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This Week in PNAS: Sep 4, 2013

Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.

Source ground waters can provide the bacterial fodder for microbial communities present in associated springs, according to a study slated to appear online this week in the Proceedings of the National Academy of Sciences. Investigators from the US and The Netherlands used 16S and 18S ribosomal RNA sequencing to assess microbial diversity in samples from three highly basic, low salinity springs in a coastal area of northern California known as The Cedars. Based on results for samples collected over several years, the team found that each spring had distinct microbial community members, which tended to reflect the shallow or deep groundwater sources feeding them. "[I]n the spring fed by deep groundwater, many of the phylotypes are members of, or most closely related to, candidate divisions or classes that are defined only by the 16S rRNA clones recovered from various environments," study authors note, "and where no cultivated microorganisms are clustered."

An international team led by investigators in the US and Germany explores structural variation patterns in primate genomes. With the help of DNA sequencing to detect polymorphisms in five chimpanzee, five orangutan, and five rhesus macaque genomes, the researchers picked up on the presence of rampant retrotransposition in the macaques, for instance. On the other hand, their structural variant maps suggested that the genomes of great apes such as chimps and orangutans are marked by non-allelic homologous recombination. By folding in transcriptome data for humans and non-human primates, the group also got a glimpse at gene duplications contributing to species-specific differences in expression in certain types of tissue.

Researchers from the Universities of Massachusetts and Pennsylvania used a high-throughput insertion tracking by deep-sequencing, or HITS, approach to look at bacterial genes contributing to Haemophilus influenzae infection in mice already infected with influenza A virus in an effort to understand and perhaps prevent such secondary infections. Using the transposon mutagenesis-based approach, the team compared genes needed for H. influenzae infection in mice with or without the pre-existing flu infection, uncovering genes involved in bacterial infection in one or both situations. "The results identify bacterial stress and metabolic adaptations required in an [IAV] co-infection model," the study's authors note, "revealing potential targets for treatment or prevention of secondary bacterial pneumonia after viral infection."