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This Week in PNAS: Jan 10, 2017

In the early, online edition of the Proceedings of the National Academy of Sciences, researchers from the UK and Australia explore associations between rare variants in the gene ERAP1 and an inflammatory spinal arthritis condition called ankylosing spondylitis. By tapping into data for 213 individuals with ankylosing spondylitis and their family members, as well as 46 control individuals with rheumatoid arthritis, the team defined four common haplotypes for variants in and around ERAP1 and compared their frequency in affected and unaffected individuals. Based on their results, the study's authors conclude that "it is common variants in ERAP1 that are mainly responsible for protection/susceptibility in [ankylosing spondylitis] rather than rare ERAP1 variants and/or unusual combinations of ERAP1 variants."

A Harvard- and Imperial College London-led team takes a look at the antigens produced by the respiratory pathogen Streptococcus pneumoniae using pangenome-wide proteomic data. With a custom proteomic array representing thousands of pneumococcal proteins designed with genomic clues from more than 600 nasopharyngeal carriage pneumococcal isolates, the researchers tested blood sera from almost three dozen healthy Americans, narrowing in on 208 antibody-binding targets produced by the pathogen. They note that more than 100 variants fell in a handful of surface or metalloprotease enzyme proteins, while other antigen-affecting variants occurred in conserved proteins. "[S]ome variable antigens rapidly diversified through mechanisms including homologous recombination, mobile genetic element transmission, and phase variation," the authors write. "Other antigens were conserved across the population and may be better candidates for simple vaccine formulations."

Finally, an international team led by investigators at Columbia University describes activating VAV1 alterations that are recurrent in peripheral T-cell lymphoma. The researchers relied on RNA sequencing data for samples from 154 individuals with peripheral T-cell lymphoma, uncovering recurrent mutations and translocations in genes that are known to occur in various sub-types of the disease. But their analyses also unearthed several fusions or mutations involving the guanine exchange factor VAV1 — changes that also turned up in a few more tumors when they considered genomic data for another 126 peripheral T-cell lymphoma cases. 

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.