THROUGH THE
Sallyport
Exposing Telltale Signs of Bioterror Large-scale outbreaks of illness are never pretty, but these days, one question may be paramount: Is the outbreak caused by a natural pathogen or one that was grown in a lab by terrorists? Discovering the answer to that question is the aim of a group of Rice researchers who have won federal support to develop a genomic test designed to provide homeland security and public health officials with the tools they need to quickly determine how to respond to an outbreak. The three-year grant is Rice’s first from the Defense Threat Reduction Agency (DTRA). “In a natural outbreak, there are classic rules of epidemiology that describe how particular types of diseases will spread,” said principal investigator Yousif Shamoo, associate professor of biochemistry and cell biology and director of Rice’s Institute of Biosciences and Bioengineering. “In a man-made outbreak, you may be faced with an actor who is continuously spreading the disease, or you might have a
Low-temperature electron micrograph of a cluster of E. coli bacteria, magnified 10,000 times.
media. And it’s the same diet every day. Our expectation is that organisms will lose certain genes that allow them to get nutrition from the soil or the gut or wherever they came from, simply because they don’t need them anymore.” In a lab, domesticated strains will outcompete the wild type, which will disappear from the lab within just a few generations. For the DTRA project, Shamoo and his students will gather wild strains of two common bacteria — Enterococcus faecalis and Escherichia coli — and domesticate each of them in the lab. Genomic snapshots will be taken throughout the process, and they’ll be analyzed for telltale patterns. “We don’t want to get into the business of trying to catalog the
“The idea is to look for common sets of responses to domestication that you would likely see for any organism that’s adapting from living in the wild to living in the laboratory.” —Yousif Shamoo
person who, knowing public health strategy, has engineered strains.” Shamoo’s lab specializes in studying how the process of evolution plays out at the molecular level. His group also studies how bacteria evolve to become drug-resistant. He said the same forces that allow drug-resistant strains of an organism to outcompete their nondrugresistant cousins in a hospital will also allow his team to discern between pathogens whose origins are in nature or the lab. That will be possible because of the way bacteria can progress through hundreds of generations in just a few weeks and rapidly adapt to new conditions. “Living out in the wild is a pretty rough existence,” Shamoo said. “By comparison, life in the laboratory is very posh. Lab-grown bacteria live in very nice conditions on agar plates eating this very rich
specific changes that take place for thousands of different organisms,” Shamoo said. “The idea is to look for common sets of responses to domestication that you would likely see for any organism that’s adapting from living in the wild to living in the laboratory.” While E. faecalis and E. coli are each common, well-studied bacteria, they also come from opposite ends of their species’ genetic spectrum. The fundamental differences in their chemical and physical properties will give the researchers a broad range of genetic patterns associated with domestication. “If we find something after three years, and we want to expand the pool to include soil bacteria or other types,” Shamoo said, “we can do that and see if the patterns repeat.” —Jade Boyd
Rice Magazine
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No. 8
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2010
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