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This Week in PLOS: Mar 18, 2014

In PLOS Genetics, American researchers used genomic approaches to characterize bipolar disorder in individuals belonging to a large, well-documented Amish pedigree. Along with SNP and microsatellite data on 388 members of an Amish family, the team performed whole-genome sequencing on 50 of the study participants — data used for subsequent linkage and association analyses. The work highlighted five chromosomal regions with nominal or more tenuous ties to bipolar disorder risk, along with several candidate genes suspected of contributing to the condition.

A PLOS Pathogens study suggests that the Pichia fungus may combat some opportunistic pathogens in the mouth microbiome of individuals infected with HIV. Researchers from Case Western University and elsewhere used a combination of 16S rRNA gene sequencing, ITS sequencing, and biofilm analyses to characterize microbiomes and mycobiomes present in the mouths of a dozen HIV-positive and a dozen HIV-negative individuals and to explore interactions between organisms in those communities. Their results indicated that Pichia's presence may antagonize opportunistic pathogens such as Candida albicans and Aspergillus. "This study is the first to characterize the mycobiome and the bacteriome in the oral cavity of HIV-infected patient," they write, "and provides the first evidence that a fungus present in the same micro-environment antagonizes Candida and identifies [a] potential novel antifungal approach."

A Broad Institute and Uppsala University-led team introduces an improved version of the canine genome — and corresponding annotation — in PLOS One. Through targeted sequencing of the dog genome and a new build of available sequence data, the researchers assembled a canine genome known as canFam3.1 that spans 99.8 percent of the dog's euchromatic genome and contains some 85 million bases of sequence not present in prior versions of the genome. That reference, together with transcriptome sequences from 10 dog tissues, made is possible to define around 175,000 expressed loci, including roughly 3,000 loci not annotated in dogs previously. Along with new and known protein-coding genes, the group described a slew of antisense transcripts, potential long, intergenic non-coding RNAs, and thousands more transcripts with unknown functions.