The University of Pennsylvania's Hakon Hakonarson and colleagues used transcriptome profiles of colonic mucus to look for gene expression shifts associated with ulcerative colitis. As they report in PLOS One, the investigators relied on a gene set enrichment analysis approach to assess three sets of gene expression data generated on endoscopic colon biopsy samples with microarrays. Their analysis uncovered eight genes that were down regulated in the colonic mucosa of individuals with ulcerative colitis, along with nearly 90 sets of genes showing higher-than-usual expression in the ulcerative colitis samples. The differentially expressed genes included those involved in processes such as signaling, cell division, and immune function — a set that tended to overlap with colitis-associated genes found in a genome-wide association study of thousands more cases and controls.
A PLOS Pathogens study by researchers involved in the UK HIV Drug Resistance Database and the UK CHIC Study revealed the variable viral set points present in the plasma of individuals infected with various HIV genotypes. By bringing together quantitative genetic and population-level data for almost 8,500 HIV-positive individuals infected with HIV-1 from subtype B, the group estimated that genetic features in HIV explains almost 6 percent of the plasma viral load variance seen in such patients. "Our results suggest that in the UK epidemic, subtype B has a small but significant viral genetic effect on viral load," the study's authors say. "By allowing the analysis of large sample sizes, we expect our approach to be applicable to the estimation of the genetic contribution to traits in many organisms."
In PLOS Neglected Tropical Diseases, Spanish researchers describe conserved intergenic sequences they detected in genomes of the Chagas disease-causing protozoan parasite Trypanosoma cruzi. Using existing genome sequence data for multiple T. cruzi representatives, the team examined the features and genetic diversity found in non-protein-coding portions of the pathogen's genome. The analysis uncovered a set of highly conserved intergenic regions in T. cruzi, regardless of the lineage considered and shared intergenic sequence motifs, along with more variable intergenic sequences.