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Genomics In The Journals: Apr 14, 2011

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – A meta-analysis in PLoS Genetics ties two sites in the genome to regular caffeine consumption. Researchers from the US and Singapore brought together information on more than 47,300 individuals of European descent who were sampled through five population-based studies. The team found two genomic regions that were significantly linked to habitual, self-reported caffeine consumption: a chromosome 15 locus between CYP1A1 and the caffeine metabolizing gene CYP1A2 and a chromosome 7 locus near AHR, a gene that seems to regulate the activity of CYP1A2 and other genes.

In an effort to learn more about speciation patterns and criteria in bacteria, researchers from the US and Australia used Illumina GAII and Roche 454 platforms to sequence the genomes of nine Escherichia coli strains from four phylogenetic clades that have become adapted to living outside warm-blooded host animals. When they compared these genomes to those of other E. coli strains, the researchers found genetic clues hinting at functional differences between environmental strains, commensal strains living in animal guts, and pathogenic E. coli strains — despite phenotypic and taxonomic characteristics that are shared by all the bugs. The study appeared in the early, online version of the Proceedings of the National Academy of Sciences.

"Defining bacterial species remains a challenging problem even for the model bacterium Escherichia coli and has major practical consequences," corresponding author Konstantinos Konstantinidis, a researcher at the Georgia Institute of Technology, and co-authors wrote, explaining that the new findings "are consistent with a more stringent and ecologic definition for bacterial species than the current definition and provide means to start replacing traditional approaches of defining distinctive phenotypes for new species with omics-based procedures."

The eusocial behaviors that have independently sprung up in several insect groups coincide with accelerated evolution in specific sets of genes, according to another PNAS paper. Through a Roche 454 Life Sciences "one-gigabyte sequencing grant," researchers from the University of Illinois at Urbana-Champaign and Cornell University sequenced the transcriptomes of nine bee species known to have varying degrees of eusociality. By mapping these transcripts to the honey bee genome, the team found 212 genes with evidence of accelerated evolution in all of the eusocial bees tested, offering clues about convergent evolution patterns behind the social structure. Hundreds of other genes showed different accelerated evolution patterns depending on the bee group tested and their degree of eusociality.

"What we find is that there are some genes that show signatures of selection across the different independent evolutions (of eusocial bees)," University of Illinois researcher Gene Robinson, who was senior author on the study, said in a statement. "They might be representatives of the 'gotta have it' genes if you're going to evolve eusociality. But others are more lineage-specific."

In Science, researchers from the Universities of Liverpool and South Bohemia describe how they used linkage mapping and fluorescence in situ hybridization to track down a single site on chromosome 17 of the peppered moth, Biston betularia, that seems to shift the moth's color from mottled grey to black — a finding that they verified and refined through targeted SNP testing of peppered moths that had been collected in the UK over several years.

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

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.