Dr. William Barnes, professor of biology at Clarion University, has been selected to collaborate with the Department of Energy's Joint Genome Institute (JGI) in The Undergraduate Research Program in Microbial Genome Annotation.
One of the major initiatives at JGI is the GEBA project (A Genomic Encyclopedia for Bacteria and Archaea), which aims to sequence 100 bacterial and archaeal genomes based on the phylogenetic positions of organisms in the tree of life. The long-term goal of the GEBA project is to generate reference genomes for every major and minor group of bacteria and archaea. This could represent something on the order of 5,000 genomes.
This amount of sequencing is not beyond the capabilities of the current capacity of major genome sequencing centers, but it is beyond the current capacity for qnalysis by human experts. JGI has, therefore, developed online tools to enable "massively parallel undergraduates" to take part in the process of manual annotation.
Pedagogically, these recently sequenced genomes ideally provide a unifying thread for concepts across the life sciences curriculum. 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.
The letter of acceptance reads, "Clarion University was chosen because your application demonstrated the potential to enrich the curriculum with sequence-based research; we believe your approach has the potential to contribute to the national model for undergraduate research that we are collectively developing. This collaboration between the JGI, undergraduate faculty, and their students is a response to the call to reform undergraduate life sciences education through research experience. "
Barnes looks forward to this project because, "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."
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