Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.
In the early, online edition of the Proceedings of the National Academy of Sciences, a Massachusetts-led team used exome sequencing and bioinformatics as part of its analyses of a condition present at birth called congenital diaphragmatic hernia (CDH). Based on exome sequence data for 275 individuals with CDH, the researchers tracked down rare variants occurring in genes suspected of contributing to CDH as well as chromosomal regions that tend to be altered by deletions or duplications in those with the condition. Together with gene expression and other experiments in mouse models of the disease, the analysis highlights genes and pathways that appear to contribute to diaphragmatic development that may go awry in CDH.
Researchers at the University of Massachusetts RNA Therapeutic Institute and elsewhere uncovered blood microRNAs associated with liver damage in individuals with ischemic hepatitis or those taking acetaminophen. Using quantitative real-time PCR, the team looked at levels of almost 400 extracellular miRNAs in individuals with or without acetaminophen poisoning or ischemic hepatitis. In the process, it saw 11 miRNAs associated with liver damage — a set that showed waning expression in individuals with acetaminophen overdose that was treated with an N-acetyl cysteine antidote to the poisoning.
A comparative genomics study by French researchers indicates that viruses taken up by bacterial genomes are frequently domesticated before being degraded and replaced by newer prophages performing similar functions. The team scrutinized genome sequences from dozens of Escherichia coli and Salmonella enterica representatives to find prophages within the bacterial genomes, including more than 300 showing signs of vertical inheritance between generations of the enterobacteria. By following the fates of prophages with shared insertion sites, the investigators were able to track the inactivation and degradation of the viruses, as well as selection by bacterial hosts to maintain particular phase-associated functions. The study's authors argue that their results point to "pervasive domestication of parasites by the bacterial hosts," along with a possible role for phage domestication in bacterial adaptation.