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Workshop Notebook GCAT WORKSHOPS 2009 NSF SUPPORTED DNA MICROARRAY WORKSHOPS FOR HISTORICALLY BLACK COLLEGES AND UNIVERSITIES, HISPANIC-SERVING INSTITUTIONS AND TRIBAL COLLEGES FACULTY JULY 5 - July 11, 2009 HOST INSTITUTION: MOREHOUSE COLLEGE BIOLOGY DEPARTMENT; ATLANTA, GA INSTRUCTORS Consuelo Alvarez, Malcolm Campbell, Todd Eckdahl, Edison Fowlks, Charles Hauser, Laurie Heyer, and Anne Rosenwald Genome Consortium for Active Teaching (GCAT) NSF GRANT DBI-0520908 Awarded to Hampton University PI: Edison R. Fowlks; Co-PIs: Mary Lee Ledbetter and Anne Rosenwald and NSF GRANT DBI-0520908 Awarded to Davidson College PI: Malcolm Campbell; Co-PIs: Laurie Heyer and Todd Eckdahl By the DIRECTORATE FOR BIOLOGICAL SCIENCES NATIONAL SCIENCE FOUNDATION DR. SALLY O’CONNOR, MANAGERING PROGRAM OFFICER NSF-SPONSORED GCAT DNA MICROARRAY SUMMER WORKSHOPS FOR UNDERGRADUATE HBCU, HSI AND TRIBAL COLLEGE FACULTY TAB I. Origin of this NSF Workshop and History of GCAT 1 II. Workshop Participants and Instructors 2 III. Workshop Schedule of Dry and Wet Lab Activities 3 IV. Assessment Material 4 A. Pre-Test B. Post-Test V. Wet Lab Activities 6 A. Culturing Yeast B. Isolating RNA C. 3DNA Protocol VI. Dry Lab Activities 7 A. Magic Tool User Guide B. Magic Tool: Exploring Diauxic Shift Microarray Data C. Exploring Correlations VII. Sampling of Microarray Articles 7 VIII. Notes, Special Instructions & Directions 8 ORIGIN OF THIS NSF WORKSHOP At a curriculum gathering during summer of 2004, Drs. Fowlks and Campbell presented their perspectives on the undergraduate educational implications of the NIH Roadmap. Fowlks addressed curricular changes in undergraduate biology, as well as recruitment and training for underrepresented populations. Campbell provided an overview of activities by GCAT, a non-profit educational consortium, to bring functional genomics methods into undergraduate courses and independent student research. After the presentations, an invited representative of NSF encouraged Dr. Fowlks and Dr. Campbell to submit a proposal that would provide a microarray workshop opportunity for undergraduate faculty at minority serving institutions (MSIs). The 2005 GCAT workshop at Morehouse College was an overwhelming success based on participant and instructor evaluations (see Outcomes of Previous Workshops below), as well as comments from two NSF Program Officers (POs) who attended part of the workshop. These POs encouraged Fowlks, Campbell, and their GCAT colleagues to submit a three-year proposal for DNA microarray workshops that would have a significant impact on the introduction of genomics in undergraduate curricula, especially in MSIs. On the advice of the POs, this collaborative proposal brings Hampton University as the lead institution with Davidson College as the collaborative institution. Fowlks and Heyer will co-chair the advisory board which will focus on participant recruitment (emphasizing faculty from MSIs). Fowlks also will oversee workshop housing, transportation, and on-site facilities logistics while Campbell will focus on wet- and dry-lab curriculum, recruitment of instructors, and organization of the workshop technical aspects. As described in the budget justification, the budget will be divided according to these two functional roles. History of Genomics and GCAT Genomics first grabbed the headlines with the Human Genome Project. This monumental task was the beginning of a long process to understand how humans work. The production of any genome sequence is analogous to creating a periodic table for the chemical elements – a great start but ultimately only a parts list, failing to explain how the parts interact. Experimental data are needed to illuminate how all the genes work synergistically. One way to measure every gene’s activity simultaneously is to use DNA microarrays. DNA microarrays are produced by printing one spot of DNA for each gene onto a specially coated glass microscope slide. Each spot contains a unique DNA sequence specific for only one gene. For example, a yeast DNA microarray is composed of ~ 6,500 spots – one for each of its 6,500 genes. The investigator isolates the mRNAs and couples one color fluorescent dye to the mRNAs for one growth condition. In parallel, the investigator isolates and labels with a different color the mRNAs isolated from cells grown under a different condition. The two populations of differently colored mRNAs are mixed and allowed to base pair with the appropriate genes among the 6,500 spots on the microarray. The fluorescence for each color on every spot is quantified to produce a ratio of mRNA binding from the two growth conditions. From this list of 6,500 ratios, the investigator can determine which genes are