/22/12-10/21/17 TRANSPOSON AND TARGETED MUTATIONAL ANALYSIS OF COXIELLA BURNETII TO IDENTIFY VIRULENCE DETERMINANTS OF ACUTE AND CHRONIC DISEASE. The goal of this project is broad screen of mutant libraries of C. burnetii to identify virulence related loci responsible for intracellular growth in vitro and in vivo as well as pathotype manipulation of innate responses.

DTRA1-CMB-03 (Samuel, J.E., PI) DOD/DTRA 1/1/14-12/31/18. Q FEVER VACCINE. The recent progress in antigen characterization and definition of components of protective immunity provide the opportunity to pursue strong candidates for novel vaccines. These include both T cell and B cell dependent antigens that have shown protection in rodent models of Q fever with lead candidates formulations examined in a non-human primate model of Q fever. Based on rodent and NHP results, lead candidate vaccine compositions will undergo manufacturing development, leading to pilot lot production and validation of efficacy in animal models.

Program Director/Principal Investigator: SCHOLTHOF, Herman B.

BIOGRAPHICAL SKETCH

NAME POSITION TITLE Scholthof, Herman Bertus Professor of Plant Pathology & Microbiology eRA COMMONS USER NAME (credential, e.g., agency login) hscholthof EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) Wageningen University, The Netherlands B.S./M.S. 11/86 Plant Virology

University of Kentucky, Lexington KY Ph.D. 12/90 Molecular Virology

University of California, Berkeley CA Postdoctoral 10/94 Molecular Virology

A. Positions and Honors

Positions and Employment 1990-1994 Postdoctoral Associate/Fellow, Plant Biology, University of California at Berkeley 1994-2000 Assistant Professor, Plant Pathology and Microbiology, Texas A&M University 2000-2005 Associate Professor, Plant Pathology and Microbiology, Texas A&M University 2002 Visiting Associate Professor, Biological Chemistry and Molecular Pharmacology, Harvard Medical School (June-December) 2003 Visiting Associate Professor, Biological Chemistry and Molecular Pharmacology, Harvard Medical School (May-August) 2005- Professor, Plant Pathology and Microbiology, Texas A&M University 2009 Visiting Scientist, Boyce Thompson Institute for Plant Research, Cornell University (February-August)

Other Experience and Professional Memberships Editorial Responsibilities 1998-2001 Associate Editor Phytopathology 2001-2004 Associate Editor Molec. Plant-Microbe Interact. 2003-2004 Senior Editor Phytopathology 2004-2007 Senior Editor Molec. Plant-Microbe Interact. 2004- Editorial Board Virology 2008- Editorial Board Journal of Virology

Selected Federal Grant Proposal Panels USDA-NRI-Competitive Grants Program Plant Pathology (2x) NSF Mol. Cell. Bioscience (1x) NIH Topics in Virology (2x) NIH Special Emphasis panel (1x)

Honors 2006 Outstanding Professor, Plant Pathology and Microbiology, Texas A&M University 2007 Ruth Allen Award for innovative research, American Phytopathological Society 2009 TAMU Association of Former Students Distinguished Achievement Award for Research 2009 Fellow, American Phytopathological Society Program Director/Principal Investigator: SCHOLTHOF, Herman B.

B. Selected Peer-reviewed Publications. Everett, A, Scholthof, H.B., and Scholthof, K.-B. G. (2010). Satellite panicum mosaic virus coat protein enhances the performance of plant virus gene vectors. Virology 396:37-46.

Saxena, P., Hsieh, Y-C., Alvarado, V.Y., Sainsbury,, F., Saunders. K., Lomonossoff, G., and Scholthof, H.B. (2011). Improved foreign gene expression in plants using a virus-encoded suppressor of RNA silencing modified to be developmentally harmless. Plant Biotech. J. 9:703-712

Scholthof, K.-B.G., and Scholthof, H.B. (2011). Induction and suppression of RNA silencing: Insights from plant viral infections - A BARD Workshop Report. Plant Molec. Biol. 75:205-210

Ciomperlik, J., Omarov, R.T., and Scholthof, H.B. (2011). An antiviral RISC isolated from Tobacco rattle virus- infected plants. Virology 412:117-124

Scholthof, H.B., Alvarado, V.Y., Vega-Arreguin, J.C., Ciomperlik, J.J., Odokonyero, D., Brosseau, C., Jaubert, M., Zamora, A., and Moffett, P. (2011). Identification of an ARGONAUTE for antiviral RNA silencing in Nicotiana benthamiana. Plant Physiol., 156:1548-1555

Seaberg, B., Hsieh, Y.-C., Scholthof, K.-B.G. and Scholthof, H.B. (2012). Host impact on stability of a plant virus gene vector as measured by a newly adapted fluorescent local lesion assay. J. Virol. Meth. 179:289-94

Alvarado, V.Y., and Scholthof, H.B. (2012). AGO2: A new Argonaute compromising plant virus accumulation. Frontiers Plant Sci. 2:112

Omarov, R., and Scholthof, H.B. (2012). Biological chemistry of virus-encoded gene-silencing suppressors: an overview. In: Antiviral Resistance in Plants: Methods and Protocols. Methods in Molecular Biology 894:39-56. Eds. J. Watson & M-B. Wang.

Alvarado, V.Y., Odokonyero, D., Duncan, O., Mirkov, T.E., and Scholthof, H.B. (2012). Molecular and physiological properties associated with Zebra Complex disease in potatoes and its relation with Candidatus Liberibacter contents in psyllid vectors. PLoS ONE 7(5):e37345

Manabayeva, S.A., Shamekova, M., Park, J.-W., Ding, X.S., Nelson, R.S., Hsieh, Y.-C., Omarov, R.T., and Scholthof, H.B. (2013). Differential requirements for Tombusvirus coat protein and P19 following plant leaf versus root inoculation. Virology 439:89-96

Gao, S.-J., Damaj, M.B, Park, J.-W., Beyene, G., Buenrostro-Nava, M.T., Molina, J., Wang, X., Ciomperlik, J.J., Manabayeva, S., Alvarado, V.Y., Rathore, K.S., Scholthof, H.B., and Mirkov, T.E. (2013). Enhanced gene expression in sugarcane by co-expression of virus-encoded RNA silencing suppressors. PLoS ONE 8(6):e66046

Shamekova, M., Mendoza, M.R., Hsieh, Y.C., Lindbo, J., Omarov, R.T., and Scholthof, H.B. (2014). Tombusvirus-based vector systems to permit over-expression of genes or that serve as sensors of antiviral RNA silencing in plants. Virology 452:159–165

Principal Investigator/Program Director (Last, First, Middle): SHAW, Brian D.

NAME POSITION TITLE Shaw, Brian D. Associate Professor eRA COMMONS USER NAME bdshaw EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Michigan State University B.A. (Hons) 1988-1992 Multidisciplinary Cornell University Ph.D. 1995-2000 Plant Pathology Postdoctoral University of Georgia 2000-2003 Fungal Biology Training

A. Positions and Honors

Employment

2009- present Associate Professor. Dept. of Plant Pathology and Microbiology. Texas A&M University 2003-2009 Assistant Professor. Dept. of Plant Pathology and Microbiology. Texas A&M University 2000-2003. Post Doctoral Researcher. Dept. of Plant Biology. University of Georgia.

Other Experience and Professional Memberships American Phytopathological Society Genetics Society of America Mycological Society of America (Fellow)

Honors 2014 Fellow Mycological Society of America 2009,10,11 SLATE Award (Student Led Award for Teaching Excellence), Texas A&M University 2009 Alexopolous Prize. Mycological Society of America

B. Selected peer-reviewed publications J-H Shin, J-E Kim, M. Malapi-Wight, Y-E. Choi, B. D. Shaw and W-B Shim. 2013. Protein phosphatase 2A regulatory subunits perform distinct functional roles in the maize pathogen Fusarium verticillioides. Molecular Plant Patholoy. 14:518-529 . X. Zhou, H. Zhang,G. Li, B. D. Shaw,J.-R. Xu. 2012. The Cyclase-Associated Protein Cap1 Is Important for Proper Regulation of Infection-Related Morphogenesis in Magnaporthe oryzae. PLoS Pathog 8(9): e1002911. D.-W. Chung, C. Greenwald, S. Upadhyay, S. Ding, H. H. Wilkinson, D. J. Ebbole, and B. D. Shaw. 2011. acon-3, the Neurospora crassa ortholog of the developmental modifier, medA, complements the conidiation defect of the Aspergillus nidulans mutant. Fungal Genetics and Biology. 48: 370-376. C. J. Greenwald, T. Kasuga, N. L. Glass, B. D. Shaw, D. J. Ebbole, and H. H. Wilkinson. 2010. Temporal and spatial regulation of gene expression during asexual development of Neurospora crassa. Genetics. 2010 186: 1217–1230.

PHS 398/2590 (Rev. 09/04) Page Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle): SHAW, Brian D. C. Wang, W.-B. Shim, and B. D. Shaw. 2010. The Aspergillus nidulans striatin ortholog is required for sexual development. Fungal Genetics and Biology. 47: 789-799. S. C. Lee, S. N. Schmidtke, L. J. Dangott and B. D. Shaw. 2008. Aspergillus nidulans ArfB is linked to endocytosis and polarized growth. Eukaryotic Cell. 7: 1278-1288. Q.-M. Qin, J. Pei, V. Ancona, B. D. Shaw, T. A. Ficht, and P. de Figueiredo. 2008. RNAi Screen of Endoplasmic Reticulum-Associated Host Factors Reveals a Role for IRE1 in Supporting Brucella Replication. PLOS Pathogens. 4:e1000110 S. C. Lee and B. D. Shaw. 2008. Localization and function of ADP ribosylation factor A in Aspergillus nidulans. FEMS Microbiology Letters 283: 216-222. S. Upadhyay, and B. D. Shaw. 2008. The Role of actin, fimbrin, and endocytosis in growth of hyphae in Aspergillus nidulans. Molecular Microbiology 68: 690-705. S. Sukno, V. M. García, B. D. Shaw, and M. R. Thon. 2008. Root infection and systemic colonization of maize by Colletotrichum graminicola. Applied and Environmental Microbiology 74: 823-832. (Includes Journal Cover Illustration) U. Sagaram, B. D. Shaw, and W.-B. Shim. 2007. Fusarium verticillioides GAP1, a gene encoding a putative glycolipid-anchored surface protein, participates in conidiation and cell wall structure but not virulence. Microbiology 153: 2850-2861. S. C. Lee and B. D. Shaw. 2007. A novel interaction between N-myristoylation and the 26S proteasome during cell morphogenesis. Molecular Microbiology 63: 1039-1053. S. Upadhyay, and B. D. Shaw. 2006. A phosphoglucose isomerase mutant in Aspergillus nidulans is defective in hyphal polarity and conidiation. Fungal Genetics and Biology 43: 739- 751. (Includes Journal Cover Illustration) B. D. Shaw, G. C. Carroll, and H. C. Hoch. 2006. Generality of the prerequisite of conidium attachment to a substratum as a signal for germination among Phyllosticta species. Mycologia 98: 186-194. (Includes Journal Cover Illustration) B. D. Shaw and **S. Upadhyay. 2005. Aspergillus nidulans swoK encodes an RNA binding protein that is important for cell polarity. Fungal Genetics and Biology. 42: 862-872.

PHS 398/2590 (Rev. 09/04) Page Continuation Format Page Program Director/Principal Investigator: SHIPPEN, Dorothy E.

BIOGRAPHICAL SKETCH Provide the following information for the key personnel and other significant contributors. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Shippen, Dorothy E. Professor, Biochemistry and Biophysics eRA COMMONS USER NAME dshippen EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Auburn University, Montgomery Alabama BS 1982 Biology Univ. Alabama, Birmingham PhD 1987 Biology Univ. California, Berkeley Postdoc 1987-90 Molecular Biology Univ. California, San Francisco Postdoc 1990-91 Molecular Biology

A. PERSONAL STATEMENT My research program is focused on elucidating fundamental properties of telomeres and their engagement with the telomerase reverse transcriptase. I have studied telomeres and telomerase for 27 years, beginning with postdoctoral training in the laboratory of Dr. Elizabeth Blackburn. As a faculty member in the Biochemistry and Biophysics Department at Texas A&M University since 1991, I have investigated basic aspects of telomerase function and regulation and the role of telomere capping proteins in promoting genome stability. Our initial work employed ciliated protozoa as a model to investigate the biochemistry of telomerase. However, in the mid 1990’s my lab developed the flowering plant Arabidopsis as a new model for telomeres. A multicellular, genetically tractable eukaryote, Arabidopsis allows a broad and deep range of investigation using molecular, cytological, biochemical and evolutionary approaches. Over the years we amassed a large toolbox of telomere-specific molecular and biochemical assays to complement the powerful genetic and transgenic approaches in this system. Along the way, we discovered that Arabidopsis is extraordinarily tolerant to telomere dysfunction, a unique characteristic that has allowed us to elucidate functions and interactions of essential telomere components in a manner not possible in vertebrate systems. I have sustained continuous research funding from NIH and NSF throughout my career. With these funds I have managed a highly interactive and productive research team of postdoctoral fellows, graduate students and undergraduate students.

B. POSITIONS AND HONORS Professional Experience 1991-1997 Assistant Professor 1991-97, Dept. Biochemistry and Biophysics, Texas A&M University 1997-2002 Associate Professor 1997-02, Dept. Biochemistry and Biophysics, Texas A&M University 2002-present Professor 2002-present Texas A&M Univ., Dept. Biochemistry and Biophysics Honors, Awards and Other Professional Activities 1982 B.S. summa cum laude; AUM Outstanding Biology Undergraduate Student; 1987 Phi Kappa Phi Honor Society; 1989-91 American Cancer Society Postdoctoral Research Fellowship; 1991 American Cancer Society Senior Postdoctoral Fellowship (California Division); 1993 Texas A&M Biochemistry Graduate Association Faculty Recognition Award; 1999- 2009 Editorial Board Molecular and Cellular Biology; 2000-2005 Texas A&M Faculty Fellow; 2000-present Ad-hoc reviewer for NIH CDF-2, NDT, MGC study sections; 2001 Instructor, Burroughs Wellcome Fund/Howard Hughes Medical Institute Laboratory Management Course; Participant Arabidopsis Molecular Genetics Course, Cold Spring Harbor Laboratory; 2002 Keynote Speaker, Canadian Telomere Workshop, Vancouver, UBC; Keynote Speaker, Texas A&M Univ. Ethel Ashworth-Tsutsui Memorial Lecture for Women in Science and Engineering; NSF Committee of Visitors to evaluate Division of Molecular and Cellular Biosciences; 2002-04 Executive Committee Texas A&M Univ. Council of Principal Investigators; Texas A&M President’s Life Sciences Advisory Committee; 2002-2008 Chair, Texas A&M Univ. Molecular and Cell Biology Graduate Training Program; 2005 Featured Speaker, 47th Annual Maize Genetics Conference, Lake Geneva WI., Co-Organizer, American Society of Plant Biologist Conference on Plant Genetics, Snowbird, UT; Texas Agriculture Experiment Station Faculty Fellow; 2006 Invited Speaker, Grand Opening of the Gregor Mendal Institute, Vienna Austria; Vice Chancellor’s Award for Research; 2007 Co-Organizer Cold Spring Harbor Laboratory Telomere and Telomerase Meeting; Co-Organizer EMBO Conference on Plant DNA Repair and Recombination, Giens, France; 2008 Texas A&M Univ. Association of Former Students Award for Excellence in Research; 2009 Co-Organizer Cold Spring Harbor Laboratory Telomere and Telomerase Meeting; 2010 Keynote Speaker Anat Krauskopf Symposium, Tel Aviv University, Israel; Invited Speaker, NCI lab management workshop for new Program Director/Principal Investigator: SHIPPEN, Dorothy E. grantees; Leadership Team NSF-sponsored ADVANCE program, TAMU; Editorial Board Frontiers in Plant Genetics and Genomics; 2011 Co-Organizer Cold Spring Harbor Laboratory Telomere and Telomerase Meeting; Senior Faculty Fellow AgriLife Research, TAMU; 2014 Organizer International Plant Genomic Stability and Change Conference, Pacific Grove, CA.

