Undergraduate Research in Microbial Genome Annotation
The DOE Joint Genome Institute’s Education Program is providing opportunities for colleges and universities across the country to “adopt” bacterial genomes, such as those sequenced as part of the GEBA project, for analysis. This “Adopt a GEBA Genome” Education Program makes available a selection of recently sequenced genomes for use in undergraduate courses. The organisms ideally provide a unifying thread for concepts across the life sciences curriculum. For example, students can analyze the six open reading frames for a given fragment of DNA, compare the results of various gene calling algorithms, assign function by sequence homology, and use gene ortholog neighborhoods for comparative genomics and annotate biochemical pathways, while learning the underlying biological concepts in a variety of science courses.
Go to the "Adopt a GEBA Genome for Education" page to view information on the GEBA genomes currently available for adoption.
The goal of JGI’s Microbial Genome Annotation program is to support the use of annotation to teach the curricular standards in new ways. For example, 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 profiling 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.
2009-2010 Faculty Collaborators
The 2009-2010 Faculty Collaborators are among the first to participate in the program and to use the Integrated Microbial Genomes Annotation Collaboration Tool (IMG-ACT). The Faculty Collaborators,from institutions across the United States, came to the JGI to meet fellow participants in January 2009. These representatives from higher education institutions will adopt GEBA genomes for use in the classroom.
2009-2010 Cohort: front row (left to right): Seth Axen (DOE JGI), Edwin Kim (DOE JGI), Wendi David (Texas State University), Wei-Jen Chang (Hamilton College), Rachell Booth (Texas State University), Wendy Lacy (Saint Mary’s College), Keith Garrison (Saint Mary’s College), Ronald Walter (Texas State University), Vidya Chandrasekaran (Saint Mary’s College), Jocelyne DiRuggiero (Johns Hopkins University), Jon Schnorr (Pacific University), Lisa Sardinia (Pacific University), Matthew Domek (Weber State University), Kimberly Murphy (Waldorf College), Tim Beagley (Salt Lake Community College), Barbara May (College of Saint Benedict, Saint John’s University), Craig Oberg (Weber State University), Jean Cardinale (Alfred University), Charles Bland (Mississippi Valley State University); back row (left to right): Kirk Brown (Tracy Unified School District), Leila Hornick (DOE JGI), Abigail Newsome (Mississippi Valley State University), Brad Goodner (Hiram College), Michelle Zwolinski (Weber State University), Chloe Cai (Weber State University), Allan Hansell (Saint Mary’s College), Carin Zimmerman (City College of San Francisco), Ying-Tsu Loh (City College of San Francisco), Robert Del Vecchio (City College of San Francisco), Heather Wiatrowski (Clark University), Lori Scott (Augustana College), Angela Ghrist (Eastern Iowa Community College), Ann Hirsch (UCLA), Cheryl Kerfeld (DOE JGI), Satish Bhalla (Johnson C. Smith University), Jennifer Galovich (College of Saint Benedict, Saint John’s University), Michael McCormick (Hamilton College), Lorraine Olendzenski (Saint Mary’s College)
2008-2009 IMG-ACT Development Team
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 worked closely with undergraduate educators in a pilot program during the 2008-2009 academic year. 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, 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 2010-2011 team by Monday, November 2, 2009 (download the application)
- After acceptance, attend the workshop at the JGI (January 2010)
- Implement in 2010-2011 academic year
Not Sure You're Ready?
Many faculty find the ASM-JGI Bioinformatics Institutes, http://www.facultyprograms.org/ a useful introduction to integrating genomics and bioinformatics into the curriculum.
News Reports
Iowa college biology students to join national genome project (Waldorf College News)
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)