activated and which ones are repressed in the two growth conditions (see an animated version here: <www.bio.davidson.edu/Courses/genomics/chip/chip.html>). Measuring the genomic transcriptional response to different growth conditions is a critical step in understanding how each gene contributes to the genome’s combinatorial functional capacity. GCAT was conceived in December 1998 by Dr. A. Malcolm Campbell (Davidson College) and Dr. Mary Lee Ledbetter (College of the Holy Cross), who were inspired by Dr. Patrick Brown’s talk at the 39th Annual meeting of the American Society of Cell Biology regarding his pioneering work on DNA microarrays. DNA microarray technology has revolutionized the investigation of gene expression at the genomic level, and holds great promise for understanding the complex, systems-level regulation in many species. Many job opportunities in academia and industry are available for trained college graduates. Furthermore, the best graduate programs are looking for students with practical experience. However, microarray technology is inaccessible to many undergraduates because of limitations in funding and faculty expertise. GCAT’s mission is to make such experiments accessible to all undergraduates and we are succeeding: since 2000, about 5,000 undergraduates have performed experiments with DNA microarrays obtained through GCAT and analyzed their results with free software developed by co-PI Laurie Heyer and her undergraduate students (www.bio.davidson.edu/MAGIC). GCAT makes microarray experiments affordable through cost-sharing, provides a clearinghouse of information, raw data and analyzed results for use in teaching genomics, and represents a network of mutually supportive teachers using functional genomics. WORKSHOP #1 PARTICIPANTS Name Institution Email Address Dixon, Emily St. Lawrence Univ. [email protected] Essig, David Geneva College [email protected] Estevez, Ana St. Lawrence Univ. [email protected] Ghosh, Sibdas Dominican Univ, CA [email protected] Hammonds-Odie, Latanya Dillard Univ. [email protected] Harrison, Benjamin College U of Alaska [email protected] Holmes, Keinya Hampton Univ. [email protected] Horst, Cynthia Carroll College [email protected] Johnson-Brousseau, Sheila Dominican Univ, CA [email protected] Lodhi, Muhammad Fayetteville St. Uiv. [email protected] Louie, Maggie Dominican Univ, CA [email protected] Lu, Yuefeng Tougaloo College [email protected] McCray, Joseph Morehouse [email protected] Nagengast, Alexis Widener [email protected] Osgood, Robert Rochester Inst Tech [email protected] Peng, Chuang Morehouse College [email protected] Reyna, Nathan Ouachita Baptist U. [email protected] Santisteban, Maria UNC-Pembroke [email protected] Vanderpuye, Oluseyi Albany State Univ. [email protected] Woriax, Velinda UNC-Pembroke [email protected] Carson-Newman Wright, Stephen Coll [email protected] O WORKSHOP #2 PARTICIPANTS Name • Institution • Email Address Bayline, Ronald Wash. & Jeff. College [email protected] Bellin, Robert Coll. Of the Holy Cross [email protected] DeBerry, Candy Wash. & Jeff. College [email protected] Dwyer, Kathleen Univ. Scranton [email protected] Fahy, Michael Chapman Univ. [email protected] Fuselier, Linda MN St. Univ. [email protected] Gordon, Ethel NC A&T Univ. [email protected] Hammond, Charlotte Quinnipiac Univ [email protected] Holgado, Andrea SW OK State Univ. [email protected] Hum-Musser, Sue Western Ill. Univ. [email protected] Jenik, Pablo Franklin and Marshall [email protected] Lanni, Jennifer Wheaton College MA [email protected] LaRiviere, Frederick Washington and Lee U. [email protected] Lee, Alice Wash. & Jeff. College [email protected] Mukhtar, Hamid NC A&T Univ [email protected] Pavao, Maura Worcester State Coll [email protected] Rhode, Jennifer UNC-Ashville [email protected] Roig-Lopez, Jose Universidad del Este (UNE) [email protected] Rowland-Goldsmith, Melissa Chapman Univ. [email protected] Schisa, Jennifer Central Michigan Univ. [email protected] Singh, Minati Univ. Iowa [email protected] [email protected] Villafane, Robert Alabama State Univ [email protected] Ward, Gregg Winston-Salem St. Univ. [email protected] Watson, Fiona Washington and Lee Univ. [email protected] DNA MICROARRAY WORKSHOP FACULTY SUMMER 2009 A. Malcolm Campbell, Ph.D.; Professor; Department of Biology; Davidson College; Davidson, NC 28036; Email: [email protected] Todd T. Eckdahl, Ph.D.; Professor; Department of Biology; Missouri Western State University; St. Joseph, MO 64507-2294;Email: [email protected] Laurie J. Heyer, Ph.D.; Associate Professor; Department of Mathematics; Davidson College; Davidson, N.C. 28035-6959; Email: [email protected] Ann G. Rosenwald, Ph.D.; Assistant Professor; Department
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