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This Week in PNAS: May 26, 2015

In the early, online edition of the Proceedings of the National Academy of Sciences, University of Miami researchers discuss different co-evolutionary signatures that can occur in insect hosts and their bacterial symbionts. The team focused on holobiont signatures arising from host-symbiont collaboration, acquisition, or constraint. "Despite the current limited availability of paired genomes, these genomes support identification of signatures of holobiont genome evolution," authors of the paper explain. "As more holobiont genomes are sequenced, we anticipate that these signatures will continue to be supported and that other as yet unidentified signatures will emerge." 

High-grade serous ovarian tumors tend to produce distinct transcript isoforms, according to a team based at the University of California, San Diego. Using a custom algorithm, the researchers compared RNA sequence data for 296 high-grade serous ovarian tumors and more than 1,800 normal samples. From hundreds of suspicious isoforms, they then narrowed in on half a dozen isoforms present in most of the 12 tumors tested for follow up stages of the study that were missing from 18 normal samples. The team also saw an over-representation of transcripts from specific pathways amongst the top tumor-specific candidate isoforms, pointing processes that may be important to the disease and its progression.

Researchers from the US and Canada describe blood protein markers associated with Duchenne muscular dystrophy, a rare muscular condition caused by mutations to the X-linked gene DMD. The team assayed blood levels of more than 1,100 proteins in samples from 93 individuals with the disease and 45 without, identifying 44 proteins with distinct blood expression patterns in those with Duchenne muscular dystrophy. GenomeWeb has more on the study, here.

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.