In PLOS Genetics, University of Michigan researchers explore a gene regulatory process called RNA-directed DNA methylation (RdDM) — which uses small interfering RNAs and long non-coding RNAs to target repressive chromatin modifications to certain genes — in the model plant Arabidopsis thaliana. The team used a combination of RNA sequencing, Hi-C, and other approaches to profile gene expression and chromatin interactions in wild type Arabidopsis and mutants with altered versions of an AGO4 gene coding for a component of the RNA silencing complex. Based on their findings, the authors note that "the repression of gene expression by RdDM may involve preventing interactions between distant chromosomal regions."
For a paper appearing in PLOS Neglected Tropical Diseases, a team from Thailand, the UK, and the US outlines its search for genes influencing survival and symptom patterns in individuals with melioidosis, a serious emerging infectious disease in Southeast Asia and northern Australia involving Burkholderia pseudomallei infection. The researchers focused on toll-like receptor 5 (TLR5) genotypes in 194 individuals with acute melioidosis in Thailand, reasoning that TLR5's role in bacterial recognition might impact patient outcomes. Their analyses pointed to a potentially protective role for a TLR5 variants found in a subset of patients that was associated with somewhat lower bacterial levels and a dip in death rate.
Canadian Food Inspection Agency researchers report on results from a genomic analysis of senecavirus A (SVA) in swine-related isolates collected in Canada in 2015 for a PLOS One study. After using real-time RT-PCR to screen swabs from pigs and their surrounding environment, the team did genome sequencing on SVA isolates in two clinical swine samples and in nine samples taken from water dispenser, feeders, loading chutes, and other swine environment sites. Analyses of the new sequences, considered alongside 22 already-sequenced SVA genomes, offered a look at everything from SVA evolution to potential transmission patterns and infection sources.