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USDA gives $1 million grant for genome database at MSU

A multidisciplinary effort at Mississippi State University to create an agricultural genomic database has resulted in a million dollar grant from the U.S. Department of Agriculture.

The funding will support ongoing efforts to enlarge AgBase, an online database developed by College of Veterinary Medicine researcher Shane Burgess and College of Engineering researcher Susan Bridges. Burgess and Bridges are also co-directors of the Institute for Digital Biology at MSU.

“We could not have gotten this grant without the support of MSU's Division of Agriculture, Forestry and Veterinary Medicine as well as the College of Engineering and Office of Research,” Burgess said.

AgBase is part of an international effort to help researchers who want to understand biological function from large amounts of data generated during experiments at the genomic level. Researchers and nonacademic organizations can search the database for information needed for their individual projects. It is part of an international project organized by the Gene Ontology Consortium, which includes nonagricultural genomic data.

“Other groups have compiled databases on particular species, such as mice, fruit flies and yeast, but this is the first system to compile genomic information for multiple species related to agriculture,” Burgess said. “So far, we have information on many microbes, chickens, cows, sheep, corn, pine and poplar trees.”

Burgess, a researcher with the College of Veterinary Medicine and the Mississippi Agricultural and Forestry Experiment Station, said MSU is in the process of inviting fellows to join genomic work under way in the Institute for Digital Biology.

Fiona McCarthy, assistant research professor in the College of Veterinary Medicine's basic sciences, said when researchers completed the human genome, worldwide efforts turned immediately to other species.

“For the first time, scientists have enormous information to piece together. Instead of concentrating on small segments, we are doing whole plant or whole animal genomic work to determine what is going on,” McCarthy said. “We assist biologist by examining the research papers on a particular gene, then compile a synopsis of what is known about that gene currently.”

McCarthy said the database organizes information for scientists and presents it in a way than can be searched easily using computers.

Bridges, a professor of computer science and engineering, started her career as a biologist but transitioned to computer science about 20 years ago.

“Modern biology requires collaboration among life scientists and computer scientists. That's how they were able to sequence the human genome and how we look at genomes now,” she said.

“All of modern biology that investigates many genes of an organism simultaneously requires computers. There are thousands of genes, so they cannot be studied manually all at once,” Bridges said. “Years ago, scientists could spend their entire careers investigating one gene. Now, they look at all the genes and proteins in an organism, and they must use computers to understand and model their data.”

Burgess said additional collaborators from other segments of the university have been important in the project's success.

Harry Llull is the associate dean for public services in MSU's library and the liaison to the department of computer science and engineering.

Susan Seal, distance learning coordinator with the Extension Service, will help formulate the training component of the grant using the Internet and various workshops.

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