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This Week in PLOS: Dec 16, 2013

Researchers from Portugal, reporting in PLOS Pathogens, used genome sequencing as part of their effort to understand adaptations leading to pathogenesis in Escherichia coli. Together with mathematical modeling and experiments gauging the bug's evolution and physical features, the team's genome sequence assessments suggested that the presence or absence of a lone transposable element can spell the difference between commensal and virulent E. coli, for example, with another transposable element apparently speeding up that transition. In addition, the study's authors found that patho-adaptation can arise in fewer than 500 generations in E. coli grown in the lab.

In PLOS Genetics, researchers from the US and China describe recombination patterns detected in the dog genome using genome sequence data for 51 village dogs. Past studies have indicated that pooches lack a functional copy of the PRDM9 gene, which codes for a trimethylase enzyme that seems to situate recombination hotspots in other mammalian genomes, the study's author note. Their genetic maps suggest that broad recombination patterns in the dog genome are similar to those in other mammals, even without that PRDM9-mediated hotspot localization. But a closer look at the data also revealed a tendency for dog recombination to occur in and around regions rich in cytosine and guanine nucleotides, particularly in parts of the genome containing gene promoters.

A gene expression signature that includes the transcription factors-coding gene BACH1 can provide clues about the likelihood that individuals with triple-negative breast cancer will remain free from metastases, according to a PLOS One study. Researchers from the US and UK developed and tested this so-called BACH1 pathway metastasis signature with the help of array-based expression data for more than 1,500 individuals with breast cancer. The signature subsequently proved promising for predicting metastasis risk in individuals with tricky-to-treat triple-negative breast cancer, the study's authors report, providing information that complemented that found using existing breast cancer signatures such as Mammaprint and Oncotype.

The Scan

Follow-Up Data Requests to Biobank Participants Ineffective, Study Finds

An effort to recontact biobank enrollees for additional information reports low participation in a new BMJ Open study.

Study Finds Widespread Transmission of Resistant Bacteria in Vietnam Hospitals

A sequencing study in The Lancet Microbe finds widespread transmission of drug-resistant Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii in two Vietnam ICUs.

Novel Brain Cell Organoids Show Promise for Autism Research

University of Utah researchers report in Nature Communications on their development of brain cell organoids to study SHANK3-related autism.

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.