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This Week in PLOS: Jan 1, 2013

In PLOS One, Case Western Reserve University's Jing Li and colleagues from that center's electrical engineering and computer science department describe a method for predicting the presence of structural variation from paired-end, high-throughput sequence data. The approach, dubbed SVMiner, uses a model-based clustering approach to define a range of candidate structural variants from paired-end sequence data given structural variant features. For the new study, the investigators highlighted the feasibility of this approach for finding structural variants in both simulated and real datasets.

A team from the US and Belgium took a systems-based approach to define the gene networks that control bone-related cells in the osteoblast lineage. As they report in PLOS Genetics, the researchers used array-based bone gene expression information on inbred mouse strains from the Hybrid Mouse Diversity Panel, combined with related genomic data, to define modules of co-expressed genes contributing to various aspects of skeletal growth and development, including the function of bone-forming osteoblast cells. "These data improve our understanding of the gene networks important for osteoblast function," the study's authors say, "and demonstrates the ability of systems genetics to unravel gene networks involved in complex cellular processes."

Expression levels of the interleukin IL-22 can help predict response to vaccines targeting bovine tuberculosis, according to a PLOS Pathogens study. A team from Germany, the UK, and Canada found 668 differentially expressed genes when they compared gene expression on peripheral blood cells from vaccine-protected, vaccine-unprotected, or unvaccinated calves. In particular, they report, the efficacy of a Bacillus Calmette-Guérin vaccine produced from the Danish Mycobacterium bovis strain 1331 SSI appeared to be tied to the expression of IL-22. The results point to IL-22 as a "predictive biomarker that can be used in future experiments," researchers explain, "and also highlighted the role of T-cells producing this cytokine in protective immunity."

The Scan

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.

Study Highlights Pitfall of Large Gene Panels in Clinical Genomic Analysis

An analysis in Genetics in Medicine finds that as gene panels get larger, there is an increased chance of uncovering benign candidate variants.

Single-Cell Atlas of Drosophila Embryogenesis

A new paper in Science presents a single-cell atlas of fruit fly embryonic development over time.

Phage Cocktail Holds Promise for IBD

Researchers uncovered a combination phage therapy that targets Klebsiella pneumonia strains among individuals experiencing inflammatory bowel disease flare ups, as they report in Cell.