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This Week in PNAS: Jul 16, 2014

In a study appearing in the online edition of the Proceedings of the National Academy of Sciences this week, a team from the Genome Institute of Singapore and the National University of Singapore describes the metagenomic, metatranscriptomic, and culture-based method it used to find three anaerobic microbe strains from the Dehalococcoides mccartyi species that can detoxify polychlorinated biphenyl, or PCB, pollutants in the environment. After culturing PCB-respiring strains with the help of enrichment with a related tetracholoroethene (PCE), the researchers used sequences generated for microbes grown in the presence of PCBs and PCEs to define three different D. mccartyi strains that can remove chlorine residues from a PCB mix known as Aroclor 1260.

French researchers used transposon mutagenesis in a library of tagged Lactobacillus casei mutants to examine the functional genes involved in helping the bug take up residence in the gut of a rabbit model organism. Using this signature-tagged mutagenesis method, together with whole-genome transposon insertion site sequencing, the team focused in on 1,110 L. casei mutants, each carrying a mutation that affected a different gene. A closer look at the mutants' prevalence in rabbit intestines over time pointed to 47 main genes (belonging to five functional groups) that seemingly contribute to L. casei's ability to set up shop in the gut.

Plants from three closely related eudicot families belonging to an angiosperm plant group called Campanulaceae sensu lato contain plasmid genomes that have undergone both extensive rearrangements and insertions by new protein-coding genes, according to a study by Indiana University's Eric Knox. Knox generated draft plastid genome sequences from the leaves of more than three dozen species in Campanulaceae sensu lato families and one member of a sister group. By comparing these "plastomes" to one another and to other angiosperm plastid sequences by multiple sequence alignment, he determined that the Campanulaceae sensu lato plastomes contain dozens of open reading frames that seem to have been nabbed from the nucleus — a pattern not detected in plants from other branches of the angiosperm family tree.