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This Week in PLOS: Dec 24, 2013

Researchers from Howard University and JCVI examined the fecal microbiome of half a dozen African-American patients with and without colonic polyps. As they report in PLOS One this week, they used a combination of a 16S rRNA phylogenetic array, the HITChip, and 16s rRNA sequencing to find that the patient and healthy samples differed in the levels of Bacteroides. "This study reveals that at the pre-neoplastic stages, there is a trend showing microbiota changes between healthy and colon polyp patients at the sub-genus level," the researchers note.

RNA silencing in grapevine is resistant to lower temperatures than other plants studied, say researchers from the University of Strasbourg in France. RNA silencing, which plants use as a defense strategy, is often ineffective below 15 degrees Celsius, but in PLOS One the Strasbourg researchers show that grapevine can still steadily produce siRNAs at temperature dipping down to 4 degrees, a point at which silencing in Arabidopsis and other plants falters.

Memorial Sloan-Kettering Cancer Center's Chris Sander and his colleagues present a method for predicting how cells will respond to perturbations in PLOS Computational Biology this week. Their approach borrows from a physics statistical method called Belief Propagation, adapting it to calculate the most likely interactions. After testing their approach on simulated data, the researchers applied it to a BRAF-mutant melanoma cancer cell line and the models generated by the method were able to "reproduce and extend known pathway biology." Sander and his colleagues add that "[t]he network pharmacology approach described here provides a strong tool for a system level description of signaling events in cancer cells. Moreover, it presents a step forward in quantitative prediction of responses of cancer cells to drug perturbations."

The Scan

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.

Study Points to Synonymous Mutation Effects on E. Coli Enzyme Activity

Researchers in Nature Chemistry saw signs of enzyme activity shifts in the presence of synonymous mutations in a multiscale modeling analysis of three Escherichia coli genes.

Team Outlines Paternal Sample-Free Single-Gene Approach for Non-Invasive Prenatal Screening

With data for nearly 9,200 pregnant individuals, researchers in Genetics in Medicine demonstrate the feasibility of their carrier screening and reflex single-gene non-invasive prenatal screening approach.

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.