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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."