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This Week in PLOS: Oct 21, 2014

Researchers from the Genome Institute at Washington University and elsewhere used a systems biology-based approach to identify features in Paragonimus lung flukes aimed at more reliably diagnosing a food-borne condition called paragonimiasis, which is linked to consumption of undercooked crustaceans. As they report in PLOS Neglected Tropical Diseases, the investigators did transcriptome sequencing and mass spec-based protein profiling on the trematode P. kellicotti. Together with "immunolome" experiments that used immunoaffinity purification and liquid chromatography-mass spec assessments to track parasite protein reactivity with infected patient antibodies, these methods made it possible to narrow in on new diagnostic candidates.

For another PLOS Neglected Tropical Diseases study, Chinese researchers used genome sequencing and phylogenetics to investigate a virus from the Bunyaviridae family that caused a 2007 outbreak in that country's Henan province and has since spread to other parts of China. The team sequenced samples from a dozen patients infected with the so-called "fever, thrombocytopenia, and leukocytopenia syndrome virus," or FTLSV. Through comparisons with available sequences from other FTLSV isolates, the investigators saw evidence of FTSLV emergence in an area called Huaiyangshan stretching back to roughly the late 1700's, followed by spread to other area starting in the early part of the next century. The study's authors argue that their findings "provide new insights into the origin and spread of FTLSV in China, and provide a foundation for future virological surveillance and control."

In PLOS One, Japanese researchers introduce a new draft genome assembly for Bacillus subtilis natto — a form of the bacterial species that's used to produce a fermented soybean food by the same name. Using Pacific Biosciences long reads, the team put together a de novo assembly for the B.subtilis natto strain BEST195, which was subsequently improved using Illumina short reads. The resulting draft contains sequences that seem to have been missed in the original B.subtilis genome, which was produced for the laboratory strain Marburg 168. "[W]e found that incomplete regions in the previous genome sequence were attributed to GC-bias and repetitive sequences," the study's authors say, "and we also identified some novel genes that are found only in the new genome.