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This Week in PLOS: Apr 22, 2019

For a paper appearing in PLOS One, a team from India and Saudi Arabia explore antibiotic resistance patterns in Escherichia coli isolated from 120 children in India. The researchers focused on quinolone resistance-related region of the E. coli genome in children under five-years-old in Delhi, using multiplex PCR amplification and amplicon sequencing to profile resistance genes in E. coli found in stool samples. Based on the resistance variants they found, together with subsequent phylogenetic analyses on the E. coli isolates, the investigators saw hints that healthy children in India are carrying antibiotic-resistant forms of E. coli in their gut microbiomes. "Our observations suggest the implementation of active surveillance and stewardship programs to promote appropriate antibiotic use and [minimize] further danger," they write.

In PLOS Genetics, researchers from Novosibirsk State University and other centers in Russia describe a dozen genetic loci with apparent ties to varicose vein risk in Europeans. Using the GeneATLAS database, the researchers tracked down summary statistics from prior genome-wide association studies on more than 408,400 UK Biobank participants, including 10,861 individuals with varicose vein diagnoses and 397,594 without. After narrowing in on 14 suspicious loci with data for more than 336,100 of the individuals in Neale Lab database, they used the UK Biobank data to validate 12 loci, predict and prioritize potential causal genes, look at correlated traits, and perform in silico functional analyses.

A team from the University of Pennsylvania digs into a portion of the respiratory syncytial virus (RSV) genome involved in the production of so-called copy-back defective genomes (cbDVGs), which prompt and influence host immune responses. As they report in PLOS Pathogens, the researchers relied on a custom bioinformatic approach to focus in on cbDVG-generating parts of the RSV genome based on breakpoint and region patterns detected with available RNA sequence data, verifying the proposed functions for the cbDVG-related sequences in a mini-genome system and recombinant virus experiments. Based on these and other results, the authors suggest that "sequences encoded in the viral genome determine the location of cbDVG formation and, therefore, the generation of cbDVGs is not a stochastic process."

The Scan

Foxtail Millet Pangenome, Graph-Based Reference Genome

Researchers in Nature Genetics described their generation of a foxtail millet pangenome, which they say can help in crop trait improvement.

Protein Length Distribution Consistent Across Species

An analysis in Genome Biology compares the lengths of proteins across more than 2,300 species, finding similar length distributions.

Novel Genetic Loci Linked to Insulin Resistance in New Study

A team reports in Nature Genetics that it used glucose challenge test data to home in on candidate genes involved in GLUT4 expression or trafficking.

RNA Editing in Octopuses Seems to Help Acclimation to Shifts in Water Temperature

A paper in Cell reports that octopuses use RNA editing to help them adjust to different water temperatures.