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This Week in PNAS: Dec 19, 2017

In Proceedings of the National Academy of Sciences online, researchers from the University of Vienna, Utrecht University, and elsewhere explore microbial communities in Atlantic Ocean samples at different depths in the water column using metaproteomics, metagenomics, and single-cell genomics. The team used mass spectrometry, metagenomic sequencing, and targeted 16S ribosomal RNA sequencing to assess Atlantic Ocean samples, folding in available genomic, functional, other data to get a look at microbial representatives and protein expression in samples collected at more than a dozen depths between 100 meters (328 feet) and 5,000 meters (16,404 feet). "[O]ur data suggest that, while the phylogenetic composition of the microbial community is depth stratified, the composition and substrate specificities of transporters considered in this study are ubiquitous while their relative abundance changes with depth," the authors note.

A team from the National Institute of Genetics in Japan takes a look at genetic features behind the toe webbing and syndactyly, or fused digits, found in mice from a spontaneous mutant dubbed Hammer toe. Using linkage analyses inverse PCR-based structural variant analyses, ATAC-seq profiling on open chromatin, and other approaches, the researchers narrowed in on a 150,000 base fragment of non-coding sequence from chromosome 14 that had been inserted upstream of the Sonic hedgehog promoter. With CRISPR/Cas9-based gene editing on developing mouse embryos, they hammered out the specific enhancer regions contributing to the syndactyly in these mice. The authors say these and other results "provide unequivocal evidence that interchromosomal translocation is able to generate enhancer activity for a developmental gene, which ultimately leads to morphological alteration."

Finally, Chinese researchers report on apparent ties between a microRNA called miR-351 and a Schistosoma infection complication called hepatic fibrosis — a liver condition prompted by activation of a liver cell type known as hepatic stellate cells. Following from miRNA clues gleaned from an earlier study, the team tracked miR-351 expression in liver samples from a mouse model of human liver fibrosis over different stages of S. japonicum infection. Though the miRNA expression dipped early on in the infection process, the authors explain, it ratcheted up later on during the infection process, apparently contributing to hepatic stellate cells activation and liver fibrosis via vitamin D receptor targeting.