C. SELECTED PEER-REVIEWED PUBLICATIONS (from 60 total) Five most relevant to the current application: Surovtseva Y, Shakirov EV, Vespa L, Osbun N, Song X and Shippen DE (2007) Arabidopsis POT1 associates with the telomerase RNP and is required for telomere maintenance. EMBO J 26:3653-3661. PMCID: PMC1949013 Song, X., Leehy, K., Warrington, R.T., Lamb, J.C., Surovtseva, Y. and Shippen, D.E. (2008) STN1 protects chromosome ends in Arabidopsis. Proc Natl Acad Sci USA 105:19815-19820. PMCID: PMC2604966 Surovtseva YV, Churikov D, Boltz KA, Song X, Lamb J, Warrington R, Leehy K, Heacock M, Price CM and Shippen DE (2009) Conserved telomere maintenance component 1 interacts with STN1 and protects chromosome ends in higher eukaryotes. Mol Cell 36:207-218. PMCID: PMC2768651 Cifuentes-Rojas C, Kannan K, Tseng L and Shippen DE (2011) Two TER subunits for Arabidopsis telomerase and the TER binding activity of POT1a. Proc Natl Acad Sci USA 108:73-78. PMCID: PMC3017190 Cifuentes-Rojas C, Nelson AD, Kannan K, Boltz KA, She X and Shippen DE (2012) An alternative telomerase RNA represses enzyme activity in response to DNA damage. Genes Dev 26:2512-2523. PMID: 23109676

Other significant publications (since 2010): Shakirov EV, Perroud P-F, Nelson AD, Cannell ME, Quatrano RS and Shippen DE (2010) Protection of telomeres is required for telomere integrity in the moss Physcomitrella patens. Plant Cell 22:1838-1848. PMCID: PMC2910979 Banks et al. (103 authors) (2011) The compact Selaginella genome identifies changes in gene content associated with the evolution of vascular plants. Science 332: 960-963. PMCID: PMC3166216 Lamb JC, Nelson, AD Kobrossly P and Shippen DE (2011) Parameters affecting telomere-mediated chromosomal truncation in Arabidopsis thaliana. Plant Cell 23:2263-2272. PMCID: PMC3160034 Boltz KA, Leehy K, Song X, Nelson AD and Shippen DE (2012) ATR and the CST telomere complex cooperate to maintain telomeres and genome integrity in Arabidopsis. Mol Biol Cell 23:1558-68 PMID: 22357613 Shakirov EV and Shippen DE (2012) Selaginella telomeres: conserved and unique features in an ancient land plant lineage. Front Plant Sci 3:161. doi: 10.3389/fpls.2012.00161 PMID: 22833748 Beilstein MA, Brinegar AE and Shippen DE (2012) Evolution of the Arabidopsis telomerase RNA. Front Genet 3:188. Epub 2-12 Sep 24. PMID: 23015808 Leehy K, Lee JR, Song X, Renfrew K and Shippen DE (2013) Meristem Disorganization 1 encodes TEN1, a telomere capping protein that modulates telomerase processivity in Arabidopsis. Plant Cell, 25:1343-1354. PMID: 23572541 Jasti M,* Boltz KA*, Townley J and Shippen DE (2014) Poly(ADP-Ribose) polymerases are dispensable for telomere regulation in Arabidopsis thaliana.*Equal contribution. PLoS One 9:e888872. PMID: 24551184 Renfrew KB, Song X, Lee JR, Arora A and Shippen DE. POT1a and components of CST engage telomerase and regulate its activity in Arabidopsis. PLoS Genetics, in press. González-García MP, Pavelescu I, Canela A, Sevillano J, Leehy KA, Nelson ADL, Shippen DE, Blasco M and Caño- Delgado A. Telomere length gradients preserve the meristematic potential and stem cell function in the root of Arabidopsis thaliana. Submitted. Lee JR, Zhang J, Yang K, Lee SY and Shippen DE Arabidopsis TEN1 is a molecular chaperone that promotes telomere integrity. In preparation. Beilstein MA, Renfrew KB, Song X, Shakirov EV and Shippen DE. Evolution of the telomerase-associated protein POT1a is characterized by positive selection to reinforce protein-protein interaction. In preparation. Xu H, Nelson ADL and Shippen DE A transposable element in TER2 controls telomerase activity in Arabidopsis thaliana. In preparation.

D. RESEARCH SUPPORT Ongoing: NIH R01-GM065383 “Telomere structure and function in Arabidopsis” 12/10-11/14 $920,000 (direct costs) D. Shippen (PI)

NSF (MCB-1052018) “Negative regulation of telomerase in Arabidopsis” 4/11-3/15 $730,000 (total costs) D. Shippen (PI)

Cancer Prevention Research Institute of Texas (CPRIT-RP130639) “A role for noncoding RNA in the regulation of telomerase in breast cancer” 6/13-5/2015 $199,912 (direct costs) D. Shippen (PI) and R. Fuchs-Young (Co-PI)

Pending: NIH R01-GM065383 “Telomere structure and function in Arabidopsis” 1/15-12/18 $1,174,302 (direct costs requested) D. Shippen (PI) Competitive Renewal Program Director/Principal Investigator (Last, First, Middle): SIEGELE, Deborah A.

NAME POSITION TITLE Siegele, Deborah A. Associate Professor eRA COMMONS USER NAME (credential, e.g., agency login) Dept. of Biology dsiegel Texas A&M University EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Northwestern University, Evanston, IL B.A. 1976 Biochemistry University of Wisconsin, Madison, WI Ph.D. 1989 Molecular & Cell Biology Harvard Medical School, Boston, MA Post-doc. 1989-92 E. coli mol. genetics

A. Positions and Honors. Employment 1992-1997 Assistant Professor, Dept. of Biology, Texas A&M University, College Station, TX 9/2003- Graduate Advisor, Dept. of Biology, Texas A&M University, College Station, 8/2006 TX 1996-present Member, Graduate Faculty of Genetics, Texas A&M University, College Station, TX 2002-present Member, Professional Program in Biotechnology, Texas A&M University 1997-present Associate Professor, Dept. of Biology, Texas A&M University, College Station, TX

Other Experience and Professional Memberships EcoliHub Steering Committee, 2006-2009 Member, Genetics Society of America Board of Directors, 2013-2015 American Society for Microbiology Genetics Society of America

Honors Support on NIH Cell and Molecular Biology Training Grant, University of Wisconsin 1983-85 NIH Postdoctoral Fellowship, 1990-1992

B. Selected peer-reviewed publications (Graduate students and undergraduates as shown.) 1) Hu, J.C., G. Sherlock, D.A. Siegele, S.A. Aleksander, C.A. Ball, J. Demeter, S. Gouni, N.M. Liles, B.K. McIntosh, H. Mi, A. Muruganujan, F. Wymore, and P.D. Thomas. (2014) PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. Nucleic Acids Res. 42(Database issue):D677-84. 2) Lim, B., R. Miyasaki, S. Neher, D.A. Siegle, K. Ito, P. Walter, Y. Akiyama, T. Yura, and C.A. Gross. (2013) Heat shock transcription factor sigma32 co-opts the signal recognition particle to regulate protein homeostasis in E. coli. PLoS Biol. 11:31001735. 2) Renfro DP, McIntosh BK, Venkatraman A, Siegele DA & Hu JC (2012) GONUTS: the Gene Ontology Normal Usage Tracking System. Nucleic Acids Res 40: D1262-9. PMCID: PMC3245169 4) McIntosh BK, Renfro DP, Knapp GS, Lairikyengbam CR, Liles NM, Niu L, Supak AM, Venkatraman A, Zweifel AE, Siegele DA & Hu JC (2012) EcoliWiki: a wiki-based community resource for Escherichia coli. Nucleic Acids Res 40: D1270-7. PMCID: PMC3245172 5) Siegele, D.A., S. Bain, and W. Mao (2010) Mutations in the flhD gene of Escherichia coli K-12 do not cause the reported effect on cell division. FEMS Microbiol. Lett. 309:94-9.

PHS 398/2590 (Rev. 11/07) Page Biographical Sketch Format Page Program Director/Principal Investigator (Last, First, Middle): SIEGELE, Deborah A. 6) Hu, J.C, Karp, P. Keseler, I, Krummenacker, M, and Siegele DA (2009) What we can learn about Escherichia coli through application of Gene Ontology. Trends in Microbiology. 7:269-78. PMCID: PMC357575 7) Reference Genome Group of the Gene Ontology Consortium (2009) The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLoS Comput Biol. 2009 Jul;5(7):e1000431. PMCID: PMC2699109 8) Typas, A., R.J. Nichols, D.A. Siegele, M. Shales, S.R. Collins, B. Lim, H. Braberg, N. Yamamoto, R. Takeuchi, B.L. Wanner, H. Mori, J.S. Weissman, N.J. Krogan, and C.A. Gross (2008) High- throughput, quantitative analyses of genetic interactions in E. coli. Nature Methods 5:781-787. 9) Champion, M.M., C.S. Campbell, D.A. Siegele, D.H. Russell, and J.C. Hu (2003) Proteome analysis of Escherichia coli K-12 by two-dimensional native-state chromatography and MALDI- MS. Mol. Microbiol. 47: 383-96. 10) Arnold, C.N., J. McElhanon, A. Lee, R. Leonhart, and D.A. Siegele (2001) Global analysis of Escherichia coli gene expression during the acetate-induced acid tolerance response. J. Bacteriol. 183: 2178-86. 11) Mao, W. and D.A. Siegele (1998) Genetic analysis of the stationary phase-induced mcb operon promoter in Escherichia coli. Mol. Microbiol. 27:415-24. 12) Siegele, D.A. and J.C. Hu (1997) Gene expression from plasmids containing the araBAD promoter at subsaturating inducer concentrations represent mixed populations. Proc. Natl. Acad. Sci. USA 94:8168-72. 13) Siegele, D.A. and L.J. Guynn (1996) Escherichia coli proteins synthesized during recovery from starvation. J. Bacteriol. 178: 6352-6. 14) Siegele, D.A., K.R. Imlay, and J.A. Imlay (1996) The stationary-phase-exit defect of cydC (surB) mutants is due to the lack of a functional terminal cytochrome oxidase. J. Bacteriol. 178: 6091-6.

PHS 398/2590 (Rev. 11/07) Page Continuation Format Page Program Director/Principal Investigator: SITCHERAN, Raquel

BIOGRAPHICAL SKETCH Provide the following information for the Senior/key personnel and other significant contributors. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Sitcheran, Raquel Assistant Professor eRA COMMONS USER NAME (credential, e.g., agency login) raquel_sitcheran

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.)

DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable)

Columbia University, New York, NY A.B. 05/92 Molecular Biology University of California, San Francisco, CA Ph.D. 06/00 Physiology & Genetics University of North Carolina at Chapel Hill, NC Postdoc 07/06 Molecular & Cell Biology

A. POSITIONS & HONORS Positions and Employment 1994 – 2000 Graduate Student with Keith R. Yamamoto, PhD, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 2000 – 2006 Postdoctoral Fellow with Albert S. Baldwin, PhD, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 2006 – 2009 Research Associate, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 2009 – present Assistant Professor, Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX

Honors 1994 – 1996 Eugene Cota Robles Graduate Student Fellowship 2000 – 2001 Lineberger Comprehensive Cancer Center Postdoctoral Fellowship 2001 – 2004 Cancer Research Institute Postdoctoral Fellowship 2002 Keystone Scholarship Award for “NF-κB: Bench to Bedside” Meeting 2004 Keystone Scholarship Award for “NF-κB: Biology and Pathology” Meeting 2004 American Society for Cell Biology Minority Affairs Committee Travel Award 2005 Joseph S. Pagano Award, Lineberger Cancer Center, UNC Chapel Hill 2008 Keystone Symposia Minorities Affairs Committee (MAC) Travel Award & Best Poster Award (3rd place)

Program Director/Principal Investigator: SITCHERAN, Raquel

C. PUBLICATIONS

1. Vassar, R., Chao S.K., Sitcheran R., Nunez J.M., Vosshall L.B., Axel R. (1994). Topographic organization of sensory projections to the olfactory bulb. Cell 79(6):981-991. PMID:8001145 2. Sitcheran R., Kralli A., Yamamoto K.R. (2000). A genetic analysis of glucocorticoid receptor signaling: Identification and characterization of ligand-effect modulators in Saccharomyces cerevisiae. Genetics 156: 963-972. PMCID:PMC1461341 3. Sitcheran R., Cogswell P., Baldwin, A.S. (2003). NF-κB mediates inhibition of mesenchymal cell differentiation through a posttranscriptional gene silencing mechanism. Genes & Development. 17(19):2368-2373. PMCID:PMC218074 4. Sun K., Welniak L.A., Panoskaltisis-Mortari A., O’Shaughnessy M.J., Liu H., Barao I., Riordan W., Sitcheran R., Wksocki C., Serody J.S., Blazar B.R., Sayers T.J., Murphy W.J. (2004). Inhibition of acute graft-vs.-host disease with promotion of anti-tumor effects by the proteosome inhibitor, Bortezomib, after allogeniec bone marrow transplantation. PNAS 101(21):8120-5. PMCID:PMC419567 5. Lorcher A., Lee T.L., Ticker J.L., Howard A., Geoghegen J., Chen Z., Sunwoo J., Sitcheran R., Chuang E.Y., Mitchell J.B., Baldwin A.S. Jr., Van Waes C. (2004). Nuclear Factor-κB is an important modulator of the altered gene expression profile and malignant phenotype in squamous cell carcinoma. Cancer Research 64(18):6511-23. PMID:15374962 6. Sitcheran R., Gupta P., Fisher P.B., Baldwin A.S. (2005) Positive and negative regulation of EAAT2 expression requires NF-κB: a role for N-myc in TNFα-controlled repression. EMBO Journal, 24:510- 20. PMCID:PMC548660 7. Steinbrecher K.A., Harmel-Laws E., Sitcheran R., Baldwin A.S. (2007). Loss of epithelial RelA results in deregulated intestinal proliferative/apoptotic homeostasis and susceptibility to inﬂammation. Journal of Immunology. 15;180(4):2588-99. PMID:18250470 8. Sitcheran R.*, Comb W.C., Cogswell P.C., Baldwin A.S.* (2008). An essential role for the EGF receptor in glutamate receptor signaling to NF-κB. Molecular and Cellular Biology. 28(16):5061-70. PMCID: PMC2519702 9. Williams K.L., Lord C.A., Savitzky D. Sitcheran R., Calame K, Wright J.R., Ting J.P.Y. (2009). Blimp- 1 regulates TLR- mediated repression of the NLRP12 gene in myeloid cells. Journal of Immunology. 182(5):2948-58. PMCID:PMC2701146 10. O’Shaughnessy M.J., Bogtenhuber, C., Sun, K., Sitcheran R., Baldwin A.S., Murphy W.J., Dang L., Jafee B., Palmer E., Serody J.S., Blazar B.R. (2009). Ex vivo inhibition of NF-κB signaling in alloreactive T-cells prevents graft-versus-host disease. Amer. J. Transplantation. Mar;9(3):452-62. PMCID:PMC2680009 11. Comb, W., Sitcheran, R. Cogswell, P. Baldwin, A.S. (2011). IKK-Dependent, NF-κB-Independent Control of Expression of Key Autophagic Genes. Oncogene. Apr 7;30(14):1727-32. PMCID: PMC3369814. 12. Lee DW, Ramakrishnan D, Valenta J, Parney IF, Bayless KJ, Sitcheran R. (2013) The NF-κB RelB protein is an oncogenic driver of mesenchymal glioma. PLoS One 8(2):e57489. doi: 10.1371/journal.pone.0057489. Epub 2013 Feb 25. PMICD: PMC3581451 13. Cherry EM, Lee DW, Jung J, Sitcheran R. (2014) TWEAK promotes glioma cell invasion through activation of NF-κB-inducing kinase (NIK) and non-canonical NF-κB signaling. Submitted to Molecular Cancer.

