Two papers published in one day. First, "Adaptive evolution and functional redesign of core metabolic proteins in snakes" by Castoe, Jiang, Gu, Wang, and Pollock has been published at PLoS ONE.

Original news postings : A Blog Around the Clock, UC Denver;

News articles and blog postings:Not Exactly Rocket Science, ScienceDaily, NewsWise, NIH, ICM Natural History Log, The Herptile Blog, Genetic Archaeology, ReptileGeeks; also news service hits at UC Denver, FirstScience, Biology News Net,SiloBreaker, SiloBreaker2, EurekAlert, AScribe, Health News Digest, PhysOrg, ScienceCentric, BiochemistryWire, HandsNet.

We demonstrate that mitochondrially-encoded oxidative phosphorylation proteins in snakes (particularly cytochrome oxidase subunit I, or COI) have endured a remarkable process of evolutionary redesign, swith unprecedented levels of positive selection, coevolution, convergence, and reversion at functionally critical residues. This provides an exceptionally clear and dramatic example of adaptive evolution in a core metabolic protein to date, and implies that strong molecular and physiological adaptation may be linked. Snakes have been recently identified as an excellent model for studying extreme metabolic and physiological regulation, and we suggest that they are an excellent model for studying molecular adaptation as well.

Second, a pre-press version of "Identification of repeat structure in large genomes using repeat probability clouds" by Gu, Castoe, Hedges, Batzer, and Pollock has been published at Analytical Biochemistry. We introduce a rapid approach to analyzing repeat structure in large eukaryotic genomes. The method can analyze the entire human genome on a desktop computer in less than half a day. The approach is based on understanding the evolutionary relationships among repetitive elements, the largest contributor to repeat sequences, and should be a useful tool for repetitive element and genome structure research.

We welcomed Vijetha Vemulapalli to the lab this March. Vijetha is a PhD candidate in the Computational Bioscience Program and comes from the Computational Omics Lab at Indiana University.

The Consortium for Comparative Genomics (CCG) is now operational. We have purchased a Roche/454 FLX next-generation sequencer, and it was installed Monday December 17. We should be accepting samples in mid-January, 2008. Please contact David.Pollock at uchsc.edu for pricing, collaboration, and other information (and see our web page, which will be updated shortly).

Sample files and executable software (.zip format) for P-clouds manuscript (in review).

Supplementary data for Wang ZO and Pollock DD, " Coevolutionary patterns in cytochrome c oxidase subunit I depend on structure and functional context" J Molecular Evolution, 2007

Pollock Lab and NLM Training Grant Postdoctoral Fellow Todd Castoe was quoted in a Science "Focus on Careers" article by Laura Bonetta: "Training postdocs: communication is key", (2007, Science 317:1239). "My adviser is giving me a lot of firsthand experience with the practicalities of running a lab. We talk about why we should finish specific projects and how that relates to current and future grants. We look at a pile of new data and decide what direction is most profitable to follow up," he says. "I get to see the larger picture."

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