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This Week in PNAS: Mar 16, 2010

In the this week's PNAS Early Edition, researchers at Stanford University report their method for mining developmentally regulated genes using Boolean implications, MiDReG. "MiDReG uses two gene expression-based seed conditions that mark the initial and the terminal stages of a given differentiation pathway and combines the statistically inferred Boolean implications from these seed conditions to identify the relevant genes," the authors write, adding that they validated their method by applying it to B-cell development. The authors suggest that by using MiDReG they've identified novel gene candidates for the future study of B-cell development. "These data demonstrate the power of MiDReG in predicting functionally important intermediate genes in a given developmental pathway that is defined by a mutually exclusive gene expression pattern," the authors conclude.

Researchers in Japan describe the molecular cloning of Sdr4, a rice quantitative trait locus and regulator involved in seed dormancy and the domestication of rice. They found Sdr4 expression to be positively regulated by OsVP1, among other characteristics, which, when combined, suggest that it acts as an intermediate regulator in the seed maturation program. The team also discusses their results with respect to "possible selection of the allele during the domestication process."

In PNAS this week, a pair of researchers at the University of California, San Francisco, presents their method to label and isolate N-terminal peptides from human plasma and serum, which "dramatically reduces the complexity of the sample by eliminating internal peptides." The team writes that, with their method, it's possible to identify substrates from specific proteases with the exogenous addition of the protease along with N-terminal isolation and quantitative mass spectrometry. "In this way we identified proteins cleaved in human plasma by membrane-type serine protease 1, an enzyme linked to cancer progression," the authors write.

Researchers report their examination of IRF-5, a transcription factor critical for the induction of the antiviral and inflammatory response, and its role in the regulation of B-cell differentiation. Using a murine model, the team also shows that IRF-5 plays a role in the stimulation of Blimp-1 expression "Analysis of the profile of transcription factors associated with plasma cell differentiation shows down-regulation of Blimp-1 expression, a master regulator of plasma cell differentiation, which can be reconstituted with ectopic IRF-5," the authors write, adding that their results highlight the transcription factor as a regulator of B-cell terminal differentiation.

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.