NAME POSITION TITLE Skare, Jon T. Professor and Associate Chair eRA COMMONS USER NAME jskare EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of California at Irvine, Irvine, California B.S. 1986 Biology Washington State University, Pullman, WA Ph.D. 1992 Microbiology Univ. of Calif. at Los Angeles, Los Angeles, CA Post-Doc 1992-1996 Microbial Pathogenesis

Personal Statement

Current research in the Skare laboratory focuses on the pathogenesis of the Lyme disease spirochete, Borrelia burgdorferi. Specific questions are designed to address (i) the ability of B. burgdorferi to modulate gene expression as it adapts to the diverse environments is occupies in nature (e.g., both arthropod vectors and mammals), (ii) the role of the borrelial oxidative stress response to promote survival in ticks and mammals, and (iii) the importance of surface exposed proteins in the colonization and dissemination of the bacterium following infection in mammalian hosts. Molecular genetics approaches, coupled with in vivo imaging technology, are used to evaluate the role of genes and gene products in borrelial pathogenesis.

1. Positions/Employment, Memberships and Honors.

Professional Experience: 1996-2002 Assistant Professor, Department of Medical Microbiology and Immunology, College of Medicine. Texas A&M University Health Science Center, College Station, TX. 1997-present Full Member, Faculty of Genetics, Texas A&M University, College Station, TX. 2002-2006 Associate Professor, Department of Medical Microbiology and Immunology, College of Medicine. Texas A&M University Health Science Center, College Station, TX. 2006-present Professor, Department of Microbial Pathogenesis and Immunology, College of Medicine. Texas A&M Health Science Center, College Station, TX. 2012-present Associate Chair, Department of Microbial Pathogenesis and Immunology, College of Medicine. Texas A&M Health Science Center, College Station, TX.

Selected Awards and Honors:

1994-1996 Individual National Research Service Award, NIAID 1997-1999 Editorial Board, Infection and Immunity 1998-2002 Scientist Development Grant, the American Heart Association, National Award 2002 & 2004 ad hoc Reviewer for the Bacteriology and Mycology 1 Study Section, NIAID 2003 Manuscripts cited by Faculty of 1000 (Ojaimi et al., 2003 and Labandeira-Rey et al., 2003) 2004-2007 Peer Review Panel, Immunology and Microbiology, American Heart Association 2004 Invited speaker, Gordon Research Conference, Biology of Spirochetes 2006 Invited speaker, Gordon Research Conference, Biology of Spirochetes 2006-present ad hoc Reviewer for “Topics in Bacterial Pathogenesis”, NIAID (11 times) 2008-2010 Editorial Advisory Board, Molecular Microbiology 2008 Chair of site visit, Science Foundation of Ireland 2009-present ad hoc Reviewer for Special Emphasis Panel for Study Section Members (6 times) 2009 Manuscript featured in MicroCommentary in Molecular Microbiology (Hyde et al., 2009) 2009-2017 Editorial Board, Infection and Immunity 2010 Manuscript featured in Infection and Immunity Spotlight, Jan. 2010 issue (Hyde et al., 2010) 2010-present Review Editor, Frontiers in Cellular and Infection Microbiology 2011 Manuscript featured in Infection and Immunity Spotlight, Mar. 2011 issue (Wu et al., 2011) 2012-2015 Editorial Advisory Board, Molecular Microbiology 2013 Texas A&M HSC, College of Medicine, Excellence in Research Award, 2013

2. Selected Publications (from over 40 manuscripts and reviews).

1. Skare, J. T., Shang, E. S., Foley, D. M., Blanco, D. R., Champion, C. I., Mirzabekov, T., Sokolov, Y., Kagan, B. L., Miller, J. N. and M. A. Lovett. 1995. Virulent strain associated outer membrane proteins of Borrelia burgdorferi. J. Clin. Invest. 96(11):2380-2392. PMCID: PMC185890 2. Labandeira-Rey, M. and J. T. Skare. 2001. Decreased Infectivity in Borrelia burgdorferi strain B31 is Associated with the Loss of Either Linear Plasmid 25 or 28-1. Infect. Immun. 69(1): 446-455. PMCID: PMC97902 3. Labandeira-Rey, M. Seshu J., and J. T. Skare. 2003. The Absence of Linear Plasmid 25 (lp25) or 28-1 (lp28-1) of Borrelia burgdorferi Dramatically Alters the Kinetics of Experimental Infection Via Distinct Mechanisms. Infect Immun. 71(8):4608-4613. PMCID: PMC166013 4. Seshu, J., Esteve-Gassent, M. D., Labandeira-Rey, M., Kim, J. H., Trzeciakowski, J. P., Höök, M. and J. T. Skare. 2006. Inactivation of the Fibronectin Adhesin Gene bbk32 Significantly Attenuates the Infectivity Potential of Borrelia burgdorferi. Mol Microbiol. 59(5):1591-1601. PMID: 16468997 5. Weening E. H., Parveen. N., Trzeciakowski, J. P., Leong, J. M., Höök, M., and J. T. Skare. 2008. Borrelia burgdorferi Lacking DbpBA Exhibit an Early Survival Defect During Experimental Infection. Infect. Immun. 76(12):5694-5705. PMCID: PMC2583571 6. Hyde, J.A., Shaw, D.K., Smith, R., Trzeciakowski, J.P., and J. T. Skare. 2009. The BosR regulatory protein of Borrelia burgdorferi interfaces with the RpoS regulatory pathway and modulates both the oxidative stress response and pathogenic properties of the Lyme disease spirochete. Mol Microbiol. 74(6): 1344-1355. PMCID: PMC2805275 7. Hyde, J.A., Weening, E.H., Chang, M.H., Trzeciakowski, J.P., Höök, M., Cirillo, J.D., and J. T. Skare. 2011. Bioluminescent imaging of Borrelia burgdorferi in vivo demonstrates that the fibronectin binding protein BBK32 is required for optimal infectivity. Mol Microbiol. 82(1): 99-113. PMCID: PMC3183165 8. Moriarty, T. J., Shi, M., Lin, Y.-P., Ebady, R., Zhou, H., Odisho, T., Hardy, P.-O., Salman-Diligimen, A., Wu, J., Weening, E.H., Skare, J. T., Kubes, P., Leong, J., and G. Chaconas. 2012. Vascular binding of a pathogen under shear force through mechanistically distinct sequential interactions with host macromolecules. Mol Microbiol. 86(5): 1116-1131. PMCID: PMC3508296

3. Research Support.

CURRENT:

1. R01-AI042345; J.T. Skare, PI 04/25/09-03/31/15 (no cost extension) NIH/NIAID “Genetic Mechanisms in Borrelia burgdorferi Pathogenesis” The major goals of this project are to characterize the response of B. burgdorferi to oxidative stress in the context of the global regulatory protein BosR and linked genes in the bosR-containing operon.

2. R21-AI095935; J.T. Skare, PI 04/01/12-03/31/15 (no cost extension) NIH/NIAID “ “An Intracellular Niche for Borrelia burgdorferi” The goal of this project is to determine if invasion in non-innate immune cells promotes escape from clearance and contributes to borrelial persistence in vivo.

3. R21-AI113200-01; J. Skare, PI 05/15/14-04/30/16 NIH/NIAID “A New Mammalian-specific Function for OspC in Lyme borreliosis” The major goals of this grant are to characterize novel OspC binding activity to host thrombospondin proteins.

4. R21-AI101740; J. Hyde, PI 07/01/12-06/30/15 (no cost extension) NIH/NIAID “In vivo Dual Bioluminescence Reporter System of Infectious Borrelia burgdorferi” The major goals of this grant are to track the expression of various virulence determinants and regulatory loci during active infection in live mice.

5. Contract HHSN2722010000241; J. Cirillo, PI 03/22/10-03/21/17 NIH/NIAID “Animal Models of Infectious Diseases” The objectives of this contract are to provide services under contract to NIH for investigators who wish to utilize animal models for the study of infectious disease virulence mechanisms, vaccines and therapeutics. Dr. Skare directs work designed to test spirochete infections.

Principal Investigator STELLY, David M.

NAME POSITION TITLE Stelly, David M. Associate Professor of Soil & Crop Science at Texas eRA COMMONS USER NAME A&M University (TAMU)

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of Wisconsin B.Sc. 1975 Genetics Iowa State University M.Sc. 1979 Plant Breeding & Cyto. Plant Breeding & Plant University of Wisconsin Ph.D 1983 Gene.

A. Positions and Honors. Positions and Employment 2000-present Professor, Faculty of Molecular & Environmental Plant Sciences (MEPS) 1997-2000 Professor, Dept. Forest Sciences FRSC: (joint appt.) 1993-present Professor, Dept. Soil & Crop Sciences (SCSC), and Faculty of Genetics (GENE) 1996-2006 Director, Laboratory for Plant Molecular Cytogenetics (LPMC) 1989-1993 Associate Professor, SCSC, and GENE 1983-1989 Assistant Professor, SCSC, and GENE

HONORS, AWARDS AND MEMBERSHIPS 1995: Cotton Genetics Award 2008: Cotton Genetics Award (member of 3-person team) 2002: International Cotton Genome Initiative (ICGI) - First elected Chair 2007: Elected Chair, Science & Technology, Plant Breeding Coordination Committee (2007-2009) 2009 Elected as Secretary (2010), Vice-President (2011), President (2012) and Past-President (2013), National Association of Plant Breeders. 2009-: Chair, P&T Committee, Dept. Soil & Crop Sciences, TAMU 2012: Elected as Co-Chair 2013-2015 and Chair 2015-17, International Cotton Genome Initiative (ICGI)). 2013: Research Award for 2012, Dept. Soil & Crop Sciences, TAMU Memberships: AAAS, Crop Science Society of America, National Association of Plant Breeders, Int'l Cotton Genome Initiative, Sigma Xi

B. Selected peer-reviewed publications (in chronological order).

ILLUSTRATIVE RECENT PUBLICATIONS OF LAB RESEARCH (*postdoc & †student) 1. Bell, A.A., A.F. Robinson, J. Quintana, N.D. Dighe†, M.A. Menz, D.M. Stelly, X. Zheng†, J.E. Jones, C. Overstreet, E. Burris, R.G. Cantrell, and R.L. Nichols. 2014. Registration of LONREN-1 and LONREN-2 Germplasm Lines of Upland Cotton Resistant to Reniform Nematode. J. Plant Reg. XXX- XXX. doi:10.3198/jpr2013.11.0069crg 2. Bell, A.A., A.F. Robinson, J. Quintana, S.E. Duke, J.L. Starr, D.M. Stelly, X. Zheng†, S. Prom, V. Saladino, O.A. Gutiérrez, S.R. Stetina and R.L. Nichols. 2014. REGISTRATION OF BARBREN-713 Germplasm Line of Upland Cotton Resistant to Reniform and Root-Knot Nematodes.

PHS 398/2590 (Rev. 09/04) Page 1 Biographical Sketch Format Page Principal Investigator STELLY, David M. 3. De Donato, M. †, R.A. Brenneman, D.M. Stelly, J.E. Womack and J.F. Taylor. 2004. A methodological approach for the construction of a radiation hybrid map of bovine chromosome 5. Genetics and Molecular Biology, 27, 1, 22-32. 4. Dighe, N.† , A.F. Robinson, A.A. Bell, M. Menz, R. Cantrell and D.M. Stelly. (2009.) Linkage mapping of resistance to reniform nematode in cotton (Gossypium hirsutum L.) following introgression from G. longicalyx (Hutch. & Lee). Crop Science 49:1151-1164. 5. Gao, W. †, Z. J. Chen, J. Z. Yu, D. Raska, R. J. Kohel, J. E. Womack, and D. M. Stelly. 2004. Wide- cross whole-genome radiation hybrid (WWRH) mapping of cotton (Gossypium hirsutum L.). Genetics 167 (3): 1317-1329. 6. Gao, W. †, Z. J. Chen, J. Z. Yu, R. J. Kohel, J. E. Womack, D. M. Stelly. 2006. Wide-cross whole- genome radiation hybrid mapping of the cotton (Gossypium barbadense L.) genome, Molecular Genetics and Genomics 275:105-113. DOI: 10.1007/s00438-005-0069-5 (New method to physically map the cotton genome.) 7. Guan X, Lee JJ, Pang M, Shi X, Stelly DM and Z. Jeffrey Chen. 2011. Activation of arabidopsis seed hair development by cotton fiber-related genes. PLoS ONE 6(7): e21301. doi:10.1371/journal.pone.0021301 (towards an A.t. platform for exploring fiber dev. control) 8. Ji, Y. †, X, Zhao, A, H. Paterson, H. J, Price and D. M. Stelly. 2007. Integrative mapping of Gossypium hirsutum L. by meiotic flourescent in situ hybridization of a tandemly repetitive sequence (B77). Genetics 176: 115-123. 9. Kim, J. †, P. E. Klein, R. R. Klein, H. J. Price, J. E. Mullet, and D. M. Stelly. 2005. Chromosome identification and nomenclature of Sorghum bicolor. Genetics 169: 1169–1173. doi: 10.1534/genetics.104.035980. 10. Kim, J.-S. †, M. N. Islam-Faridi *, P. E. Klein, D. M. Stelly, H. J. Price, R. R. Klein, and J. E. Mullet. 2005. Comprehensive molecular cytogenetic analysis of sorghum genome architecture: distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice. Genetics 171:1963- 1976. 11. Lee, J. J.,O. S. S. Hassan, W. Gao †, N. E. Wei, R. J. Kohel, X-Y Chen, P. Payton, S-H Sze, D. M. Stelly, Z. J. Chen. 2006. Developmental and gene expression analyses of a cotton naked seed mutant, Planta 223:418-432. 12. Mei, M., N. H. Syed, W. Gao †, P. M. Thaxton, C. W. Smith, D. M. Stelly and Z. J. Chen. 2004. Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium). Theor Appl Genet 108:280–291. 13. Page, J.T., M.D. Huynh, Z.S. Liechty, K. Grupp, D. Stelly, A.M. Hulse†, H. Ashrafi, A. Van Deynze, J. Wendel, and J.A. Udall. 2013. Insights into the evolution of cotton diploids and polyploids from whole- genome re-sequencing. G3: GENES, GENOMES, GENETICS 3:1809-1818. 14. Paterson, A H., et al. (D. M. Stelly). 2012. The cotton genomes, their polyploidies, and the evolution of spinnable fibers. Nature 492:423-428. (x. useful resource for cotton genomics) 15. Saha, S., Stelly, D.M., Raska, D.A., Wu, J., Jenkins, J.N., McCarty, Jr., J.C., Makamov, A., Gotmare, V., Abudurakhmonov, I., Campbell, B.T. 2012. Chromosome substitution lines: Concept, development and utilization in the genetic improvement of upland cotton. In: Abdurakhmoov, I.Y., editor. Plant Breeding. InTech. p. 107-128. (uses of hypoaneuploids) 16. Van Deynze, A., K. Stoffel, M. Lee, T.A. Wilkins, A. Kozik, R.G. Cantrell, J.Z. Yu, R.J. Kohel, D.M. Stelly. Sampling nucleotide diversity in cotton. BMC Plant Biology 2009, 9:125-136. (Early SNP development in cotton.) 17. Yu, J., Kohel, R.J., Fang, D.D., Cho, J., Van Deynze, A., Ulloa, M., Hoffman, S.M., Pepper, A.E., Stelly, D.M., Jenkins, J.N., Saha, S., Kumpatla, S.P., Shah, M.R., Hugie, W.V., Percy, R.G. 2012. A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome. Genes, Genomes, Genetics 2:43-58. doi: 10.1534/g3.111.001552 http://www.g3journal.org/content/2/1/43.abstract (useful resource)

