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This Week in PNAS: Sep 11, 2013

In a study appearing in the early, online edition of the Proceedings of the National Academy of Sciences, a Max Planck Institute for Evolutionary Anthropology-led team describe an improved ancient DNA extraction method used to help sequence the mitochondrial genome from a more than 300,000-year-old cave bear bone found in a permafrost-free cave in Spain. Using the silica-based approach, plus a single-stranded DNA preparation scheme, the researchers generated more than 16,300 bases of mitochondrial sequence from fragmented DNA in the sample — a sequence that they used to sniff out the Middle Pleistocene cave bear's relationship with cave bears that lived more recently in western Europe during the Late Pleistocene period.

Our sister publication GenomeWeb Daily News has more on the study here.

Swiss researchers present a massively parallel microchemostat array approach they developed for following yeast proteomic changes over time and under changing conditions. The continuous culture microfluidic system made it possible to assess protein abundance, protein localization, and other cell features in up to 1,152 yeast strains with different GFP-tagged proteins at 20-minute time intervals. Using that approach, the group assessed thousands of GFP-tagged yeast strains treated with the DNA replication stressor methyl methanesulfonate or exposed to other stressful conditions. "Our microchemostat platform enables the large-scale interrogation of proteomes in flux," the study's authors note, "and permits the concurrent observation of protein abundance, localization, cell size, and growth parameters on the single-cell level for thousands of microbial cultures in one experiment."

The University of California, Santa Barbara's Boris Shraiman teamed up with investigators from the Max Planck Institute for Developmental Biology to look at coalescence, genetic diversity, and adaptation in sexually reproducing populations under selection. With the help of a computational approach that considers how loci influence the recombination dynamics of other nearby loci in linkage disequilibrium with them, the study's authors found that "simple patterns emerge from the collective effect of many loci and that these patterns can be used to infer evolutionary parameters from sequence data."