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Collaborative, networked labs to tackle intestinal bacterium




Traditional rivals on the football field, three Michigan universities now are working together to perform the most complete functional analysis of an organism done in a single project.

In just one year, scientists at Michigan State University, Wayne State University and U-M will map at least 80 percent of the intestinal bug Campylobacter jejuni with a networked effort that melds the latest equipment and techniques in genomics, proteomics and bioinformatics.

Strains of C. jejuni bacteria cause more than 2 million attacks of bacterial diarrhea per year in the United States; that’s more cases of food poisoning than salmonella and shigella combined. While the bacterium’s genome recently has been mapped by the UK’s Sanger Centre, that is only the start of understanding how pathogenic versions of it operate and cause illness, and what makes them more harmful than other strains of the bug. Though Campylobacter commonly occurs in cattle, sheep, chickens, wild birds and even insects, it is not very well understood.

C. jejuni’s genome consists of 1.6 million basepairs and an estimated 1,650 proteins—22 percent of which are expected to be novel. The ultimate goal of this project by the networked Michigan labs is to generate an interaction map of C. jejuni that is linked to large sets of functional data. The group expects that the resulting resource will provide new insights into the biology of this and other pathogens and contribute to development of methods to control them.

“Instead of looking only at gene sequences, we’re going to be discovering the function of those genes,” says Philip Andrews, director of the Michigan Proteome Consortium, the state-funded lab leading the Campylobacter project.

The Proteome Consortium headed by Andrews is one of five state-supported labs under the “Core Technology Alliance,” which were established with the state of Michigan’s share of tobacco settlement money. This highly networked, collaborative set of labs is intended to help grow a life sciences economy in the state by providing equipment and techniques that are out of reach for most academic and private-sector researchers.

The Campylobacter effort, in addition to being an important public health project, also is a proof-of-concept test for networked laboratory collaboration. A host of networking issues, including intellectual property, information infrastructure and communication systems, will be identified and hopefully resolved. The group hopes that the distributed laboratory in this consortium will become a model for making the best use of biotechnology resources.

Four of the five labs will participate in the Campylobacter project. The fifth lab, at the Van Andel Research Institute in Grand Rapids, specializes in cancer research and transgenic animal models.

The Campylobacter project also will be used as a test-bed for different hardware and software platforms and protocols, Andrews says. The labs will develop new technologies and evaluate which of the new technologies and tools are most effective for generating functional data. They also are developing software that allows management and cross-correlation of large, complex datasets of the types generated by large-scale functional studies.

Having worked out the kinks on this smaller organism, “then we’ll then be poised to go on to larger organisms,” says Dr. Mark R. Hughes, leader of Wayne State’s genomics core.
For more information on the Michigan Proteome Consortium, visit http://www.proteomeconsortium.org and the Core Technologies Alliance at http://www.ctaalliance.org.

The principal investigators include Andrews and Brian Athey, director of the Michigan Center for Biological Information, who leads the bioinformatics component.

 

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