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This Week in Nucleic Acids Research: Sep 3, 2014

In Nucleic Acids Research online, a team from Denmark and Hong Kong introduces a database designed to discern links between human disease features and small molecules found in plant-based food sources. The resource, dubbed NutriChem, was developed using a systems chemical biology approach that tapped into data from 21 million published abstracts involving plant-based foods, phytochemicals found in plants, and human disease phenotypes. "To the best of our knowledge this database is the only resource linking the chemical space of plant-based foods with human disease phenotypes," the study's authors say, "and provides a foundation for understanding mechanistically the consequences of eating behaviors on health."

University of Warwick researchers present a method called MosaicSolver that mines high-throughput sequence data to find recombination events and related mosaicism in viral genomes. The team demonstrated the veracity of this approach — which relies on geometric information gleaned from read pileup patterns — using small interfering RNA profiles, RNA sequence data, and genome sequence information associated with two honeybee viruses: the honeybee deformed wing virus and the Varroa destructor virus 1. There, the MosaicSolver helped in uncovering recombinant forms of two parent viruses within samples that contained multiple viruses.

Researchers in Germany relied on RNA sequencing and transposon mutagenesis sequencing to characterize coding and non-coding transcripts and delineate a core set of essential genes in the gonorrhea-causing human pathogen Neisseria gonorrhoeae. In the process, the team documented almost 830 apparently essential genes in N. gonorrhoeae, for example — a set that included more than 100 genes with yet unknown functions. "Our basic analyses focused on growth conditions on rich medium," the investigators note, "however, the full potential of the approach will be exploited in future by investigating different infection conditions."