PHS 398/2590 (Rev. 09/04) Page 2 Continuation Format Page Principal Investigator STRAIGHT, Paul D.

NAME POSITION TITLE Straight, Paul D. Assistant Professor eRA COMMONS USER NAME

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Lewis & Clark College B.Sc. 1992 Cell Biol., Biochemistry University of Colorado, Boulder Ph.D. 2000 Mol, Cell. & Dev. Biology Harvard Medical School Postdoc. 2001-2007 Microbiology

A. Positions and Honors. Positions and Employment 2007 - 2008 Instructor, Harvard Medical School and Broad Institute 2008 - present Assistant Professor

AWARDS, HONORS, EDITORIAL, REVIEW AND ADVISORY BOARD APPOINTMENTS

2011-2012 Faculty Recognition Award, Biochemistry Graduate Association 2008 New England Biolabs, New Faculty Startup Award 2006 US/EU Task Force Fellowship for Biotechnology, Funds for International Research 2003-2005 NSF Postdoctoral Fellowship in Microbial Biology and Depression (NARSAD), Young Investigators Award.

B. Selected peer-reviewed publications (in chronological order).

Vargas-Bautista C, Rahlwes K, and Straight PD. Differential Regulation of the B. subtilis pks Genes in Motilie and Non-motile Subpopulations Controlled through Spo0A and DegU. (2014) J. Bacteriology 196 (4):717-728. PMID: 24187085.

Hoefler BC, Konganti K, and Straight PD. Draft Genome Sequence of Streptomyces sp. Mg1 Assembled Using PacBio Sequencing. (2013) 1(4). PMID: 23908282.

Meyer RE, Kim S, Obeso D, Straight PD, Winey M, and Dawson DS. Mps1 and Ipl1/Aurora B Act Sequentially to Correctly Orient Chromosomes on the Meiotic Spindle of Budding Yeast. (2013) Science, 339(6123):1071-1074, PMID: 23371552.

Gonzalez DJ, Xu Y, Yang Y-L, Esquenazi E, Liu W-T, Edlund A, Duong T, Du L, Molnár I, Gerwick WH, Jensen PR, Fischbach M, Liaw C-C, Straight P, Nizet V, and Dorrestein PC. Observing the invisible through imaging mass spectrometry, a window into the metabolic exchange patterns of microbes (2012) J. of Proteomics, 75(16):5069-5076. PMID: 22641157.

Barger SR, Hoefler BC, Cubillos-Ruiz A, Russell WK, Russell DH, Straight PD. Imaging secondary metabolism of Streptomyces sp. Mg1 during cellular lysis and colony degradation of competing Bacillus subtilis. (2012) Antonie van Leeuwenhoek, 102(3):435-445. PMID: 22777252.

PHS 398/2590 (Rev. 09/04) Page 1 Biographical Sketch Format Page Principal Investigator STRAIGHT, Paul D. Hoefler BC, Gorzelnik KV, Yang J, Hendricks N, Dorrestein PC, Straight PD. Enzymatic resistance to the lipopeptide surfactin as identified through imaging mass spectrometry of bacterial competition. (2012) Proc. Natl. Acad. Sci., 109(32):13082-7, PMID: 22826229.

Liu WT, Yang YL, Xu Y, Lamsa A, Haste NM, Yang JY, Ng J, Gonzalez D, Ellermeier CD, Straight PD, Pevzner PA, Pogliano J, Nizet V, Pogliano K, Dorrestein PC. 2010. Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis. Proc. Natl. Acad. Sci., 107(37):16286-90, PMID: 20805502.

Yang YL, Xu Y, Straight P†, Dorrestein PC†. 2009. Translating metabolic exchange with imaging mass spectrometry. Nat. Chem. Biol., 5(12):885-7, PMID: 19915536. †Co-corresponding authors.

Straight PD and Kolter R. 2009. Interspecies Chemical Communication in Bacterial Development. Annu Rev Microbiol, 63:99-118, PMID: 19566421.

Yin J,* Straight PD,* Hrvatin S, Dorrestein PC, Bumpus S, Jao C, Kelleher NL, Kolter R, Walsh CT. 2007. Genome-wide high-throughput mining of natural-product biosynthetic gene clusters by phage display. Chem. Biol.,14(3):303-12, PMID: 17379145. *These authors contributed equally to the work.

Butcher RA, Schroeder FC, Fischbach MA, Straight PD, Kolter R, Walsh CT, Clardy J. 2007. The identification of bacillaene, the product of the PksX megacomplex in Bacillus subtilis. Proc. Natl. Acad. Sci., 104(5):1506-9, PMID: 17379145.

Straight PD, Fischbach MA, Walsh CT, Rudner DZ, and Kolter R. 2007. A Singular Enzymatic Megacomplex from Bacillus subtilis. Proc. Natl. Acad. Sci., 104(1): 305-310, PMID: 17190806.

Dorrestein PC, Bumpus SB, Calderone CT, Garneau-Tsodikova S, Aron ZD, Straight PD, Kolter R, Walsh CT, and Kelleher NL. 2006. Facile Detection of Acyl and Peptidyl Intermediates on Thiotemplate Carrier Domains via Phosphopanntetheinyl Elimination Reactions during Tandem Mass Spectrometry. Biochemistry, 45(42): 12756-12766, PMID: 17042494. Straight PD, Willey JM, and Kolter R. 2006. Interactions Between Streptomyces coelicolor and Bacillus subtilis: The Role of Surfactants in Raising Aerial Structures. J. Bacteriology, 188(13): 4918-4925, PMID: 16788200.

Dorrestein PC, Blackhall J, Straight PD, Fischbach MA, Garneau-Tsodikova S, Edwards DJ, McLaughlin S, Lin M, Gerwick WH, Kolter R, Walsh CT, and Kelleher, NL. 2006. Activity Screening of Carrier Domains within Nonribosomal Peptide Synthetases Using Complex Substrate Mixtures and Large Molecule Mass Spectrometry. Biochemistry, 45(6): 1537-1546, PMID: 16460000.

Yin J, Straight PD, McLoughlin SM, Zhou Z, Lin AJ, Golan DE, Kelleher NL, Kolter R, and Walsh, CT. 2005. Genetically encoded short peptide tag for versatile protein labeling by Sfp phosphopantetheinyl transferase. Proc. Natl. Acad. Sci. 102(44): 15815-15820, PMID: 16236721.

Winey M, Morgan GP, Straight PD, Giddings TH Jr., Mastronarde DN. 2005. Three dimensional ultrastructure of Saccharomyces cerevisiae meiotic spindles. Mol. Biol. Cell, 16(3): 1178-88, PMID: 15635095.

Straight PD, Giddings TH Jr., Winey M., 2000. Mps1p regulates meiotic spindle pole body duplication in addition to having unique roles during sporulation. Mol. Biol. Cell, 11:3525-3537, PMID: 11029053.

Wolfsberg TG, Straight PD, Genera RL, Huovila AP, Primakoff P, Myles DG and White JM. ADAM, a widely distributed and developmentally regulated gene family encoding membrane proteins with a disintegrin and metalloprotease domain. Dev. Biology, 1997, 169(1): 378-383, PMID: 7750654. PHS 398/2590 (Rev. 09/04) Page 2 Continuation Format Page Principal Investigator/Program Director (Last, First, Middle): TESH, Vernon L.,

NAME POSITION TITLE Tesh, Vernon Lewis Professor eRA COMMONS USER NAME

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of Virginia, Charlottesville, VA B.A. 1976 Biology Emory University, Atlanta, GA Ph.D. 1988 Microbiol. & Immunol. Uniformed Services University of the Health post-doc 1988-1992 Microbiology Sciences, Bethesda, MD

A. Positions and Honors

Positions

1976-1979 Lab technician, Pathology Clinical Labs., University of Virginia Hospital, Charlottesville VA 1979-1983 Supervisor, Anaerobic Bacteriology and Parasitology Labs, University of Virginia Hospital, Charlottesville, VA 1979-1983 Instructor, Medical Technology Program, University of Virginia Hospital, Charlottesville, VA 1983-1988 Graduate Student, Department of Microbiology and Immunology, Emory University, Atlanta, GA 1988-1992 Post-doctoral Fellow, Department of Microbiology, Uniformed Services University of the Health Sciences, Bethesda, MD 1992-1998 Assistant Professor, Department of Medical Microbiology and Immunology, Texas A&M Health Science Center, College Station, TX 1998-2005 Associate Professor, Department of Medical Microbiology and Immunology, Texas A&M Health Science Center, College Station, TX 2001-pres. Member, Center for Food Safety, Institute for Food Safety and Engineering, Texas A&M University, College Station, TX 2005-pres. Professor, Department of Microbial and Molecular Pathogenesis, Texas A&M Health Science Center, College Station, TX 2006-pres. Member, Faculty of Genetics, Texas A&M University, College Station, TX 2011-2013 Associate Dean for Faculty Affairs and Curriculum Management, College of Medicine, Texas A&M Health Science Center, Bryan, TX 2013-pres. Vice President for Academic Affairs, Texas A&M Health Science Center, Bryan, TX

B. Selected Peer-reviewed Publications (in chronological order, from a total of 62)

1. Lee, S.-Y., R.P. Cherla, I. Caliskan, and V.L. Tesh. Shiga toxin 1 induces apoptosis in the human myelogenous leukemia cell line THP-1 by a caspase 8-dependent, TNF receptor-independent mechanism. Infection and Immunity 73:5115-5126 (2005) (PMID 16041028).

2. Cherla, R.P., S.-Y. Lee, P.L. Mees, V.L. Tesh. Shiga toxin 1 induced cytokine production is mediated by MAP kinase pathways and translation initiation factor eIF4E in the macrophage-like THP-1 cell line. Journal of Leukocyte Biology 79:397-407 (2006) (PMID 19788417).

PHS 398/2590 (Rev. 09/04) Page Biographical Sketch Format Page Principal Investigator/Program Director (Last, First, Middle): TESH, Vernon L., 3. Lee, S.-Y., R.P. Cherla, and V.L. Tesh. Simultaneous induction of apoptotic and survival signaling pathways in macrophage-like THP-1 cells by Shiga toxin 1. Infection and Immunity 75:1291-1302 (2007) (PMID 17194804).

4. Lee, S.-Y., M.-S. Lee, R.P. Cherla and V.L. Tesh. Shiga toxin 1 induces apoptosis through the endoplasmic reticulum stress response in human monocytic cells. Cellular Microbiology 10:770-780 (2008) (PMID 18005243).

5. Cherla, R.P., S.-Y. Lee, R.A. Mulder, M.-S. Lee and V.L. Tesh. Shiga toxin 1-induced proinflammatory cytokine production is regulated by the phosphatidylinositol 3-kinase/Akt/ mammalian target of rapamycin signaling pathway. Infection and Immunity 77:3919-3931 (2009) (PMID 19596774).

6. Lee, M.-S., R.P. Cherla, D. Leyva-Illades, and V.L. Tesh. Bcl-2 regulates the onset of Shiga toxin 1-induced apoptosis in THP-1 cells. Infection and Immunity 77:5233-5244 (2009) (PMID 19752028).

7. Leyva-Illades, D., R.P. Cherla, C. Galindo, A.K. Chopra, and V.L. Tesh. Global transcriptional response of macrophage-like THP-1 cells to Shiga toxin type 1. Infection and Immunity 78:2454-2465 (2010) (PMID 20351145)

8. Lee, M.-S., R.P. Cherla, E.K. Lentz, D. Leyva-Illades, and V.L. Tesh. Signaling through C/EBP homologous protein and death receptor 5 and calpain activation differentially regulate THP-1 cell maturation- dependent apoptosis induced by Shiga toxin type 1. Infection and Immunity 78: 3378-3391 (2010). PMID: 20515924; PMCID: PMC2916263.

9. Lentz, E.K., R.P. Cherla, V. Jaspers, B.R. Weeks, and V.L. Tesh. Role of TNF-α in disease using a mouse model of Shiga toxin-mediated renal damage. Infection and Immunity 78: 3689-3699 (2010). PMID: 20605983.

10. Stearns-Kurosawa, D.J., V. Collins, S. Freeman, V.L. Tesh, and S. Kurosawa. Distinct physiologic and inflammatory responses elicited from baboons after challenge with Shiga toxin type 1 or 2 from enterohemorrhagic Escherichia coli. Infection and Immunity 78: 2497-2504 (2010) (PMID 20308301)

11. Lentz, E.K., R.P. Cherla, M.-S. Lee, and V.L. Tesh. Differential response of the human renal proximal tubular epithelial cell line HK-2 to Shiga toxin types 1 and 2. Infection and Immunity 79: 3570-3580 (2011).

12. Lee, M.-S., R.P. Cherla, M.H. Jenson, D. Leyva-Illades, M. Martinez-Moczygemba and V.L. Tesh. Shiga toxins induce autophagy leading to differential signaling pathways in toxin-sensitive and toxin-resistant human cells. Cellular Microbiology 13: 1479-1496 (2011).

