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This Week in PNAS: Mar 28, 2017

Stanford University researchers introduce a transcribed genome array (TGA) approach to tease out biophysical interactions between RNA binding proteins and the broader transcriptome with a hardware and software system that builds from the Illumina MiSeq flow cell as a biochemical platform. The team's proof-of-principle analyses applied TGA to track transcriptome-wide binding affinities for the Saccharomyces cerevisiae RNA-binding protein Vts1, which is conserved in animals and appears to regulate some developmental features. "Our work couples transcriptome-wide measurements of binding affinity, sequence, and structural determinants of binding, and phenotypic outcomes to provide a comprehensive portrait of Vts function," the authors write, noting that the approach "is easily extensible to other RNA-binding proteins involved in disease and development, and facilitates diverse applications in systems biochemistry."

A team from Houston Methodist Research Institute, Arizona State University, and elsewhere describe a strategy for quantifying levels of antigen peptides associated with active Mycobacterium tuberculosis infections in blood samples from infected individuals. The so-called NanoDisk-MS approach relies on nanodisk-bound antibodies that enrich for peptides specific to active M. tuberculosis cases, the researchers explain, followed by high-throughput mass spectrometry. They demonstrated the specificity and sensitivity of the method in samples from participants with or without HIV infections who were participating in a tuberculosis surveillance study in Texas.

Investigators from Finland and Canada find evidence of balancing selection for variants in two brain-expressed genes implicated in mammalian behavior: Avpr1a and Oxtr, which fall in vasopressin and oxytocin pathways, respectively. The team used the bank vole (Myodes glareolus) as a model, tracking reproductive success in field studies of voles with variable-length microsatellite polymorphisms in regulatory regions of Avpr1a and Oxtr. Though population density was also a factor, the experiments suggested long Avpr1a regulatory region-associated microsatellites (RRAM) and short Oxtr RRAMs boosted reproductive success in male bank voles, while females with short Avpr1a RRAMs and longer Oxtr RRAMs were more successful. "[B]alancing selection through sexually antagonistic fitness effects and density-related social influences is capable of maintaining microsatellite length polymorphisms at both genes," the authors suggest.

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.