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Mass Spec and Microarrays: Genomics and Proteomics Find Home at Biodefense Powwow

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Genomics and proteomics may have lost some of their luster on Wall Street in recent months, but on Aliceanna Street at the American Society for Microbiology Biodefense conference in March these subdisciplines found a home. Along with several oral presentations, a good 20 percent of the posters described how large-scale gene and protein analysis could be used to better understand pathogens and how to combat them.

Many researchers have pinned their hopes on using proteomics and DNA microarray technologies for rapidly detecting the presence of potential pathogens. Nancy Valentine, a scientist in the environmental technology division of Pacific Northwest National Laboratory, says her group is applying MALDI mass spectrometry to identify various pathogenic bacteria.

Although Valentine’s group was able to accurately identify the bacteria even when the organisms were grown under disparate conditions, she says using mass spec to detect an airborne pathogen will require more sensitive technology. Getting an accurate identification still requires waiting for enough of the pathogen to accumulate, she says.

Other proteomics practioners are hoping to aid in the search for new vaccines to protect against bioterror agents. At the University of California, Irvine, Luis Villareal is leading an effort to develop a broadly applicable strategy for expressing the entire proteomes of pathogenic viruses, starting with smallpox. Villareal and his group at UC Irvine’s Center for Virus Research are employing an in vitro technique, gene activation by PCR, to express viral proteins in a 96-well format. With sufficient funding to purchase the oligonucleotide reagents, he says the technology is capable of expressing 2,000 proteins a week. Villareal plans to array the proteins on slides to allow other researchers to develop antibodies against them for use as potential vaccines.

Scientists are also tying their more basic research in genomics and proteomics to biodefense. In separate posters, researchers at Lawrence Livermore National Laboratory described their analysis of the genomes of Francisella tularensis (responsible for typhoid fever), and Brucella abortus (responsible for undulant fever). In a presentation, Michel Desjardins, of the University of Montreal and Caprion Pharmaceuticals, described his success in using proteomics to identify a previously uncharacterized process by which the human body fights infectious disease. Insight into the mechanism, he says, should help researchers develop treatments for diseases ranging from salmonella to tuberculosis.

— John S. MacNeil

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