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This Week in PLoS: Apr 6, 2009

In PLoS One this week, scientists used comparative gene expression analysis to determine a possible signature that could serve as a biomarker to distinguish between patients with stable idiopathic pulmonary fibrosis and those where the disease progressed rapidly. Comparing the SAGE profiles in stable and progressive disease, they identified a SAGE molecular expression signature of 134 transcripts that could distinguish between the two stages, including overexpressed genes, surfactant protein A1, two members of the MAPK-EGR-1-HSP70 pathway that regulate cigarette-smoke induced inflammation, and Plunc (palate, lung and nasal epithelium associated).

Also in PLoS One, Arizona State University researchers discovered genetic clues to the division of labor in honey bees, who turn out to be collectors of nector or pollen, but not both. Using a combination of backcross QTL analysis, behavioral and anatomical phenotyping, candidate gene expression studies, and backcross confirmation of gene-to-anatomical trait associations, they showed that two genes, PDK1 and HR46, are directly related to ovary size, "a central reproductive trait that correlates with the nectar and pollen foraging bias of workers," they write.

Scientists at WashU have created a new computational program named RSSVM (RNA Sampler+Support Vector Machine), which uses Support Vector Machines to identify functional RNA motifs from random RNA secondary structures. They applied RSSVM to several Shewanella genomes and identified 166 putative regulatory RNA motifs in the 5' untranslated regions in S. oneidensis, a microbe with great potential in bioremediation and alternative energy, they say. Their work was published in PLoS Computational Biology.

Using "high-density time sampling," research led by scientists at the Institute for Translational Medicine and Therapeutics at the University of Pennsylvania studied the interplay between circadian rhythms and gene expression. Using microarrays to profile the circadian transcriptome from the mouse liver and two immortalized cell lines, they identified over 3,000 different transcripts in the mouse liver "that cycle with a period length of approximately 24 hours." Surprisingly, they write in the author summary in PLoS Genetics, they also identified two classes of genes "which cycle with period lengths of 12 and 8 hours; i.e., harmonics of the circadian clock. Importantly, we were able to identify harmonics in five other tissue types."

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.