Current Research

Utpal Banerjee's project provides opportunities for course-based research to large numbers of early-stage undergraduates and high school students through UCLA's Undergraduate Research Consortium in Functional Genomics. In a separate course recently developed as part of the program, students "deconstruct" research presentations in a guided process that helps them learn about the concepts and techniques of experimental science.

Our 2002 and 2006 HHMI professor grants supported projects that provided inquiry-based science instruction to more than 1,000 freshmen and sophomores at the University of California, Los Angeles (UCLA). Roughly half participated in our flagship program, the Undergraduate Research Consortium in Functional Genomics (URCFG), in which students most with minimal preparation in the life sciences—conducted original, publishable research on genes and development of the fruit fly Drosophila melanogaster. The URCFG has three components. The first is an introductory course that provides research training for up to 30 students in each 10-week quarter and includes complementary instruction in genetics, bioinformatics, laboratory ethics, and science writing. The second component is an advanced program in which selected students from the introductory course participate in graduate-level research for multiple years. The third component is a summer program that offers an introductory research-training experience to talented high school students and undergraduates from UCLA and other universities.

At the end of each quarter, selected URCFG students can move on to do more extensive research either in our advanced URCFG program or in other laboratories on campus through the recently created minor in biomedical research. The students work on projects emanating from the introductory program. The goal is that each student eventually will author at least one scientific manuscript.

Collectively, these students have completed two major research projects. During the 2002 grant cycle, they conducted a genome-wide screen for genes important in Drosophila eye development and analyzed more than 2,100 lethal mutations for eye defects. The students created 3,000 independent strains of Drosophila and conducted 150,000 genetic crosses. The Drosophila strains created by the students are curated at the Kyoto Drosophila Genomic Resource Center and are available to the entire research community via the internet. This project resulted in articles published in Plos Biology and Genetics, with 134 and 264 undergraduate authors respectively.

For the 2006 grant cycle, we used a novel cell-lineage tracing system, G-TRACE, to permanently mark cells that express a gene of interest at any point during development. This system was developed by students from the advanced program and is described in a paper in Nature Methods. Students from the introductory and summer programs have used G-TRACE to determine expression patterns for more than 700 Drosophila genes and trace the lineage cells expressing these genes during development of the brain, wing, eye and blood. They have collected over 30,000 digital microscopic images and documented their results in a database that will be made publicly available. When published, this work will have over 250 URCFG student authors.

In addition to our undergraduate program, an 8-week summer program has trained a small number of local high school students. These students work on the G-TRACE project alongside undergraduates from the Los Angeles area who attend other institutions and have come home for the summer. Future activities will focus on expanding the summer program through interaction with other local high schools and additional coordination with UCLA’s minority outreach program.

We would like to further increase the number of students who receive research-based instruction. With our new grant, we will expand a new teaching method that we call “research deconstruction.” Students are taught to analyze real data from current research that is presented to them in the form of a high-level seminar by invited faculty members. The seminar presentation is videotaped and made available on a classroom Web site for the students to review. Not surprisingly, the presentation is initially too complex for most students to comprehend. But during the 10 hours of classroom time, a course instructor dissects the presentation, using segments from the videotape. A remarkable transformation occurs during this period, as students identify questions and hypotheses from the seminar, explore the experimental approaches used, and analyze the data. They begin to see the logic of the research and experience the excitement of discovery as the implications of each experiment become clear.

Over the past three years, we have used this method to provide research-based instruction to over 500 undergraduates, most of whom were first- and second-year students who had minimal preparation in the life sciences. Like the URCFG, the research deconstruction course has allowed us to identify students with promise and provide them with an opportunity to do more extensive independent research. Moreover, external assessments indicate that students from the URCFG and research deconstruction courses report comparable strong gains in important areas, such as analyzing data, interpreting results, and understanding the role of evidence in the construction of knowledge

This strategy can be adapted to a variety of research topics and is scalable to class sizes of over 100 students, making it an approach that can be adopted by a variety of institutions. We are excited by the potential that research deconstruction has to teach the logic of scientific inquiry to large numbers of students. To facilitate adoption by other institutions, we intend to create a Web-based repository of seminars, deconstruction classes, and resources for educators interested in developing similar courses. We will also develop general education courses built around the research deconstruction concept in an effort to offer research-based instruction to a broader segment of the student population.

Related HHMI Project Publications

Clark, I. E., et al. 2009. "Deconstructing' Scientific Research: —A Practical and Scalable Pedagogical Tool to Provide Evidence-Based Science Instruction." PLoS Biology 7(12): e1000264.

Evans, C.J., et al. 2009. "G-TRACE: Rapid Ga14-Based Cell Lineage Analysis in Drosophila". Nature Methods 6:603-605.

Call, G.B., et al. 2007. "Genome-wide Clonal Analysis of Lethal Mutations in the Drosophila melanogaster Eye: Comparison of the X Chromosome and Autosomes." Genetics 177: 689-697.

Liao, T.S., et al. 2006. "An Efficient Genetic Screen in Drosophila to Identify Nuclear-Encoded Genes with Mitochondrial Function." Genetics 174:525-33.

Chen, J., et al. 2009. "Discovery-Based Science Education: Functional Genomic Dissection in Drosophila by Undergraduate Researchers." PLoS Biology 3:e59.

Research Summary

My research focuses on the fields of Drosophila genetics and developmental biology. Our lab has recently reported that hematopoietic stem cells are maintained within a microenvironment and that the “stemness” of these cells is maintained through the combined action of a Niche Signal, generated by Hedgehog (Hh), a local signal Wingless/Wnt signal and a reverse signal from the differentiating cells. Myeloid cells are ideal for the study of response to many kinds of stresses. Hypoxia-related factors and free radicals (ROS) play a role both in hematopoietic development and in stress response. Similarly, blood cells use NF-kB derived inflammatory response to injury at distant sites. Developmental mechanisms are reused for stress, injury and inflammatory responses by the myeloid systems. In the past, our laboratory has identified components of signal transduction pathways that participate in oncogenesis. We have also studied the role of the mitochondrion in controlling cell-cycle. Currently we study transition of metabolic states during Drosophila development.

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