13. Leyva-Illades, D., R.P. Cherla, M.-S. Lee, and V.L. Tesh. Dual specificity phosphatase expression and its effect on mitogen-activated protein kinases and chemokine expression elicited by Shiga toxin type 1. Infection and Immunity 80: 2109-2120 (2012).

14. Stearns-Kurosawa, D.J., S.-Y. Oh, R.P. Cherla, M.-S. Lee, V.L. Tesh, J. Papin, J. Henderson, and S. Kurosawa. Distinct renal pathology and chemotactic phenotype after challenge with enterohemorrhagic Escherichia coli Shiga toxins in non-human primate models of hemolytic uremic syndrome. American Journal of Pathology 182: 1227-1238 (2013).

22. Lee, M.-S., and V.L. Tesh. Shiga toxin-induced regulatory immune responses. J. Microbiol. 51: 724-730 (2014).

PHS 398/2590 (Rev. 09/04) Page Continuation Format Page BIOGRAPHICAL SKETCH Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Threadgill, David W. Professor eRA COMMONS USER NAME (credential, e.g., agency login) david_threadgill EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable)

Texas A&M University, College Station, TX B.S. 05/83 Zoology Texas A&M University, College Station, TX Ph.D. 05/89 Genetics Case Western Reserve University, Cleveland, OH Postdoc 06/96 Developmental Biology

A. Positions and Honors Positions and Employment 1996-2000 Assistant Professor, Department of Cell Biology, Vanderbilt University, Nashville, TN 2000-2008 Assistant, Associate Professor, Department of Genetics, University of North Carolina, Chapel Hill, NC 2008-2013 Professor and Head, Department of Genetics, North Carolina State University, Raleigh, NC 2013- Professor, Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 2013- Professor, Department of Cellular and Molecular Medicine, Texas A&M University Health Science Center, College Station, TX 2013- Director, Whole Systems Genomics Initiative, Texas A&M University, College Station, TX Other Experience and Professional Memberships 1997- Member, American Association for Cancer Research 1998- Steering committee member, NCI Mouse Models of Human Cancer Consortium 2000-2013 Member, Lineberger Comprehensive Cancer Center, UNC 2002 Co-founder, Complex Trait Community (CTC) 2003-2008 Member and Director of Transomics Research Core, Center for Environmental Health and Susceptibility 2004 Co-chair, NCI Director’s Think Tank on Susceptibility and Resistance to Cancer 2005-2008 Member, NIH Cancer Genetics Study Section 2007-2010 Secretariat member (elected), International Mammalian Genome Society 2007- Member, Society for Toxicology 2008- Member, Environmental Mutagen Society 2008- Editorial board, Cancer Prevention Research 2009- Associate editor, Genetics 2010-2013 Editorial board, Genetics Research 2010- Editorial board, Frontiers Genetics 2011- Editorial board, Mammalian Genome 2010-2012 President (elected), International Mammalian Genome Society 2010-2012 National Institutes of Health College of CSR Reviewers Honors 1998-2000 March of Dimes Basil O'Conner Award 1998-2000 V Foundation Scholar 2005 UNC-Lineberger Comprehensive Cancer Center Clinical/Translational Research Award 2004-2008 Jefferson Pilot Scholar Award 2010 Society of Toxicology award for most influential paper published in 2009 affecting the science of risk assessment (Genome Research 19:1507-1515) 2011 Fellow (elected) of the American Association for the Advancement of Science 2013- Tom and Jean McMullin Chair in Genetics, Texas A&M University Health Science Center, College Station, TX B. Peer-reviewed Publications (Selected from >140 peer-reviewed publications; Postdocs, graduate students and undergraduate students as shown) Lee DK, Yu M, Lee E, Kim H, Yang Y, Kim K, Paniccia C, Kurie JM, Threadgill DW. 2009. Tumor-specific apoptosis caused by deletion of the ERBB3 pseudo-kinase in the intestinal epithelium. Journal Clinical Investigation 119:2702-2713 La Merrill M, Kuruvilla BS, Pomp D, Birnbaum LS, Threadgill DW. 2009. Dietary fat alters body composition, mammary development, and cytochrome p450 induction after maternal TCDD exposure in DBA/2J mice with low-responsive aryl hydrocarbon receptors. Environmental Health Perspectives 117:1414-1419 Munger SC, Aylor DL, Syed HA, Magwene PM, Threadgill DW, Capel B. 2009. Systems genetic analysis reveals key nodes in the transcription network governing sex determination in mammals. Genes and Development 23:2521-2536 LaMerrill MA, Harper R, Birnbaum LS, Cardiff RD, Threadgill DW. 2010. Maternal dioxin exposure combined with a diet high in fat increases mammary cancer incidence. Environmental Health Perspectives 118:596- 601 Gordon RR, Merrill ML, Hunter KW, Sørensen P, Threadgill DW, Pomp D. 2010. Dietary fat-dependent transcriptional architecture and copy number alterations associated with modifiers of mammary cancer metastasis. Clinical Experimental Metastasis 27:279-293 Eversley CD, Clark T, Xie Y, Steigerwalt J, Bell TA, de Villena FP, Threadgill DW. 2010. Genetic mapping and developmental timing of transmission ratio distortion in a mouse interspecific backcross. BMC Genetics 11:98 Bradford BU, Lock EF, Kosyk O, Kim S, Uehara T, Harbourt D, DeSimone M, Threadgill DW, Tryndyak V, Pogribny IP, Bleyle L, Koop DR, Rusyn I. 2011. Interstrain differences in the liver effects of trichloroethylene in a multistrain panel of inbred mice. Toxicological Sciences 120:206-217 Aylor DL, Valdar W, Foulds-Mathes W, Buus RJ, Verdugo RA, Baric RS, Ferris MT, Frelinger JA, Heise M, Frieman MB, Gralinski LE, Bell TA, Didion JD, Hua K, Nehrenberg DL, Powell CL, Steigerwalt J, Xie Y, Kelada SN, Collins FS, Yang IV, Schwartz DA, Branstetter LA, Chesler EJ, Miller DR, Spence J, Liu EY, McMillan L, Sarkar A, Wang J, Wang W, Zhang Q, Broman KW, Korstanje R, Durrant C, Mott R, Iraqi FA, Pomp D, Threadgill D, Pardo-Manuel de Villena F, Churchill GA. 2011. Genome Research 21:1213-1222 Zhang X, Tamasi J, Lu X, Zhu J, Chen H, Tian X, Lee TC, Threadgill DW, Kream BE, Kang Y, Partridge NC, Qin L. 2011. Epidermal growth factor receptor plays an anabolic role in bone metabolism in vivo. Journal Bone Mineral Research 26:1022-1034 Rinella ES, Bankaitis ED, Threadgill DW. 2012. Dietary calcium supplementation enhances efficacy but also toxicity of EGFR inhibitor therapy for colon cancer. Cancer Biology Therapy 13:130-137 Rinella ES, Threadgill DW. 2012. Efficacy of EGFR inhibition is modulated by model, sex, genetic background and diet: implications for preclinical cancer prevention and therapy trials. PLoS One 7:e39552 Eversley CD, Xie Y, Pearsall RS, Threadgill DW. 2012. Mapping five new Susceptibility to Colon Cancer (Scc) loci using a mouse inter-specific backcross. G3: Genes, Genomes and Genetics 2:1577-1584 Bautz DJ, Broman KW, Threadgill DW. 2013. Identification of a Novel Polymorphism in X-Linked Sterol-4- alpha-carboxylate 3-dehydrogenase (Nsdhl) Associated with Reduced HDL Cholesterol Levels in I/LnJ Mice. G3: Genes, Genomes and Genetics 3:1819-1825 Ferris MT, Aylor DL, Bottomly D, Whitmore AC, Aicher LD, Bell TA, Bradel-Tretheway B, Bryan JT, Buus RJ, Chesler EJ, Haagmans BL, McMillan L, Miller DR, Rosenzweig E, Valdar W, Wang J, Churchill GA, Threadgill DW, McWeeney SK, Katze MG, de Villena FPM, Baric RS, Heise MT. 2013. Modeling host genetic regulation of influenza pathogenesis in the Collaborative Cross. PLoS Pathogens 9:e1003196 DeSimone MC, Rathmell WK, Threadgill DW. 2013. Pleiotropic effects of the trichloroethylene-associated P81S VHL mutation on metabolism, apoptosis and ATM-mediated DNA damage response. Journal of the National Cancer Institute 105:1355-1364 Phillippi J, Xie Y, Miller DR, Bell TA, Zhang Z, Lenarcic AB, Aylor DL, Krovi SH, Threadgill DW, de Villena FP, Wang W, Valdar W, Frelinger JA. 2014. Using the emerging Collaborative Cross to probe the immune system. Genes Immunity 15:38-46 Donohoe DR, Holley D, Collins LB, Montgomery SA, Whitmore AC, Hillhouse A, Curry KP, Renner SW, Greenwalt A, Ryan EP, Godfrey V, Heise MT, Threadgill DS, Han A, Swenberg JA, Threadgill DW, Bultman SJ. 2014. A Ggnotobiotic mouse model demonstrates that dietary fiber protects against colorectal tumorigenesis in a microbiota- and butyrate-dependent manner. Cancer Discovery [Epub ahead of print]

BIOGRAPHICAL SKETCH Provide the following information for the Senior/key personnel and other significant contributors. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Threadgill, Deborah Assistant Professor eRA COMMONS USER NAME (credential, e.g., agency login) Deborah_Threadgill EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) Texas A&M University B. S. 1980 Animal Sciences Purdue University M. S. 1985 Cytogenetics Texas A&M University Ph.D. 1990 Genetics Case Western Reserve University Post-doc 1990-1993 Virology Case Western Reserve University Post-doc 1993-1996 Immunology

A. Positions and Honors. Professional Positions: 1996-1998 Research Assistant Professor Dept. of Medicine, Division of Infectious Diseases, Vanderbilt University School of Medicine

1998-2000 Research Assistant Professor Dept. of Cell Biology, Vanderbilt University School of Medicine

7/2000-9/2008 Research Assistant Professor, Dept. of Genetics, University of North Carolina School of Medicine

10/2008-7/2013 Assistant Professor, Dept. of Microbiology, North Carolina State University

8/2013-present Assistant Professor, Dept. of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University

Other Experience Review/Advisory Boards: NSF SBIR “Biotech and Chemical Technologies” 2009, NSF SBIR “Assays and Quantitative Methods” 2007, NSF SBIR “Biotech Products/Processes” grant review panel 2006

Research mentor for Seeding Postdoctoral Innovators in Research and Education (SPIRE), an IRACDA sponsored program at UNC, Research mentor for Promoting Minority Advancement in the Biomedical Sciences (PMABS) at UNC

Honors, Awards, Fellowships: 1991-1993 Recipient of a NIAID Institutional Post-Doctoral Fellowship in Virology 1998-1999 Recipient of a CNRU pilot grant (Vanderbilt University) 1999-2000 Recipient of an NSF POWRE individual faculty development award

B. Selected peer-reviewed publications (in chronological order). [*postdoctoral trainees, SSPIRE fellows]

1. Palyada, K, Threadgill, D, Stintzi A. 2004. The iron and Fur regulons of Campylobacter jejuni studied by genome-wide transcripts profiling. J. Bacteriol. 186: 4714-29.

2. Poly, F, Threadgill, D, and Stintzi, A. 2004. Identification of Campylobacter jejuni ATCC 43431 specific genes by whole microbial genome comparisons. J. Bacteriol. 186: 4781-95.

3. Poly, F, Threadgill, D, and Stintzi, A. 2005. Genomic Diversity in Campylobacter jejuni: Identification of C. jejuni 81-176-Specific Genes. J Clin Microbiol. 43:2330-8.

4. Rinella ES, Eversley CD, *Carroll IM, *SAndrus JM, Threadgill DW, Threadgill DS. 2006. Human epithelial-specific response to pathogenic Campylobacter jejuni. FEMS Microbiol Lett. 262:236-43.

5. *Carroll, IM, *SAndrus, JM, Bruno-Bárcena, JM, Klaenhammer, TR, Hassan, HM and Threadgill, DS. 2007. Anti-inflammatory properties of Lactobacillus gasseri expressing manganese superoxide dismutase using the interleukin 10-deficient mouse model of colitis. Am J Physiol Gastrointest Liver Physiol. 293:G729-38.

6. *SLaGier, MJ and Threadgill DS. 2008. Identification of novel genes in the oral pathogen Campylobacter rectus. Oral Microbiol Immunol. 23:406-12.

7. *Carroll IM, Threadgill DW and Threadgill DS. 2009. The gastrointestinal microbiome: a malleable third genome of mammals. Mamm Genome 20: 395-403

8. Lippert E, Karrasch T, Sun X, Allard B, Herfarth HH, Threadgill D, Jobin C. 2009. Gnotobiotic IL-10; NF-kappaB mice develop rapid and severe colitis following Campylobacter jejuni infection. PLoS One.4(10):e7413.

9. Arce RM, Diaz PI, Barros SP, Galloway P, Bobetsis Y, Threadgill D, Offenbacher S. 2010. Characterization of the invasive and inflammatory traits of Oral Campylobacter rectus in a murine model of fetoplacental growth restriction and in trophoblastic cultures. J of Reprod. Immunol. 84:145-53.

10. Sun X, Threadgill D, Jobin C. 2012. Campylobacter jejuni induces colitis through activation of mammalian target of rapamycin signaling. Gastroenterology. 142:86-95.

11. *SLaGier MJ and Threadgill, DS. 2014. Identification and characterization of an Invasion Antigen B Gene from the oral pathogen Campylobacter rectus. Indian J Microbiol. 54:33-40.

