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This Week in PNAS: Feb 13, 2013

Soil and manure from pig farms where antibiotics are commonly used are prone to harboring antibiotic resistance genes, according to a study in the early, online edition of the Proceedings of the National Academy of Sciences. Researchers from China and the US assessed manure, manure compost, and manure compost-treated soil samples from three large Chinese swine farms, using quantitative PCR arrays to test for 244 antibiotic resistance genes. The search uncovered signs of 149 different antibiotic resistance genes, the group reports, with sequences from a subset of these genes being especially enriched at the commercial swine farm site samples compared to control manure and soil samples Based on the patterns they saw, Michigan State University microbial ecology researcher James Tiedje, the study's senior author, and colleagues concluded that "diverse, abundant, and potentially mobile [antibiotic resistance genes] in farm samples suggest that unmonitored use of antibiotics and metals is causing the emergence and release of [antibiotic resistance genes] to the environment."

In another PNAS study, the University of Oxford's Zoltán Molnár and colleagues from the UK explore gene expression during brain development in mice, focusing on part of the cerebral cortex called the subplate zone. Using array- and RNA sequencing-based data from brain samples collected during mouse embryonic development and in post-natal and adult mice, the researchers gained clues about subplate function by finding genes with distinct expression profiles in that brain area during at least one of the developmental stages considered. Moreover, the group also saw enhanced mouse subplate expression for several of the same genes implicated in past studies of autism and schizophrenia, prompting them to argue for "the importance of the study of transient features of the developing brain to better understand neurodevelopmental disorders."

A team from the UK and the US performed genome-wide copy number analyses on multiple samples from within individual tumors taken from 11 individuals with glioblastoma. Based on alterations across different parts of each tumor, the investigators put together tumor-specific phylogenies and tracked genetic glitches signifying cancer progression in each patient. "Our results reveal the genome-wide architecture of intra-tumor variability in [glioblastoma] across multiple spatial scales and patient-specific patterns of cancer evolution, with consequences for treatment design," the study's authors wrote in a paper slated to appear online this week in PNAS.