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This Week in PNAS: Sep 13, 2016

In the early, online edition of the Proceedings of the National Academy of Sciences, a team led by investigators from the Catholic University of Korea describes recurrent mutations in the serine/threonine kinase enzyme-coding gene AKT1 in a benign lung tumor condition called pulmonary sclerosing hemangioma. Starting with exome sequencing on pulmonary sclerosing hemangioma and matched normal samples from 44 individuals, the team identified AKT1 mutations in more than 40 percent of tumors — results they confirmed through testing on two dozen more pulmonary sclerosing hemangiomas. A smaller proportion of tumors had recurrent mutations in the beta-catenin gene, and non-recurrent alterations turned up across many genes implicated in cancer.

Investigators from Iowa State University, the National University of Singapore, and the Genome Institute of Singapore search for sources of hyper-virulence in the foodborne and animal pathogen Campylobacter jejuni. Using a directed evolution approach, the team did whole-genome sequencing on virulent strains — known for escaping the intestinal tract to produce system-wide infection and spontaneous abortion in pregnant ruminant animals — and less virulent strains, all grown in a guinea pig model. Through sequencing and comparison of almost 100 C. jejuni isolates, the study's authors narrowed in on point mutations in the outer membrane protein-coding gene porA that appeared to boost virulence in the bug.

Finally, an international team introduces a neurological syndrome that appears to be caused by autosomal recessive mutations in the glutamate pyruvate transaminase 2 enzyme-coding gene GPT2. The researchers used a combination of linkage mapping and exome sequencing to search for suspicious mutations in two large families that contained individuals with features such as microcephaly, intellectual disability, tremors, and progressive motor problems. In affected individuals, they tracked down loss-of-function GPT2 mutations, prompting follow-up studies of mice missing the gene. Without the gene, which is normally expressed more highly after birth, the mice had both muted brain growth and shifts in brain metabolite patterns.

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.