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This Week in PNAS: Sep 4, 2012

In PNAS, investigators at Caltech present a dynamic and predictive Boolean computational model of gene regulatory networks in sea urchin development. This model, the researchers say, "provides a direct test of whether the observed dynamic sequence of spatial and temporal gene expression can be computed by using the information included in the GRN model." Further, they report that the model did indeed predict gene expression patterns for regulatory genes during embryo development, and that the model could determine outcomes that are known to occur due to regulatory perturbations. "The formalism presented here provides a general means of representing in silico the genomic regulatory system underlying animal body plan development and further applications may be anticipated, ranging from evolution to synthetic developmental biology," the investigators add.

Tsinghua University's Sen Song and colleagues write in PNAS that the way that many phylogenies have been constructed, using concatenation methods, leads to incongruent results. They report that coalescent methods that accommodate gene heterogeneity "yield more consistent results." Focusing on the unresolved root of the branch of eutherian mammals, the researchers found support for a "eutherian root between Atlantogenata and Boreoeutheria and support ungulate polyphyly and a sister-group relationship between Scandentia and Primates."

Also in PNAS, researchers at the University of Washington School of Medicine report on their development of a new method, called Duplex Sequencing, to reduce errors generated by next-generation sequencing. This approach tags and sequences the two strand of complementary DNA independently, and if there are true mutations, the researchers note that they should appear at the same spot. They further estimate that this approach has a theoretical background mutation rate that is less than one error per 109 nucleotides. "Moreover, Duplex Sequencing can be generalized to essentially any sequencing platform: a double-stranded tag can be incorporated into other existing adapters or for sequencing approaches that do not require adapters, a double-stranded tag can be ligated onto a duplex DNA sample before sequencing," the researchers add.