Undergraduate Research in Microbial Genome Annotation
Part of the vision of the JGI’s Education Program is to have colleges and universities across the country “adopt” bacterial genomes, such as those sequenced as part of the GEBA project, for analysis. The organism ideally will provide a unifying thread for concepts across the life sciences curriculum. For example, students can analyze the six possible open reading frames for a given fragment of DNA, compare the results of various gene calling algorithms, assign function by sequence homology, and consider if there is evidence for operon structure while learning these concepts in introductory molecular biology courses.
The plan is to use annotation to teach the curricular standards in new ways. In biochemistry courses, students can examine and annotate fundamental metabolic pathways, whereas in microbiology, pathways, structures, and systems characteristic of the organism’s lifestyle will be traced. Novel genes and pathways can be discovered by examining clusters of hypothetical proteins in a comparative genomics context (that will include phylogenetic and ecological considerations), perhaps in an undergraduate course dedicated to bioinformatics. All bacterial genomes are full of novelties; moreover, the GEBA organisms are relatively unusual and from poorly investigated parts of the tree of life, so the likelihood of exciting discoveries and interesting variations on the classical pathways is high. The JGI believes that involving students in annotation in a calibrated, stepwise way will provide a new research-based approach to teaching fundamental concepts in the life science curriculum.
Faculty advisors: front row (left to right), Zhaohui Xu (Bowling Green State University), Sharyn Freyermuth (University of Missouri-Columbia), Kelynne Reed (Austin College), Jayna L. Ditty (The University of St. Thomas), Christopher Kvaal (St. Cloud State University), Cheryl Bailey (University of Nebraska), Sabine Heinhorst (University of Southern Mississippi), Kathleen Scott (University of South Florida), Cheryl Kerfeld (DOE JGI). Back row, Robert Britton (Michigan State University), Erin Sanders-Lorenz (University of California, Los Angeles), Rick Johns (Northern Illinois University), A. Malcolm Campbell (Davidson College), Brad Goodner (Hiram College), Stuart Gordon (Hiram College), Edwin Kim (DOE JGI).
In conjunction with the pilot phase of GEBA sequencing, the JGI has launched its pilot project for undergraduate educators. In October 2007, faculty from 12 colleges and universities across the US met at the JGI to consider how annotation could be incorporated in their courses, to discuss the challenges inherent in getting faculty from multiple courses to collaborate, and to discuss the tools for annotation, the IMG Annotation Concepts Tool (IMG/ACT). Collectively the faculty will use their spring 08 courses to annotate the genome of a chemolithoautotrophic bacterium and will reconvene at the JGI in June 2008 to discuss the experience and write up their results.
The long-term goal of the JGI’s Education program is to build on the annotation with bacterial characterization and functional genomics, including both insertional mutagenesis and protein overexpression with subsequent biochemical and biophysical characterization.
Timeline to Participate
- Apply to be part of the 2009-2010 team by November 1, 2008 (download the application)
- After acceptance, attend the workshop at the JGI (January 2009)
- Implement in 2009-2010 academic year
News Reports
College Students Engage in Research in Pilot Program (NSTA News Digest)
Program targets undergrads to make an early start on science (Nature)
UCLA Science Students in Pilot Federal Program Will Conduct Original Research in Laboratory Classes (UCLA)
