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This Week in Nature: Sep 7, 2017

In Nature Neuroscience this week, a team of US and Canadian researchers reports the creation of a multi-omic neuroscience resource using quantitative trait locus (xQTL) analyses on a set of RNA sequence, DNA methylation, and histone acetylation data from the brains of 411 older adults. The investigators identified SNPs significantly associated with gene expression, DNA methylation, and histone modification levels — including many SNPs that influence multiple molecular features. They also used the resource, called xQLT Service, to reanalyze published genome-wide association studies, uncovering 18 new schizophrenia and two new bipolar susceptibility variants.

And in Nature Biomedical Engineering, scientists from Rice University, Thermo Fisher Scientific, and Yale University describe a new multiplexed method for the enrichment and detection of rare DNA variants. The temperature-robust, PCR-based method — dubbed blocker displacement amplification — selectively amplifies all sequence variants, including single-nucleotide variants, within a roughly 20-nucleotide window by 1,000-fold over wild-type sequences, allowing for easy detection and quantitation of hundreds of potential variants originally at or less than 0.1 percent in allele frequency. The method is compatible with inexpensive thermocycler instrumentation and employs a rationally designed competitive hybridization reaction to achieve comparable enrichment performance across annealing temperatures ranging from 56 degrees to 64 degrees Celsius, the researchers state.

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.