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This Week in PLoS: Nov 9, 2009

Scientists led by Bruce Conklin at the Gladstone Institute of Cardiovascular Disease in San Francisco used exon tiling arrays and computational analysis to study how alternative splicing affects differentiating stem cells. "To identify specific splicing events that may determine cell-type-specific differentiation," they analyzed splicing profiles of human embryonic stem cells and derived cardiac and neural precursor cells and found "unique groups of genes with clear implications for the biology of cardiomyocyte function and the maintenance of pluripotent ESCs," including those involved in cytoskeletal remodeling, RNA splicing, muscle specification, and cell cycle checkpoint control as well as genes with serine/threonine kinase and helicase activity. Their work appears this week in PLoS Computational Biology.

Stanford University's Alfred Spormann is lead author on a paper in PLoS Genetics that looked at how microbes adapt to environmental pollutants. In this work, they report the first complete genome sequences of microorganisms able to respire vinyl chloride, a carcinogen and widespread groundwater pollutant: Dehalococcoides sp. strains VS and BAV1. Notably, they write, the vinyl chloride reductase encoding genes, vcrAB and bvcAB, were found in "distinct genomic islands with different predicted integration sites, suggesting that these genes were acquired horizontally and independently by distinct mechanisms."

In work led by Lucy Collinson at the London Research Institute of Cancer Research UK and appearing this week in PLoS One, scientists used a special kind of electron microscopy to get a better look at blood vessel fusion events in zebrafish. In their work, they showed that the point of fusion between developing blood vessels in zebrafish can be identified using first live confocal microscopy and then focused ion beam/scanning electron microscopy (FIB/SEM) and serial block face/scanning electron microscopy (SBF/SEM). Their method, they say, allows for the first time "visualization of the ultrastructure of a time-limited biological event within the context of a whole organism."

Also published in PLoS One this week is an effort to understand the function of viroid-derived small RNAs, which are 21-24 nt small RNAs associated with plant infection by circular, non-protein-coding RNAs called viroids. Scientists led by those at the Italian National Research Council sequenced sRNAs isolated from Vitis vinifera infected by Hop stunt viroid (HSVd) and Grapevine yellow speckle viroid 1 (GYSVd1). From their analysis, they determined that different Dicer-like enzymes target viroid RNAs and that "viroid RNAs may interact with host enzymes involved in the RNA-directed DNA methylation pathway, indicating more complex scenarios than previously thought for both vd-sRNAs genesis and possible interference with host gene expression," they say in the abstract.

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.