A team from Italy, Portugal, France, and Australia explore PCR-based methods for diagnosing a condition called ocular onchocercosis in dogs and cats. As they report in PLOS Neglected Tropical Diseases, the researchers standardized a quantitative real-time PCR assay to detect DNA from the ocular onchocercosis-causing parasite Onchocerca lupi. They applied the approach to skin samples from nearly three dozen O. lupi-infected dogs, 21 uninfected dogs, and 152 uninfected cats. They also analyzed samples from blackflies, mosquitoes, and midges that may carry such parasites, comparing the sensitivity of the qPCR method with conventional PCR-based efforts to pick up O. lupi. Based on results from the analyses, the authors note that the qPCR assay "could represent an important step forward in the diagnosis of onchocercosis, in carnivores and in insect species acting as potential intermediate hosts."
In PLOS One, researchers from Fisheries and Oceans Canada and the University of Victoria present findings from a genomic analysis of Chinook salmon, Oncorhynchus tshawytscha. The team sequenced and assembled a reference genome using genetic material for a female Chinook salmon from a hatchery in Chilliwack. Together with transcriptome sequences for 18 salmon tissues and a comparison with sequences from the coho salmon, the 2.4 billion-base-pair Chinook salmon genome made it possible to identify protein-coding genes, repetitive elements, chromosomal fusions, and other genome features. "The genome will provide fisheries researchers and managers the full spectrum of nucleotide sequence variation to exploit in research into the adaptive capacity of the species," the authors say.
Finally, for a paper appearing in PLOS Genetics, researchers from the J. Craig Venter Institute, University of California, San Diego, and elsewhere take a look at nearly a dozen methods for phasing the human genome. By comparing performance features and metrics such as accuracy and haplotype block lengths for 11 experimental and/or computational phasing approaches, relative to a gold standard, phased "Genome in a Bottle," they identified some of the most successful phasing strategies. "[O]ur comparisons show that a hybrid or combined approach that leverages population-based phasing … works well," the team says, "and is improved with the additional of genome-wide sequence read or parental genotype data."