12. Donohoe DR, Holley D, Collins LB, Montgomery SA, Whitmore AC, Hillhouse A, Curry KP, Renner SW, Greenwalt A, Ryan EP, Godfrey V, Heise MT, Threadgill DS, Han A, Swenberg JA, Threadgill DW, Bultman SJ. 2014. A Gnotobiotic Mouse Model Demonstrates that Dietary Fiber Protects Against Colorectal Tumorigenesis in a Microbiota- and Butyrate-Dependent Manner. Cancer Discov. 29. pii: CD-14-0501. [Epub ahead of print]

BIOGRAPHICAL SKETCH

NAME POSITION TITLE Turner, Nancy Delane Associate Professor

eRA COMMONS USER NAME: [email protected] EDUCATION/TRAINING INSTITUTION AND LOCATION DEGREE YEAR(s) FIELD OF STUDY Texas A&M University, College Station BS 1978 Animal Science Texas A&M University, College Station MS 1984 Animal Nutrition Texas A&M University, College Station PhD 1995 Nutrition

A. Personal Statement Dr. Turner’s research focuses on identifying dietary bioactives that suppress colon carcinogenesis and inflammatory bowel disease. She has experience studying the regulation of proliferation and apoptosis in colonocytes, and the impact of dietary and microbe-derived metabolites on gene transcription and epigenetic profile in colonocytes. Current research is designed to understand how diet influences the intestinal environment, with particular attention to the interaction between the microbiota and the colon epithelia. The most recent outcomes of the work have identified dietary interventions containing polyphenolic molecules that protect against colon disease through the establishment of beneficial bacterial populations that produce desirable microbial metabolic byproducts. Those modifications were found to contribute to a beneficial host metabolomic profile indicative of improved glucose tolerance in overweight and obese human subjects. B. Positions and Honors Positions 1996-1998 Assistant Research Scientist, Animal Science Department, Texas A&M University 1998-2003 Research Assistant Professor, Animal Science Department, Texas A&M University 2003- Associate Professor, Nutrition and Food Science Department, Texas A&M University Professional Committee Memberships, Leadership Positions, and Honors 1999 Ethel Ashworth-Tsutsui Memorial Award for Mentoring 2002-2003 Member, USDA/NRI program review panel 2004 Ad hoc reviewer, USDA’s NRI program on Improving Human Nutrition for Optimal Health 2005-2008 Chair, Intercollegiate Faculty of Nutrition 2005 Ad hoc reviewer, USDA’s NRI program on Improving Human Nutrition for Optimal Health 2006 Ad hoc member for the Chemo/Dietary Prevention Study Section, NIH 2007-2010 Secretary/Treasurer for Nutrition Sciences Council of ASN 2008-2011 Chair-Elect, Chair, and Past-Chair of the ASN Diet & Cancer Research Interest Section 2009 Member, NSBRI Postdoctoral review panel 2009-2013 Councilor of the Society for Experimental Biology and Medicine 2011 Ad hoc reviewer, National Medical Research Council of Singapore 2011-2012 Member of the NASA Oxidative Stress and Damage Working Group 2012 Nutrition & Food Science Department Award for Mentoring 2013 President-Elect, TAMU chapter of Sigma Xi Editorial and Review Experience Editorial positions: 1999-2002 Editorial Board for Journal of Animal Science 2000-2013 Associate Editor of Nutrition Notes (American Society for Nutrition) 2002 Guest co-Editor of Nutrition 2010-present Editorial Board for Advances in Nutrition 2011-2012 Guest editor of Molecules: Bioactive Compounds 2013 Guest editor of Nutrients: Dietary Fiber and Nutrition

Ad hoc reviews: Journal of Nutrition; Advances in Nutrition; Cancer Prevention Research; Nutrition and Cancer; BMC Cancer; American Journal of Clinical Nutrition; Molecular Carcinogenesis; Journal of Nutritional Biochemistry; Experimental Biology and Medicine; Integrative Cancer Therapies; Biochimica et Biophysica Acta; Cancer Letters; European Journal of Clinical Nutrition; European Journal of Nutrition; Carcinogenesis; Journal of Nutrigenetics and Nutrigenomics; Current Metabolomics; Clinical and Experimental Metastasis; British Journal of Nutrition; American Journal of Physiology–Regulatory, Integrative and Comparative Physiology; BMC Gastroenterology; Nutrition Research; Medical Oncology; Cell Biochemistry and Function; Lipids; Gravitational and Space Biology; Acta Astronautica; Journal of Medicinal Food; Molecular Nutrition and Food Research; Food and Chemical Toxicology; Aviation, Space and Environmental Medicine; Journal of Applied Physiology; Food and Chemical Toxicology; Amino Acids C. Peer-reviewed publications (Selected from the last 4 years out of 60). 1. Warren, C.A., K.J. Paulhill, L.A. Davidson, J.R. Lupton, S.S. Taddeo, M.Y. Hong, N. Wang, R.J. Carroll, R.S. Chapkin, and N.D. Turner. 2009. Quercetin may suppress rat aberrant crypt foci formation by suppressing inflammatory mediators that influence proliferation and apoptosis. Journal of Nutrition 139:101-105. PMCID: PMC2714375 2. George, N.I., J.R. Lupton, N.D. Turner, R.S. Chapkin, L.A. Davidson, and N. Wang. 2010. Evaluation of fecal mRNA reproducibility via a marginal transformed mixture modeling approach. BMC Bioinformatics 11:13. PMCID: PMC2827371. 3. Leonardi, T., J. Vanamala, S.S. Taddeo, L.A. Davidson, M.E. Murphy, B.S. Patil, N. Wang, R.J. Carroll, R.S. Chapkin, J.R. Lupton, and N.D. Turner. 2010. Apigenin and naringenin suppress colon carcinogenesis through the aberrant crypt stage in azoxymethane-treated rats. Experimental Biology and Medicine 235:710-717. PMCID: PMC2885760 4. Cho, Y.M., H. Kim, N.D. Turner, J.C. Mann, J. Wei, S.S. Taddeo, L.A. Davidson, N. Wang, M. Vannucci, R.J. Carroll, R.S. Chapkin, and J.R. Lupton. 2011. A chemoprotective fish oil/pectin diet temporally alters gene expression profiles in exfoliated rat colonocytes throughout oncogenesis. Journal of Nutrition 141:1029-1035. PMCID: PMC3095137 5. Austin, D.L., N.D. Turner, C.M. McDonough, and L.W. Rooney. 2012. Effects of brans from specialty sorghum varieties on in vitro digestibility of soft and hard sorghum endosperm porridges. Cereal Chemistry 89:190-197. 6. Jeffery, J.L., N.D. Turner, and S.R. King. 2012. Carotenoid bioaccessibility from nine raw carotenoid-storing fruits and vegetables using an in vitro model. Journal of the Science of Food and Agriculture DOI 10.1002/jsfa.5768. PMID: 22806183 7. Lemlioglu-Austin, D., N.D. Turner, C.M. McDonough, and L.W. Rooney. 2012. Effects of sorghum [Sorghum bicolor (L.) Moench] crude extracts on starch digestibility, estimated glycemic index (EGI), and resistant starch (RS) contents of porridges. Molecules 17:11124-11138. PMID: 22986923. 8. Cho, Y., N.D. Turner, L.A. Davidson, R.S. Chapkin, R.J. Carroll, and J.R. Lupton. 2012. A chemoprotective fish oil/pectin diet enhances apoptosis via Bcl-2 promoter methylation in rat azoxymethane-induced carcinomas. Experimental Biology & Medicine 237:1387-1393. PMCID: PMC3999967. 9. Turner, N.D., L.E. Ritchie*, R.S. Bresalier, and R.S. Chapkin. 2013. The microbiome and colorectal neoplasia – environmental modifiers of dysbiosis. Current Gastroenterology Reports 15(9):346. PMCID: PMC3807587. 10. Cho, Y., N.D. Turner, L.A. Davidson, R.S. Chapkin, R.J. Carroll, and J.R. Lupton. 2014. Colon cancer cell apoptosis is induced by combined exposure to the n-3 fatty acid DHA and butyrate through promoter methylation. Experimental Biology and Medicine 239:302-310. PMCID: PMC3999970. 11. Morgan, J.L.L., L.E. Ritchie, B.E. Crucian, C. Theriot, H. Wu, S.M. Smith, N.D. Turner, and S.R. Zwart. 2014. Increased dietary iron and radiation in rats promotes oxidative stress, localized and systemic immune system responses, and alters colon mucosal environment. FASEB Journal 28:1486-1498. PMID: 24334706. Select relevant earlier works 12. Wu, G., Y.-Z. Fang, S. Yang, J.R. Lupton, N.D. Turner. 2004. Glutathione metabolism and its implications for health. Journal of Nutrition 134:489-492. PMID: 14988435 13. Vanamala, J., G. Cobb, N.D. Turner, J.R. Lupton, K.S. Yoo, L.M. Pike, and B.S. Patil. 2005. Bioactive compounds of grapefruit (Citrus paradisi cv Rio Red) respond differently to postharvest irradiation, storage and freeze drying. J. Agric. Food Chem. 53:3980-3985. 14. Vanamala, J., T. Leonardi, B.S. Patil, S.S. Taddeo, M.E. Murphy, L.M. Pike, R.S. Chapkin, J.R. Lupton, and N.D. Turner. 2006. Suppression of colon carcinogenesis by bioactive compounds in grapefruit. Carcinogenesis 27:1257-1265. 15. Crim, K.C., L.M. Sanders, M.Y. Hong, S.S. Taddeo, N.D. Turner, R.S. Chapkin, and J.R. Lupton. 2008. Upregulation of p21Waf1/Cip1 expression in vivo by butyrate administration can be chemoprotective or chemopromotive depending on the lipid component of the diet. Carcinogenesis 29:1415-1420. PMCID: PMC2659529 BIOGRAPHICAL SKETCH Provide the following information for the Senior/key personnel and other significant contributors. Follow this format for each person. DO NOT EXCEED FOUR PAGES.

NAME POSITION TITLE Welsh, C. Jane Professor, Veterinary Integrative Biosciences and eRA COMMONS USER NAME (credential, e.g., agency login) Neuroscience CJWelsh Assistant Dean for Graduate Studies

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable.) DEGREE INSTITUTION AND LOCATION MM/YY FIELD OF STUDY (if applicable) University of London, U.K. B.Sc. (Hons) 06/76 Microbiology University of London, U.K. Ph.D. 10/81 Immunology/Biochem. King’s College Hospital, U.K. Postdoc 1979-1981 Autoimmune liver Dept. of Pathology, Cambridge, U.K. Postdoc 1982-1985 Rheumatoid arthritis Dept. of Pathology, Cambridge, U.K. Postdoc 1985-1989 Multiple sclerosis

B. Positions and Honors POSITIONS 1988-1989 Special Supervisor in Pathology, Newnham College, Cambridge University 1989- Visiting Assistant Professor (1989-1991), Assistant Professor (1991-2000); Associate Professor (2000-2006), Professor (2006-present) Dept. of Veterinary Integrative Biosciences and Dept. of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University 1991- Member of the Faculty of Neuroscience and Graduate Faculty, Texas A&M University 1998- Member of the Genetics Faculty, Biotechnology Faculty and Executive Committee of the Faculty of Virology, Texas A&M University 2002- Departmental Graduate Advisor 2006- Associate Department Head, Dept. Veterinary Integrative Biosciences 2007- Joint appointments in the Dept. Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M Health Science Center and Dept. Psychology, Texas A&M University 2011- Chair of the Texas A&M Institute for Neuroscience 2011- Assistant Dean for Graduate Studies, College of Veterinary Medicine HONORS AND ACTIVITIES 2001 Alzheimer’s Association Grant Reviewer 2003 Biotechnology and Biological Sciences Research Council, UK NIH Brain Disorders and Clinical Neuroscience Special Emphasis Panel (ZRG1-NMB) 2004 NSF Fellowship Review Panel, NMSS Pilot Grant Reviewer 2005 2008 & 2009 NSF Graduate Fellowship Review Panel 2006 NIH Brain Disorders and Clinical Neuroscience Special Emphasis Panel 2007 2008 2009 American Heart Association Grant Review Panel 2009 NIH Clinical Neuroimmunology and Brain Tumor Grant Review Panel 2010 NSF Grant Reviewer 2010 Texas A&M University’s (TAMU) Women’s Progress Award for faculty 2011 NIH P50 Reviewer 2011 TAMU Women’s Faculty Outstanding Mentoring Award 2012 TAMU Association of Former Students Distinguished Achievement Award for Graduate Mentoring 2013 Fast Forward MS Grant reviewer & 2013 Italian Multiple Sclerosis Society Editorial Board: Brain, Behavior and Immunity Ad hoc reviewer for: J. Infectious Diseases, Infection and Immunity, J. Virology, American Journal of Physiology: Heart and Circulation, Clinical and Diagnostic Laboratory Immunology, J. Neuroimmunology, Neuroimmunomodulation, Brain Behavior and Immunity, PNAS, Neurotoxicology, Developmental Neuroscience, Neuropathology and Applied Neurobiology, Toxicology in Vitro, J. Neuroscience, Plos One

C. Publications relevant to the current application Villarreal D, Young CR, Storts R, Ting JW & Welsh CJR (2006) A comparison of the neurotropism of Theiler’s virus and poliovirus in CBA mice. Microbial Pathogenesis, 41: 133-143. PMID 16935465 Mi W, Young CR, Storts R, Steelman A, Meagher MW & Welsh CJR (2006) Stress alters pathogenecity and facilitates systemic dissemination of Theiler’s virus. Microbial Pathogenesis 41: 149-156. PMID 16949789 Fuller, A, Yahikozawa, H, So EY, Dal Canto M, Koh CS, Welsh CJ & Kim BS (2007) Castration of male C57L/J mice increases susceptibility and estrogen treatment restores resistance to Theiler's virus-induced demyelinating disease. J Neurosci Res. 85: 871-881. PMID 17253641 Young EE, Prentice TW, Satterlee D, McCullough H, Sieve AN, Johnson RR, Welsh TH, Welsh CJR, & Meagher MW (2008) Glucocorticoid exposure alters the pathogenesis of Theiler's murine encephalomyelitis virus during acute infection. Physiology and Behavior 95: 63-71. PMID 18538803 Steelman AJ, Dean DD, Young CR, Smith R, Prentice TW, Meagher MW & Welsh CJR. (2009). Restraint stress modulates virus specific adaptive immunity during acute Theiler’s virus infection. Brain, Behavior and Immunity 23: 830-843. PMID 19348911 Welsh CJ, Steelman AJ, Mi W, Young CR, Dean DD, Storts R, Welsh TH, Meagher MW (2010). Effects of stress on the immune response to Theiler’s virus – implications for virus-induced autoimmunity. Neuroimmunomodulation. 17: 169-172. Meagher MW, Sieve AN, Johnson RR, Satterlee D, Belyavskyi M, Mi W, Prentice T W, Welsh TH, & Welsh CJR (2010). Neonatal maternal separation disrupts viral clearance from the CNS during acute Theiler’s virus infection in adolescent mice. Behavior Genetics 40: 233-249. PMID 20135342 Vichaya EG, Young EE, Reusser NM, Cook JL, Steelman AJ, Welsh CJR, & Meagher MW (2011) Social Disruption Induced Priming of CNS Inflammatory Response to Theiler's Virus is Dependent upon Stress Induced IL-6 Release. J. Neuroimmunology, 239: 44-52. PMID 2200153 Rodrigues A, Welsh CJ, Varner P, Concha-Bermejillo A, Ambrus A, Edwards J (2012) Identification of the target cells and sequence of infection during experimental infection of ovine fetuses with Cache Valley virus. Journal of Virology, 86: 4793-4800. PMID 22379096 Young EE, Vichaya EG, Reusser, NM, Cook JL, Steelman AJ, Welsh CJR, Meagher MW (2013) Chronic social stress impairs virus specific adaptive immunity during acute Theiler’s virus infection. J. Neuroimmunology. 254, 19-27 Gomez FP, Steelman AJ, Young CR, Welsh CJ (2013) Hormones and immune system interactions in demyelinating diseases. Hormones and Behavior, 63: 315-321. Rodrigues Hoffmann AF, Dorniak P, Filant J, Dunlap KA, Bazer FW, Concha-Bermejillo A, Welsh CJ, Varner P, Edwards JF. (2013) Ovine Fetal Immune Response to Cache Valley Virus Infection. J. Virol. 87: 5586-92 Steelman AJ, Smith R, Welsh CJ, Li J (2013) Galectin-9 is Up-regulated in Astrocytes by TNF and Promotes Encephalitogenic T-cell Apoptosis. J Biol. Chem. 288 (33): 23776-87. Brinkmeyer-Langford C, Rodrigues A, Steelman AJ, Young CR, Meagher MW, Welsh CJR (2014) Consequences of perinatal bisphenol A exposure in a mouse model of multiple sclerosis. Autoimmunity 47, 57-66. Johnson RR, Maldonado-Bouchard S, Prentice TW, Bridegam P, Fenan R, Young CR, Steelman AJ, Welsh TH, Welsh CJ, Meagher MW (2014) Neonatal experience interacts with adult social stress to alter acute and chronic Theiler's virus infection. In press Brain, Behavior and Immunity S0889-1591(14)00068-3. doi: 10.1016/j.bbi.2014.03.002. [Epub ahead of print]. Taylor A, Welsh CJR, Young CR, Spoor EM, Kerwin SC, Griffin JF, Levine GJ, Cohen ND, and Levine JM (2014) Cerebrospinal fluid inflammatory cytokines in naturally-occurring canine spinal cord injury. In press Journal of Neurotrauma.

