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This Week in PLoS: Sep 19, 2011

This week in PLoS Pathogens, researchers at the University of California, Berkeley, "provide the first direct evidence that a pathogenicity island-encoded sRNA, IsrM, is important for Salmonella invasion of epithelial cells, intracellular replication inside macrophages, and virulence and colonization in mice." The team shows that Salmonella in which isrM has been deleted "is defective in bacteria invasion," and as a result, suggest "sRNAs may represent a distinct class of virulence factors that are important for bacterial infection in vivo."

Over in PLoS Medicine, an international team led by investigators at the University of Sydney reports its study of treatment response on more than 800 chronic hepatitis C patients — 417 individuals with PegIFN/R treatment-induced clearance and 493 who showed treatment failure — as well as "234 individuals with spontaneous clearance," in which it found that "genotyping for IL28B, HLA-C, and KIR genes improves prediction of HCV treatment response."

The Institute of Cancer Research's Nick Orr and his colleagues this week show that "genetic variants at chromosomes 2q35, 5p12, 6q25.1, 10q26.13, and 16q12.1 influence the risk of breast cancer in men." In a PLoS Genetics paper, Orr et al. say that while breast cancer is heterogeneous, "the relative risks associated with loci identified to date show subtype and, based on these data, gender specificity."

Researchers in France this week present "an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame," MACSE — multiple alignment of coding sequences accounting for frameshifts and stop codons. "MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure," the team writes in PLoS One, adding that the approach "has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence."

The Scan

Missed Early Cases

A retrospective analysis of blood samples suggests early SARS-CoV-2 infections may have been missed in the US, the New York Times reports.

Limited Journal Editor Diversity

A survey finds low diversity among scientific and medical journal editors, according to The Scientist.

How Much of a Threat?

Science writes that need for a provision aimed at shoring up genomic data security within a new US bill is being questioned.

PNAS Papers on Historic Helicobacter Spread, Brain Development, C. difficile RNAs

In PNAS this week: Helicobacter genetic diversity gives insight into human migrations, gene expression patterns of brain development, and more.