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This Week in Science: Jun 26, 2015

In this week's Science, a team led by University of California, Berkeley, researchers report on how Cas9, the enzyme used by the genome-editing tool CRISPR to make double-strand breaks in DNA, does its work. The scientists studied the crystal structures of Cas9 from the bacteria Streptococcus pygoenes bound to a guide RNA at 2.9 angstroms resolution. They discovered a series of distinct conformational changes in the enzyme when it is bound to the guide RNA that carries it to its intended site, priming it for interaction with targeted DNA.

Also in Science, Stuart Black, the vice president of research integrity at the Laura and John Arnold Foundation, argues for transparency in science to address the growing problem of reproducibility. He calls for the creation of free, open-source, infrastructural tools that will allow scientists to more easily incorporate transparency into their daily workflows, as well as the support of the government and public sectors in developing such resources. The Scan has more on transparency efforts here.

Meanwhile, in Science Translational Medicine, Johns Hopkins University researchers describe how DNA in blood and saliva can be used to reliably detect head and neck cancers. Using genome sequencing, the researchers identified either tumor-specific mutations or genes from the human papillomavirus, which is known to cause about a quarter of head and neck cancers, in saliva, blood, or both from 93 cancer patients. Saliva proved highly effective for detecting oral cancer, while blood was the better biofluid for detecting common cancers of the throat and neck. Additionally, follow-up of a subset of treated patients allowed the researchers to detect tumor DNA months before any clinical evidence of recurrence emerged. GenomeWeb has more on this 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.