D. Research Support Ongoing Research Support

NIH/NINDS RO1 NS060822 12/01/2007-3/30/14 (includes two year no-cost extension) Mary Meagher (PI) Impact of stress-induced cytokines on an animal model of MS Goals: This grant examines the role of cytokines in mediating the adverse effects of social stress on Theiler’s virus infection. Role Co-PI

NAME POSITION TITLE Westhusin, Mark E. Professor eRA COMMONS USER NAME mwesthusin EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Kansas State University B.S. 1980 Animal Science Texas A&M University M.S. 1983 Veterinary Physiology Texas A&M University Ph.D 1986 Veterinary Physiology

A. Personal Statement.

I have been involved with the development and application of animal biotechnology and Assisted Reproductive Technologies (ARTs) for the past 30 years, and provided leadership for numerous research projects. My laboratory is best known for research involving animal cloning which resulted in our group cloning more different animal species than any other institution in the world, including the world’s first cat and first white-tailed deer. More recently my research focus has switched to improving the technology for producing transgenic livestock in which specific genes have been targeted for silencing by RNA interference. My laboratory group has already produced genetically modified offspring expressing transgenes encoding various shRNAs in sheep, pigs, goats and cattle. We have also successfully utilized RNAi to silence the expression of various genes involved with epigenetic reprogramming during preimplantation development in cattle, then determine the effects on development. More recently we have utilized TALENs and the CRISPR/Cas system to induce targeted mutations in genes critical for normal development. Over the course of my career I have served as chair or co-chair for 14 PhD students and 5 MS students. I have also served on the committees of numerous additional graduate students, mentored 5 postdoctoral fellows, and served as advisor for numerous undergraduate students conducting research in my lab. Given these and other experiences I am ideally suited to participate in the proposed project.

B. Positions and Honors.

Positions and Employment January 1986 - December 1986. Farm Manager/Director of Research, International Cattle Embryos, Inc. Mountain Home, AK. March 1987 - December 1991. Research Scientist, Granada Biosciences, College Station, TX July 1989 - April 1, 1992. Adjunct Professor, Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX. April 1, 1992 – August 31, 1998. Assistant Professor, Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX September 1, 1998 – April 2007. Associate Professor, Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX April 2007 – Present. Professor, Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX

C. Selected peer-reviewed publications (selected from > 70 peer-reviewed publications).

Most relevant to the current application 1. Shin T, Kraemer D, Pryor J, Liu L, Rugila J, Howe L, Buck S, Murphy K, Lyons L, Westhusin M. 2002. A cat cloned by nuclear transplantation. Nature 415:859. 2. Golding MC, Long CR, Carmell MA, Hannon GJ, Westhusin ME. 2006. Suppression of prion protein in livestock by RNA interference. Proc Natl Acad Sci. 14: 5285-5290. PCMID PMC1459347

3. Westhusin ME, Shin T, Templeton JW, Burghardt RC, Adams LG. 2007. Rescuing valuable genomes by animal cloning: a case for natural disease resistance. J. of Anim Sci. 85:138-142. 4. Tessanne K, Golding MC, Long C, Peoples M, Hannon G, Westhusin M. 2011. Production of transgenic calves expressing an effective shRNA targeting myostatin. Mol Reprod Dev. 3:176-85. PMCID: PMC3288734. 5. Cornetta K, Tessanne K, Long C, Yao J, Satterfield C, Westhusin M. 2013. Transgenic sheep generated by lentiviral vectors: safety and integration analysis of surrogates and their offspring. Transgenic Res. 4:737-745. PMCID: PMC3606283

Additional recent publications of importance to the field 1. Hill JR, Burghardt RC, Jones K, Long CR, Looney CR, Shin T, Spencer TE, Thompson JA, Winger QA, Westhusin ME. 2000. Evidence for placental abnormality as the major cause of mortality in first- trimester somatic cell cloned bovine fetuses. Biol Reprod. 6:1787-1794. 2. Hill JR, Winger QA, Long CR, Looney CR, Thompson JA, Westhusin ME. 2000. Develpmental rates of male bovine nuclear transfer embryos derived from adult and fetal cells. Biol Reprod. 5:1135-1140. 3. Hill JR, Burghardt RC, Jones K, Long CR, Looney CR, Shin T, Spencer TE, Thompson JA, Winger QA, Westhusin ME. 2000. Evidence for placental abnormality as the major cause of mortality in first- trimester somatic cell cloned bovine fetuses. Biol Reprod. 6:1787-1794. 4. Jones KL, Hill J, Shin TY, Liu L, Westhusin M. 2001. Hypomethylation of karyoplasts for bovine nuclear transplantation. Mol Reprod Dev. 2:208-213. 5. Betts DH, Bordignon V, Hill JR, Winger Q, Westhusin ME, Smith LC, King WA. 2001. Reprogramming of telomerase activity and rebuilding of telomere length in cloned cattle. Proc Natl Acad Sci. 98:1077- 1082. PCMID 2001 PMC14711. 6. Long CR, Walker SC, Tang RT, Westhusin ME. 2003. New commercial opportunities for advanced reproductive technologies in horses, wildlife, and companion animals. Therio 59:139-149. 7. Westhusin M, Hinrichs K, Choi YH, Shin T, Liu L, Kraemer D. 2003 Cloning Companion Animals (Horse, Cat, Dog). Cloning and Stem cells. 5:301-317. 8. Golding MC and Westhusin ME. 2003. Analysis of DNA (cytosine5) methyltransferase mRNA sequence and expression in bovine preimplantation embryos, fetal and adult tissues. 2003. Gene Expr Patterns 5:551-558. 9. Liu J, Westhusin M, Long C, Johnson G, Burghardt R, Kraemer D. 2010 Embryo production and possible species preservation by nuclear transfer of somatic cells isolated from bovine semen. Theriogenology 9:1629-1635. 10. Golding MC, Williamson GL, Stroud TK, Westhusin ME, Long CR. 2011. Examination of DNA methyltransferase expression in cloned embryos reveals an essential role for Dnmt1 in bovine development. Mol Reprod Dev. 5:306-317.

D. Research Support. (last 3 years)

Ongoing Research Support

1R24RR032683-01 Long (PI) 9/10/2011-7/31/2015 NIH- NCRR Inducible Tissue Specific Transgene Expression in Large Animal Biomedical Models The goal of this project is to produce a porcine model of human disease via tissue specific inducible expression of transgenes. Role: Co-PI

1RO1HD058969 NIH-NIHCD Westhusin (PI) 04/15/2010 - 02/28/2015 Functional Analysis of the Embryonic Epigenome in a Non-Rodent Model The major goals of this project are to characterize the expression and function of genes and proteins during early embryonic development in bovine embryos which are responsible for nuclear reprogramming and establishment of the epigenome e.g. DNA methyltransferases, Histone deacetylases and related proteins. Role: PI

Principal Investigator/Program Director (Last, first, middle): WILSON, Van G.

NAME Wilson, Wilson G. POSITION TITLE Professor and Vice Dean for Research and eRA COMMONS USER NAME Graduate Studies WILSONVAN EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) Georgia Institute of Technology, Atlanta, GA B.S. 1975 Applied Biology Case Western Reserve University, Cleveland, OH Ph.D. 1980 Microbiology State University of New York (SUNY) at Post- Stony Brook, NY doctoral 1980-1983 Virology

Please refer to the application instructions in order to complete sections A, B, and C of the Biographical Sketch.

A. Positions and Honors

Positions

1/1980-3/1983 Postdoctoral Research Fellow with Dr. Peter Tegtmeyer at SUNY-Stony Brook. Recipient of NIH post-doctoral training fellowship T32 CAO9121. 3/1983-1/1/20008 Assistant Professor to Professor in the Department of Medical Microbiology and Immunology (Renamed Microbial Pathogenesis and Immunology in 2013), College of Medicine, Texas A&M Health Science Center 4/1/2006-Present Vice Dean for Research and Graduate Studies, College of Medicine, Texas A&M Health Science Center

Honors

Summa Cum Laude (1975) Beta Beta Beta (1975) NIH Predoctoral Fellowship (1975-1980) NIH Post-doctoral Fellowship (1980-1982) NIH Young Investigator Travel Award (1989) Sigma Xi Outstanding New Member Award (1994) Merck/Association for Academic Minority Physicians Summer Research Fellowship to Support John A. Sandoval (1997) College of Medicine 2005 Distinguished Teaching Award (2006)

Editorial Boards: Virus Research

Journal Reviews: Antimicrobial Agents and Chemotherapy; BBA Gene Structure and Expression; Biochemical Journal; Biochemistry; BioTechniques; Cellular and Molecular Life Sciences; Cold Spring Harbor Protocols; EMBO Journal; EMBO Reports; Expert Reviews in Molecular Medicine; FEBS Letters, FEMS Microbiology Letters; Gene Therapy; Journal of Cellular Physiology; Journal of Clinical Microbiology; Journal of General Virology; Journal of Virology; Molecular Biology of the Cell; Molecular and Cellular Biochemistry, Molecular and Cellular Proteomics; Nature Reviews Molecular Cell Biology;

Principal Investigator/Program Director (Last, first, middle): WILSON, Van G.

Neuron; Nucleic Acids Research; Plasmid; PloS One; Proteomics; Radiation Research; Targeted Proteins Database; Virology; Virus Research

Grant Reviews: Arkansas Science & Technology Authority; Civilian Research & Development Foundation; Department of Veterans’ Affairs; National Research Council AID Program; Netherlands Genomic Initiative; NIH (Experimental Virology Study Section - Ad Hoc); NSF (Biochemical Approaches); Thomas and Kate Miller Jeffress Memorial Trust; The Wellcome Trust; UK Medical Research Council

B. Recent Publications

1. Rosas-Acosta, G., Deyrieux, A., Russell, W.K., Russell, D., and V.G. Wilson. 2005. A universal strategy for proteomic studies of SUMO and other ubiquitin-like modifiers. Molecular & Cellular Proteomics 4:56-72. PMID: 15576338; NIHMSID: 411341 2. Deyrieux, A., Rosas-Acosta, G., Ozbun, M. and V.G. Wilson. 2007. Sumoylation dynamics during keratinocyte differentiation. Journal of Cell Science 120: 125-136. PMID:17164289; NIHMSID:411353 3. Wu, Y.-C., Roark, A.A., Bian, X.-L., and V.G. Wilson. 2008. Modification of papillomavirus E2 proteins by the small ubiquitin-like modifier family members (SUMOs). Virology 379:329-338. PMCID: PMC2562504 4. Wilson, V.G. and P. Heaton. 2008. The Ubiquitin Proteolytic System - A Focus on SUMO. Expert Review of Proteomics 5:121-135. PMCID:PMC3467698 5. Wu, Y.-C., Bian, X.-L., Heaton, P.R., and V.G. Wilson. 2009. Host Sumoylation Level Influences Papillomavirus E2 Protein Stability. Virology 387:176-183. Chosen by Faculty of 1000. PMID:19251296; NIHMSID: 411346 6. Schmidt, C., Kim, D., Ippolito, G.C., Naqvi, H.R., Probst, L., Mathur, S., Rosas-Acosta, G., Wilson, V.G., Oldham, A.L., Poenie, M., Webb, C.F., and P.W. Tucker. 2009. Signaling of the BCR is regulated by a lipid rafts-localized transcription factor, Bright. EMBO J. 28:711-724. PMCID: PMC2666038 7. Nanos-Webb, A., Deyrieux, A., Bian, X.-L., Rosas-Acosta, G. and V.G. Wilson. 2010. Cloning the Human SUMO1 Promoter. Molecular Biology Reports 37:1155-1163. PMCID: PMC3083827 8. Bian, X.-L. and V.G. Wilson. 2010. Common Importin Alpha Specificity for Papillomavirus E2 Proteins. Virus Research 150:135-137. PMCID: PMC2859985 9. Heaton, P.R., Deyrieux, A.F., Bian, X-L., and V.G. Wilson. 2011. HPV E6 Proteins Target Ubc9, the SUMO Conjugating Enzyme. Virus Research 158:199-208. PMCID:PMC3103646 10. Heaton, P.R. Rosas-Acosta, G., and V.G. Wilson. 2012. Analysis of global sumoylation changes during keratinocyte differentiation. PLoS ONE 7(1): e30165. doi:10.1371/journal.pone.0030165. PMCID:PMC3264615 11. Tidwell, J.A., Schmidt, C., Heaton, P.R., Wilson, V.G., and P.W. Tucker. 2011. Characterization of a new ARID family transcription factor (Brightlike/ARID3C) that co-activates Bright/ARID31- mediated immunoglobulin gene transcription. Molecular Immunology 49:260-272. PMCID:PMC3205283 12. Wilson, V. G. 2011. Cell culture assay for transient replication of human and animal papillomaviruses. In Current Protocols in Microbiology. John Wiley & Sons. Eds. R. Coico, T. Kowalik, J.M. Quarles, B. Stevenson, and R.K. Taylor. 13. Wilson, V.G. 2012. SUMOylation at the Host-Pathogen Interface. Biomolecules 2, 203-227, 2012. PMCID: PMC3685863 14. Wilson, V.G. 2013. Growth and Differentiation of HaCaT Keratinocytes. In Epidermal Cells: Methods and Protocols (Methods in Molecular Biology series). Humana Press. Ed. K. Turksen.

The PI has an additional 67 peer-reviewed publications, 15 book chapters, and has edited 2 books on sumoylation.

PHS 398/2590 (Rev. 09/04, Reissued 4/2006) Page Continuation Format Page Program Director/Principal Investigator (Last, First, Middle): Womack, James E.

NAME POSITION TITLE Womack, James E. Distinguished Professor of Veterinary Pathobiology eRA COMMONS USER NAME (credential, e.g., agency login) and of Genetics JEWOMACK EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable)

Abilene Christian University B.S. 1964 Mathematics Ed.

Oregon State University Ph.D. 1968 Genetics

A. Personal Statement I am a geneticist with expertise in comparative genomics and the genetic basis for variation in susceptibility to infectious diseases. My laboratory is committed to the One Medicine concept and the study of genome evolution to understand similarities and differences in host response to pathogens in different species, including domestic animals, laboratory animals and humans. I am currently working on host response to Rift Valley Fever Virus in laboratory rats and have worked previously with mice as well as several livestock species including cattle and chickens.

