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True Functional Genomics as an Undergraduate Research Experience
Summary: As a researcher in the fields of Drosophila genetics and developmental biology, Utpal Banerjee studies signal transduction and transcriptional control of neural and hematopoietic development. Dr. Banerjee's HHMI project uses functional genomics to train undergraduates in all aspects of doing research and to enable them to produce high-quality data that have meaningful scientific impact. Using the Drosophila eye, undergraduates work in Dr. Banerjee's lab to examine patterns of gene expression and trace the lineage of cells during development.
HHMI PROJECT SUMMARY
Original Project (2002 grant)
The initial grant supported the development of the University of California–Los Angeles (UCLA) Undergraduate Research Consortium for Functional Genomics (URCFG) program, in which undergraduates are involved in making somatic clones of loss-of-function mutations in the Drosophila eye and creating a database of such eye mutations. The program offers a progression of courses that allows undergraduates to perform increasingly more independent research and collectively produce high-quality data that contribute to the field. An important aspect of the program is training students to train others. The more experienced undergraduates help the novices and postdoctoral instructors spend full time helping undergraduates on their research projects.
The first component of the program is an introductory genetics course in which about 30 students are newly enrolled each semester. Beginning with their first exposure to Drosophila, students quickly become experts at determining and documenting eye phenotypes by scanning light and electron microscopy for all lethal mutants and developing a cross-referenced database of their results. The course has lecture, lab, and computer lab components. Lectures, delivered both in a classroom setting and inside the laboratory, emphasize basic concepts of genetics and genomics, and also focus on central concepts—such as ethics, grant writing, and bioinformatics—that pertain to scientific research. At the end of the quarter, students interested in pursuing more research are placed into other campus labs or accepted into the advanced URCFG program.
The advanced program in genetics allows selected students to participate in a series of upper-level courses for multiple years. Students work in teams and carry on graduate-level research, analyzing genes and mutations with all the tools available for Drosophila molecular genetics. The idea is to develop the research experience of the undergraduates to the fullest extent possible, under the full-time supervision of the "teaching postdocs." The ultimate goal is for every student involved to be an author on a research article. Six of these students were coauthors on a 2006 publication in Genetics1.
During the first three years of the project, the undergraduates performed 120,000 Drosophila crosses; the resulting stocks were distributed to laboratories in the United States. The students identified 1,375 mutant phenotypes, which were the subject of an article in the February 2005 issue of PLos Biology2 One hundred-forty undergraduates were listed as authors on this publication. Their work provided the first genomewide estimate of essential genes in Drosophila that also function in eye development.
Project Update (2006 grant)
A new functional genomics project is training introductory biosciences students in modern research techniques. We have obtained over 2,000 Gal4 lines, and using an FRT/Flp-based method, we permanently mark cells in which an individual line expresses Gal4. We then trace the lineage of cells derived from this marking. This is being done in brain and blood tissues for all 2,000 genes to develop the first comprehensive genome-based comparison of gene expression pattern with lineage in these two understudied tissues in Drosophila. This database of lineage data will be made accessible to all investigators. We anticipate training 360 students, mostly freshmen and sophomores, in this program. The goal is to either help prepare students for a research career or, if they plan to pursue other careers, provide them with an appreciation of the importance of research.
Students interested in a research career have the option to pursue a new minor in biomedical research. This minor is designed to help students become involved in laboratory research at an early point in their college careers. Students are placed in a laboratory in the college or medical school for a minimum of four quarters of research, which will allow them enough time to complete a significant piece of work before graduation. In addition to research, students take courses in analysis of research literature, oral presentation of research data, science policy and ethics, and history or philosophy of science. After completing the minor, students should be well trained in both the process of scientific research and the social issues facing science today.
RESEARCH SUMMARY
My research focuses on the fields of Drosophila genetics and developmental biology. My current research interests are in signal transduction and transcriptional control of neural and hematopoietic development. Previous work from my laboratory identified the son of sevenless (sos) gene that participates in all receptor tyrosine kinase signaling pathways. Currently, my laboratory group is identifying novel means by which different signal transduction cascades combine to distinguish between neural and nonneural cell types in the Drosophila eye. We have also made critical discoveries in identifying transcription factors and signaling components that are responsible for hematopoiesis in Drosophila. Using Drosophila as a genetic model, we hope to identify basic molecular strategies that are conserved in development across species and that are disrupted in human cancers. As a new venture, we are using zebrafish as a model system to understand hematopoiesis and oncogenesis.
1. Liao, T.S., G.B. Call, P. Guptan, A. Cespedes, J. Mashall, K. Yackle, E. Owusu-Ansah, S. Mandal, Q.A. Fang, G.L. Goodstein, W. Kim, and U. Banerjee. "An Efficient Genetic Screen in Drosophila to Identify Nuclear-Encoded Genes with Mitochondrial Function." Genetics 174 (1):525-33. 2006.
2. Chen J., G.B Call, E. Beyer, C. Bui, A. Cespedes, et al. "Discovery-Based Science Education: Functional Genomic Dissection in Drosophila by Undergraduate Researchers." PLoS Biol 3 (2): e59, 2005.
Last updated March 2007
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