Undergraduate Research in Microbial Genome Analysis
The DOE Joint Genome Institute’s Education Program is providing opportunities for colleges and universities across the country to “interpret” bacterial genomes, such as those sequenced as part of the GEBA project, for analysis. This “Interpret a GEBA Genome” Education Program makes available a selection of recently sequenced genomes for use in undergraduate courses. Genomic analysis of these organisms can 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, use gene ortholog neighborhoods for comparative genomics, and annotate biochemical pathways, while learning the underlying biological concepts in a variety of science courses.
Essentially, the goal of JGI’s Microbial Genome Analysis 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 characteristics 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.
Go to the "Interpret a GEBA Genome for Education" page to view information on the GEBA genomes currently available for interpretation.
The long-term goal of the JGI’s Education program is to build on genome analysis and gene 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 2013-2014 team (download the application). Application Deadline is not yet set.
- After acceptance, attend the workshop at the JGI (2013 workshop date has not yet been set).
- Implement in 2013-2014 academic year.
Need Travel Support?
A limited number of participants can be supported by the Microbial Genome Annotation Network (MGAN). MGAN is funded by the National Science Foundation (NSF).
Not Sure You're Ready?
The JGI will be holding the JGI Genomics and Bioinformatics for Undergraduate Educators Workshop in conjunction with the JGI User Meeting. The workshop will take place March 23-26, 2013 at the JGI. Registration information coming September 2012.
Participants
2012-2013 Faculty Collaborators
The 2012-2013 cohort came to the JGI for training in the use of the Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT) in January of 2012. From the spring term of 2012 to the spring term of 2013, these faculty representatives from around the country will be implementing genome interpretation procedures into their course curriculum.
2012-2013 Cohort: Kristin Hobson (Western Michigan University), Sami Khuri (San Jose State University), Natalia Khuri (San Jose State University), Darlene Walro (Walsh University), Vicki Geiser (Mount Marty College), Laura Corey (Illinois College), Derrick Brazill (Hunter College of the City University of New York), Leslie Gregg-Jolly (Grinnell College), Sabine Reich? (San Jose State University), Cheryl Kerfeld (DOE JGI), Martina Bremer (San Jose State University), Shannon Hinsa-Leasure (Grinnell College), Christopher Kvaal (St. Cloud State University), Paul Feinstein (Hunter College of the City University of New York), Weigang Qiu (Hunter College of the City University of New York), Cleber Ouverney (San Jose State University), Amy Knobbe (Bryan LGH College of Health Sciences), Brook Milligan (New Mexico State University), Seth Axen (DOE JGI), Tom Freeland (Walsh University), Clare Congdon (University of Southern Maine), Jose de la Torre (San Francisco State University), Bryan Thines (Claremont McKenna, Pitzer, and Scripps Colleges), Lisa Moore (University of Southern Maine), Joseph Romeo (San Francisco State University), Nidhi Gadura (Queensborough Community College), Frank Cipriano (San Francisco State University), Dhana Rao (Marshall University), Jessica Rocheleau (Western New England University), Robert Ramirez (San Francisco State University), Peter Novick (Queensborough Community College), Dawn Holmes (Western New England University), Julie Aaron (DeSales University), Jiannong Xu (New Mexico State University), Joseph Colosi (DeSales University), Desiree Stanley (DOE JGI), Cheryl Bailey (University of Nebraska, Lincoln)
2011-2012 Faculty Collaborators
The 2011-2012 faculty cohort attended the training workshop at the JGI in January of 2011. Since then, they have been implementing genome annotation procedures into a wide variety of courses at their institutions.
2011-2012 Cohort: Bertrand Eardly (Penn State University, Berks), Betsy Wilson (University of North Carolina, Asheville), Cheryl Kerfeld (DOE JGI), David Roll (Roberts Wesleyan College), Jason Friday (North Iowa Area Community College), Michael LaGier (Florida Gulf Coast University), Lisa Lindert (Cal Poly San Luis Obispo), Ward Jones (Viterbo University), Scott Gabriel (Viterbo University), Alex Dekhtyar (Cal Poly San Luis Obispo), Joanna Klein (Northwestern College), Daniel Golemboski (Bellarmine University), Kari Loomis (Mars Hill College), Christopher Kvaal (St. Cloud State University), Catherine Sarisky (Roanoke College), Michael Sierk (Saint Vincent College), Sharon Lewis (Langston University), Kenneth Noll (University of Connecticut), Seth Axen (DOE JGI), Cheryl Bailey (University of Nebraska, Lincoln)
2010-2011 Faculty Collaborators
The 2010-2011 cohort attended the training workshop at the JGI in January 2010, and the faculty representatives have since been integrating the genome interpretation program into their course material. This was the first workshop to introduce IMG-ACT to international institutions, with three from Ireland, Sweden, and Grenada in attendance.
2010-2011 Cohort: Cheryl Kerfeld (DOE JGI), David Essig (Geneva College), Brad Goodner (Hiram College), Joanne Pratt (F.W. Olin College of Engineering), Rodney Austin (Geneva College), Rachael Morgan-Kiss (Miami University), Jean Huang (F.W. Olin College of Engineering), Alex Idnurm (University of Missouri, Kansas City), A. Carolin Frank (University of California, Merced), Paul O’Toole (University College Cork), Helen Donis-Keller (F.W. Olin College of Engineering), Dag Ahren (Lund University), J. Jacob Parnell (Utah State University, Logan), Kai Hung (Eastern Illinois University), Svetlana Kotelnikova (St. George's School of Medicine), Stephen Koury (University at Buffalo), Bruce Fouke (University of Illinois), William Barnes (Clarion University), Rama Dey-Rao (University at Buffalo), Anna Zimmerman (College of Charleston), Mary Shi (Tracy High School), Mark Wilson (Humboldt State University), Niraj Punjya (Tracy High School), Seth Axen (DOE JGI), Kirk Brown (Tracy High School/San Joaquin Delta College)
2009-2010 Faculty Collaborators
The 2009-2010 Faculty Collaborators were among the first to participate in the program and to use IMG-ACT. The Faculty Collaborators representing higher education institutions across the United States came to the JGI to meet fellow participants in January 2009 and have since been interpreting 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 motivating faculty from multiple courses to collaborate, and to discuss the tools for annotation, IMG-ACT. Collectively, the faculty used their spring 2008 courses to annotate the genome of a chemolithoautotrophic bacterium and reconvened at the JGI in June 2008 to discuss the experience and write up their results. These original 12 have continued to contribute to the ongoing development of IMG-ACT and recently described their experiences in an article in PLoS Biology introducing IMG-ACT.
News Reports
A Head Start for Tomorrow’s Scientists [Video] (University at Buffalo)
Roanoke selected to collaborate with the Department of Energy’s Joint Genome Institute (Roanoke College)
Genetic Research at FGCU [Audio] (WGCU Public Media)
Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum (PLoS Biology)
Genome annotation in microorganisms and metagenomic libraries as a part of an undergraduate curriculum (WINDREF Annual report 2010; p. 15-17)
Genomics Undergrads Annotate Bacteria for Government Project (UC Merced)
DOE selects UMKC School of Biological Sciences to participate in 'Adopt a Genome' project (UMKC)
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)
Biology students to take part in genome project (BGSU)
