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This Week in PLOS: Jan 9, 2017

In PLOS Genetics, researchers from the US and Uruguay consider features found in the common liver fluke, Fasciola hepatica, using genome sequencing and comparative genomics. The team generated a reference genome sequence for a liver fluke isolated from a sheep in Oregon that was also infected with Neorickettsia bacteria resembling those behind Sennetsu fever and Potomac horse fever. With the 1.14 billion base genome, re-sequenced genomes for F. hepatica isolates from Uruguay, and expression data for flukes at different life stages, the investigators identified proteins suspected of contributing to interactions with infected ruminants and other liver fluke hosts, along with evidence of potential vertical transmission of Neorickettsia endobacteria.

A PLOS Pathogens study suggests that features associated with Kaposi sarcoma-associated herpesvirus (KSHV) infection resemble those in cells exposed to low-oxygen or hypoxic conditions, which can itself activate some KSHV genes. Using a combination of RNA sequencing, quantitative RT-PCR, and other assays, an international team led by investigators at the National Cancer Institute profiled gene expression and microRNA patterns in hypoxic cells with or without KSHV, uncovering overlap between more than one-third of hypoxia- and KSHV-associated expression signatures. "KSHV harnesses a part of the hypoxic cellular response," they write, "and … a substantial portion of hypoxia-induced changes in cellular gene expression are induced by KSHV infection."

A University of Melbourne- and Oxford University-led team takes a look at genomic shifts in Salmonella enterica from the enterica sub-species and Typhi serovar (Salmonella Typhi) in Thailand since the introduction of vaccines targeting the typhoid fever-causing bacteria in the late 1970s. As they report in PLOS Neglected Tropical Diseases, the researchers did genome sequencing on almost four dozen S. Typhi isolates collected prior to national typhoid immunization began in Thailand in 1977 and in the years since. With these data, they detected 10 S. Typhi genotypes, which largely differed before and after the Thai typhoid vaccination program began. In particular, the isolates found in Thailand more recently tended to resemble those found in neighboring countries, hinting that the immunization program may have helped in ousting endemic strains in Thailand.

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.