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This Week in PLOS: Jan 20, 2014

Researchers in Portugal report on their characterization of the grapevine microbiome in PLOS One. Using 454 sequencing, the researchers examined the rDNA of the microflora living on some 50 grapevine leaves. Among the most abundant eukaryote the researchers uncovered were the early diverging fungi lineages and members of the Ascomycota phylum like Aureobasidium, while Proteobacteria, Firmicutes, and Actinobacteria were highly represented among the prokaryotes. The researchers also note that the microbial communities appear to be both highly structured and dynamic.

In PLOS Genetics, researchers led by the University of California, Los Angeles' John Novembre write that dog domestication may date back to pre-agricultural times. Using SOLiD and Illumina HiSeq platforms, he and his colleagues generated high-quality genome sequences from three gray wolves — one each from Europe, the Middle East, and East/Southeast Asia, all spots where dogs have been thought to originate — as well as from Basenji and Dingo, which are basal dog lineages, and a golden jackal as an outgroup. Through a phylogenetic analysis, the investigators found that domesticated dogs cluster together in a single group that appears to have diverged from wolves some 34,000 years ago, when most humans were still hunter-gatherers. In addition, they found that none of the wolf groups sequenced appear to be descendants of the wolf group from which dogs originated.

GenomeWeb Daily News has more on this study here.

The University of York's Deborah Smith and colleagues identified signs of sexual reproduction and inbreeding in the parasitic protozoa Leishmania genus. Leishmania mostly undergo asexual reproduction through clonal propagation, but by sequencing 11 Leishmania infantum isolates from sand flies and one patient isolate, the investigators noted a pattern of "patchy heterozygosity and SNP density" that indicated that these isolates originated from a cross between two diverse strains that then reproduce mostly clonally, with some recombination within the population. "We have thus been able to derive quantitative estimates of the relative rates of sexual and asexual reproduction during the Leishmania life cycle for the first time, information that will be critical to our understanding of the epidemiology and evolution of this genus," the researchers say.

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.