B. Positions and Honors

Positions 1968-1971 Assistant Professor, Abilene Christian College 1971-1973 Associate Professor, Abilene Christian College 1973-1975 Visiting Scientist, The Jackson Laboratory 1975-1977 Staff Scientist, The Jackson Laboratory 1977-1983 Associate Professor, Texas A&M University 1983- Present Professor, Veterinary Pathology, Texas A&M University 1987-Present W.P. Luse Professor, Texas A&M University 1989-1996 Director, Center for Animal Genetics, Institute of Biosciences & Technology 1990-1993 Interim Asst. Department Head, Veterinary Pathobiology, Texas A&M University 2001-Present Distinguished Professor, Texas A&M University 2001-2010 Director, Center for Animal Biotechnology and Genomics, Texas A&M University

Honors Alumni Citation Award, Abilene Christian University, 1983 Faculty Distinguished Achievement Award for Research, Texas A&M University, 1987 Carrington Award for Research in Cell Biology, 1990 McMaster Fellow, CSIRO, Australia, 1990 CIBA Prize for Research in Animal Health, 1993 Outstanding Texas Geneticist, Texas Genetics Society, 1996 Fellow, American Association for the Advancement of Science, 1999 National Academy of Sciences, USA, 1999 Wolf Prize in Agriculture, 2001 Distinguished Service Award, Texas Genetics Society, 2006 Outstanding Alumnus of the Year, Abilene Christian University, 2006 Dean’s Impact Award, CVM, Texas A&M University, 2007 Bush Excellence Award for Faculty in International Research, Texas A&M University, 2008 Student-Led Award for Teaching Excellence, Texas A&M University System, 2009 Elected to Sports Hall of Fame, Abilene Christian University, 2010 Faculty Distinguished Achievement Award for Graduate Student Mentoring, Texas A&M University, 2010

PHS 398/2590 (Rev. 11/07) Page Biographical Sketch Format Page Program Director/Principal Investigator (Last, First, Middle): Womack, James E. C. Selected peer-reviewed publications (from total of 350+) White, S.N., Taylor, K.H., Abbey, C.A., and Gill, C.A., and Womack, J.E.: Haploytype variation in bovine Toll-like receptor 4 and computational predication of a positively selected ligand-binding domain. Proc. Natl. Acad. Sci. USA 100:10364-10369, 2003. Raudsepp T., Lee, E.-J., Kata, S.R. Brinkmeyer, C., Mickelson, J.R., Skow, L.C., Womack, J.E. and Chowdhary, B.P.: Exceptional conservation of horse-human gene order on X chromosome revealed by high-resolution radiation hybrid mapping. Proc. Natl. Acad. Sci. USA 2386-2391, 2004. Raudsepp, T., Santani, A., Wallner, B., Kata, S.R., Ren, C., Zhang, H.-B., Womack, J.E., Skow, L.C., and Chowdhary, B.P.: A detailed physical map of the horse Y chromosome. Proc. Natl. Acad. Sci. USA 101:9321-9326, 2004. Murphy, W.J,. Larkin D.M., Everts-van der Wind A., Gurque G., Tesler G., Auvil L., Beever J.E., Chowdhary B.P., Galibert F., Gatzke L., Hitte C., Meyers S.N., Mlan D., Ostrander E.A., Pape G., Parker G.H., Raudseep T., Rogatcheva M.B., Schook L.B., Skow L.C., Welge M., Womack J.E., O’Brien S.J., Pevzner P.A., and Lewin H.A.: Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309, 613-617, 2005. Everts-van der Wind , A., Larkin, D.M., Green, C.A., Elliott, J.S., Olmstead, C., Chiu, R., Schein, J.E., Marra, MA, Womack, J.E., Lewin, H.A.: A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution. Proc Natl Acad Sci USA;102:18526-18531, 2005. Womack, J.E.: Advances in livestock genomics: Opening the barn door. Genome Research 15:1699-1705, 2005. Sugimoto, M., Fujikawa A., Womack, J.E., Sugimoto Y.: Evidence that bovine forebrain embryonic zinc finger-like gene influences immune response associated with mastitis resistance. Proc Natl Acad Sci USA 103:6454-6459, 2006. Seabury, C.M., Cargill, E.J., and Womack, J.E.: Sequence variability and protein domain architectures for bovine Toll-like receptors 1, 5 and 10. Genomics 90:502-515, 2007. Bovine Genome Sequencing and Analysis Consortium: 315 authors including Womack, J.E.: The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324:522-528, 2009. Bovine HapMap Consortium. 90 authors including Womack, J.E.: Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324:528-532, 2009. Gillenwaters, E.N., Seabury, C.M., Elliott, J.S. and Womack, J.E.: Sequence analysis and polymorphism discovery in 4 members of the bovine cathelicidin gene family. J.Hered. 100:241-245, 2009. Seabury, C.M., Seabury, P.M., Decker, J.E., Schnabel, R.D. and Womack, J.E.: Diversity and evolution of 11 innate immune genes in Bos taurus taurus and Bos taurus indicus cattle. Proc Natl Acad Sci USA 107:151-156, 2010. Fisher, C.A., Bhattarai, E.K., Osterstock, J.B., Dowd, S.E., Seabury, P.M., Vikram, M., Whitlock, R.H., Schukken, Y.H., Schnabel, R.D., Taylor, J.F., Womack, J.E., Seabury, C.M.: Evolution of the bovine TLR gene family and member associations with Mycobacterium avium subspecies paratuberculosis infection. PLoS One.:6:e27744, 2011. Jones, B.C. and Womack, J. E.: Polymorphism and haplotype structure in River Buffalo (Bubalus bubalis) Toll-like receptor 5 (TLR5) coding sequence. Anim Biotechnol. 23: 132-140, 2012. Stafuzza, N.B., Greco, A.J., Grant, J.R., Abbey, C.A., Gill C.A., Raudsepp, T., Skow, L.C., Womack, J.E., Riggs, P.K., and Amaral, M.E:. A high-resolution radiation hybrid map of the river buffalo major histocompatibility complex and comparison with BoLA. Anim Genet.10:1111, 2012 Womack, J.E., Jang, H.J., and Lee, M.O.: Genomics of complex traits. Ann N Y Acad Sci. 1271:33-36. 2012 Lee, M.O., Kim, E.H., Jang, H.J., Park, M.N., Woo, H.J., Han, J.Y., Womack, J.E.: Effects of a single nucleotide polymorphism in the chicken NK-lysin gene on antimicrobial activity and cytotoxicity of cancer cells. Proc Natl Acad Sci U S A. 120:120:12087-12092,2012 Womack, J.E.: First steps: bovine genomics in historical perspective. Anim Genet.;43 1:2-8. 2012 Jang, H.J., Seo, H.W., Lee, B.R., Yoo, M., Womack, J.E., and Han, J.Y.: Gene Expression and DNA Methylation Status of Chicken Primordial Germ Cells. Mol Biotechnol. Jun 8, 2012. Stafuzza, N.B., Abbey, C.A., Gill, C.A., Womack, J.E., and Amaral, M.E.: Construction and preliminary characterization of a river buffalo bacterial artificial chromosome library. Genet Mol Res. 11(3):3013-9. 2012

PHS 398/2590 (Rev. 11/07) Page Continuation Format Page

NAME POSITION TITLE Zimmer, Warren E. Professor, Faculty of Genetics; and Toxicology, eRA COMMONS USER NAME Texas A&M University; Department of Medical wezimmer Physiology, Texas A&M HSC

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)

DEGREE INSTITUTION AND LOCATION YEAR(s) FIELD OF STUDY (if applicable) University of Houston, Houston, TX B.S. 1977 Biology/Biochem Baylor College of Medicine, Houston, TX Ph.D. 1985 Cell & Mol. Biology Vanderbilt University, Nashville, TN Postdoc 1985-1989 Cell & Mol. Biology

Personal Statement: My lab has for many years been involved in understanding how genes are regulated during normal development and how these regulatory paradigms change in disease states. Thus, we have extensive expertise in culturing cells and transfections to examine how they regulate SMC specific genes. We have developed numerous assays including nucleic acid isolation and analysis, protein analyses through western blotting and through immunofluorescence. Prior studies from our lab have indicated that normal development is enhanced by matrix components the cells are grown upon, both in vivo and in vitro. One segment of my lab is involved in the analysis of how cells capture information from outside influences and then translates this information into biochemical signals for the cell. From these studies we have also found a smooth muscle actin is expressed in the prostate epithelial cell, from our analyses we believe this may provide a new cellular footprint for Cancer diagnosis. These studies employ the making of mouse models as well as examining human cells for expression of the smooth muscle actin and how it is structurally different from that expressed in the smooth muscle cell. With these models we are beginning to ask questions of molecular mechanisms leading to cancer, as well as developing models to test the initiation events, including environmental influences that lead to prostate cancer.

I have been able to work with undergraduate students throughout my entire career. At South Alabama we had a robust NSF funded research experience to fund students each summer for a 10-week program to work in the lab. This provided an experience for both the student and the mentor. Since coming to TAMHSC I have had the pleasure to work with numerous undergrad students. I have had several undergrad students work for pay, and many work in the lab as an intro to research class. I have been mentor for 2 undergraduate students for Honors Theses. For the past 8 years I have been the Director of the College of Medicine Summer Research Program. Our program is structured so that we have 15-25 undergraduates each summer work in labs and attend lectures or talks on the conduct of biomedical research. This has been a richly rewarding experience and we have developed a great track record of having >75% of the students going on to a career in sciences. I know from our surveys that the students believe our experience helps them chose a career path, and they feel they are better able to understand concepts in their classes, both undergraduate and graduate levels. Thus, I know the advantages the R25 funding of EHS SURP will provide and I am more than highly supportive by having students under my mentor as well as becoming a director for the experience here at TAMHSC. I am especially excited to work with the directors and faculty of the newly formed environmental research center. They have the formula for success specifically with a strong commitment to teaching and increasing awareness of STEM based careers to undergraduate students, and I am happy to support and participate with their program.

Professional Position: 2005-present Professor, Interdepartmental Faculty of Toxicology, Texas A&M University 2004-present Professor, Faculty of Genetics, Texas A&M University 2004-present Professor, Texas A&M College of Medicine, Department of Medical Physiology 2005-2010 Co-Director, Texas A&M Genetic Engineered Mouse (GEM) Facility 2003-2004 Professor, University of South Alabama, Department of Cell Biology and Neuroscience 2000-2004 Co-Director, USA COM Transgenic Animal and ES Cell Core Laboratory.

1999-2003 Adjunct Associate Professor, Baylor College of Medicine, Department of Cell and Molecular Biology. 1995-2003 Associate Professor, University of South Alabama Medical School, Department of Cell Biology and Neuroscience. 1989-1995 Assistant Professor, University of South Alabama Medical School, Department of Structural and Cellular Biology.

Publications, (Selected listing from 90 publications): 1. Stanfel MN, Moses KA, Schwartz RJ, Zimmer WE. Regulation of organ development by the NKX- homeodomain factors: an NKX code. Cell Mol Biol (Noisy-le-grand). 2005 Oct 24;Suppl 51:OL785-99. PMID 16405855 2. Stanfel MN, Moses KA, Carson JA, Zimmer DB, DeMayo F, Schwartz RJ, Zimmer WE. Expression of an Nkx3.1-CRE gene using ROSA26 reporter mice. Genesis. 2006 Nov;44(11):550-5. PMID 17078065 3. Akintola AD, Crislip ZL, Catania JM, Chen G, Zimmer WE, Burghardt RC, Parrish AR. Promoter methylation is associated with the age-dependent loss of N-cadherin in the rat kidney. Am J Physiol Renal Physiol. 2008 Jan;294(1):F170-6. PMID 17959753; http://ajprenal.physiology.org/cgi/content/full/294/1/F170 4. Zhang Y, Fillmore RA, Zimmer WE. Structural and functional analysis of domains mediating interaction between the bagpipe homologue, Nkx3.1 and serum response factor. Exp Biol Med (Maywood). 2008 Mar;233(3):297-309. doi: 10.3181/0709-RM-236. PMID 18296735; http://ebm.rsmjournals.com/cgi/content/full/233/3/297?maxtoshow=&hits=10&RESULTFORMAT=1&a ndorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&so rtspec=relevance&firstpage=297&resourcetype=HWCIT 5. Young JL, Zimmer WE, Dean DA. Smooth muscle-specific gene delivery in the vasculature based on restriction of DNA nuclear import. Exp Biol Med (Maywood). 2008 Jul;233(7):840-8. doi: 10.3181/0712-RM-331. PMID 18445769; http://ebm.rsmjournals.com/cgi/content/full/233/7/840?maxtoshow=&hits=10&RESULTFORMAT=1&a ndorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&so rtspec=relevance&firstpage=840&resourcetype=HWCIT 6. Yang J, Park Y, Zhang H, Gao X, Wilson E, Zimmer WE, Abbott L, Zhang C. Role of MCP-1 in tumor necrosis factor-alpha-induced endothelial dysfunction in type 2 diabetic mice. Am J Physiol Heart Circ Physiol. 2009 Oct;297(4):H1208-16. doi: 10.1152/ajpheart.00396.2009. PMID: 19666844; PMCID: PMC2770760 7. Verzi MP, Stanfel MN, Moses KA, Kim BM, Zhang Y, Schwartz RJ, Shivdasani RA, Zimmer WE. Role of the homeodomain transcription factor Bapx1 in mouse distal stomach development. Gastroenterology. 2009 May;136(5):1701-10. Doi: 10.1053/j.gastro.2009.01.009. PMID 19208343; PMCID: PMC2955323 8. Sun Q, Taurin S, Sethakorn N, Long X, Imamura M, Wang DZ, Zimmer WE, Dulin NO, Miano JM. Myocardin-dependent activation of the CArG box-rich smooth muscle gamma-actin gene: preferential utilization of a single CArG element through functional association with the Nkx3.1 homeodomain protein. J Biol Chem. 2009 Nov 20;284(47):32582-90. doi: 10.1074/jbc.M109.033910. PMID 19797053; PMCID: PMC2781672 9. Kojima, C., Zhang, Y., and Zimmer, W.E. Intergenic DNA elements regulate androgen-dependent expression of the murine Nkx3.1 gene. Gene Expression, 15: 89-102, 2010 PMID: 21526719 10. Landsman, L., Nijagal, A., Whitechurch, T.J., Vander Laan, R.L., Zimmer, W.E., MacKenzie, T.C., and Hebrok, M. Pancreatic mesenchyme regulates epithelial organogenesis throughout development. PLos Biol: 9, e1001143, 2011PMID: 21909240 11. Papke, C.L., Cao, J., Kwartler, C.S., Villamizar, C., Byanova, K.L., Lim, S-M., Sreenivasappa, H., Fischer, G., Pham, J., Rees, M., Wang, M., Chaponnier, C., Gabbiani, G., Khakoo, A.Y., Chandra, J., Trache, A., Zimmer, W.E., Milewicz, D.M. Loss of smooth muscle a-actin increases smooth muscle cell proliferation through altered focal adhesions, cellular relocation of p53 and increased expression and activation of platelet-derived growth factor –b. Human Mol Genetics, 22:3123-37, 2013 PMID: 23591991