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This Week in PNAS: Jan 12, 2010

In the advance, online edition of PNAS this week, Joshua Akey and his coworkers genotyped 275 dogs from 10 breeds to look for signals of artificial selection in the dog genome. In the process, they found more than 150 parts of the genome containing recent signals of selection that may influence breed variable traits such as size, coat, behavior, and physiology. As BBC News reports, they also pinpointed a gene called HAS2 that's linked to the characteristically wrinkled skin of Shar-peis.

American and Swedish researchers found an inherited genetic variant that increases the risk of aggressive prostate cancer. After comparing SNP frequencies in prostate cancer patients from four National Cancer Institute Genetic Markers of Susceptibility study populations and three independent American and Swedish study populations, they identified a chromosome 17 SNP associated with aggressive prostate cancer in all of the populations. And, they say, such findings suggest inherited variants could eventually serve as early markers for aggressive prostate cancer.

John Baross and his co-workers used 16S rRNA sequencing to explore archaea and bacteria in hydrothermal chimneys near the Mid-Atlantic Ridge. By comparing the microbes found in the so-called Lost City Hydrothermal Field over the past 1,200 years or so, they found evidence suggesting the same sequences that are rare in young chimneys are more common in the older ones, with environmental conditions in the vents apparently selecting for closely related species. "Because of the unique characteristics of the Lost City Hydrothermal Field, these data offer an unprecedented opportunity to study the dynamics of a microbial ecosystem's rare biosphere over a thousand-year time scale," they write.

Princeton University researcher David Botstein and company report on their strategy for improving the DNA microarray-based detection of sequence variants in heterozygous genomes. By exploring hybridization efficiency under different conditions and microarray probe lengths for nearly 25,000 SNPs in two yeast strains, the team found a probe melting temperature-hybridization reaction temperature-based relationship for optimizing the detection of sequence variants in mixed sequence samples.

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.