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This Week in PNAS: Oct 30, 2012

Genes in the opsin gene family share a common, early animal ancestor, according to a study in the early, online edition of the Proceedings of the National Academy of Sciences by researchers from the National University of Ireland and the University of Bristol. The team used computational methods to retrace the phylogeny of opsin family genes, which are key components of visual pigments, garnering evidence that opsin developed the ability to detect light more than an estimated 11 million years or so ago. "We traced the earliest origin of vision and we found that it originated only once in animals," senior author Davide Pisani said in a statement. "This is an astonishing discovery because it implies that our study uncovered, in consequence, how and when vision evolved in humans."

For another PNAS online study, the University of Washington's Jay Shendure and his colleagues combine optical sequencing with an in situ library construction method that involves adaptor transposition to high molecular weight DNA in a sequencing flow cell — an approach allows for long-range contiguity mapping, they report. In Escherichia coli, for instance, they produced tens of thousands of paired-end that were separated by one-, two-, or three thousand bases. Moreover, they say, results of the study demonstrate that "it is possible to stretch single molecules ranging from [three to eight thousand bases] on the surface of a flow cell before using in situ library construction, thereby enabling the production of clusters whose physical relationship to one another on the flow cell is related to genomic distance."

Finally, a team from Japan's National Institute of Advanced Industrial Science and Technology and the University of Tokyo report on results from a study exploring the range of 16S ribosomal RNA sequences that can function in E. coli and complement the bug's growth. Using an E. coli strain that was missing its own rRNA operons, researchers relied on horizontal gene transfer to transplant in new16S rRNA genes, using from DNA from metagenomic samples. Results of the analysis indicate that 16S secondary structure has a more pronounced impact on ribosomal functionality in E. coli than the degree of similarity that the transplanted 16S rRNA shares with the E. coli's natural 16S rRNA sequence.

The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.