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Genomics In The Journals: Feb 24, 2011

By a GenomeWeb staff reporter

NEW YORK - A correspondence article in the New England Journal of Medicine describes how researchers from the US and UK used high-throughput shotgun sequencing to probe a 2009-2010 salmonellosis outbreak linked to red and black peppers found in spicy meat products. By sequencing the genomes of 35 Salmonella enterica serotype Montevideo isolates, the group was able to trace the outbreak — which affected some 300 individuals across the US — back to a contaminated food processing facility.

"[Next-generation sequencing] data pointed to a domestic origin for the Montevideo strain associated with this outbreak," corresponding author Marc Allard, a microbiologist with the US Food and Drug Administration, and his co-authors wrote, "underscoring the utility of this technique in revealing subtle genotypic differences essential to the traceback of bacterial pathogens as they emerge in the food supply."

By scrutinizing molecular marker data for ants from thousands of colonies around the world, an international research team led by investigators at the US Department of Agriculture's Agricultural Research Service has unraveled the history of fire ant invasions — first from Argentina to the US and then to other parts of the world. Their mitochondrial DNA, nuclear microsatellite marker, and other data indicate that the fire ant Solenopsis invicta has been involved in at least nine invasion events originating in the southern US. The findings appear online today in Science.

Also in Science this week: a fourth round of perspectives articles on the tenth anniversary of the first human genome sequencing papers. The latest batch includes vignettes by Eric Lander, president of the Broad Institute and co-chair of the President's Council of Advisors on Science and Technology; Wellcome Trust Centre for Human Genetics Director Peter Donnelly; Princeton University researcher David Botstein; Yijun Ruan from the Genome Institute of Singapore; Harvard University Provost and neurobiologist Steven Hyman; and University of Washington researcher Mary-Claire King, among others.

In Genome Research, a British Columbia research team reports that it has used massively parallel sequencing to catalog genetic diversity in T-cell receptors in the human adaptive immune system. To do this, researchers collected a pair of blood samples, one week apart, from study participants and used the Illumina GAIIx to sequence libraries made from messenger RNA in these samples. The analysis uncovered more than a million T-cell receptor sequences in one of the individuals. By comparing these sequences with those in samples from two other participants, the team also started homing in on sequences that seem to be shared between individuals.

"This shows that certain sequences are more favored than others, most likely because they are more effective in recognizing specific types of infections or mutations," senior author Robert Holt, a researcher affiliated with the BC Cancer Agency and Simon Fraser University, said in a statement.

Genomics In The Journals is a new weekly feature pointing readers to select, recently published articles involving genomics and related research.

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