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This Week in PLOS: Oct 29, 2012

In an essay in PLOS Biology, a team from Cold Spring Harbor Laboratory argues that high-throughput DNA sequencing may offer a window into the connections between neurons in the mouse brain. The team outlines the nuts and bolts of its proposed sequencing-based method, dubbed "barcoding of individual neuronal connections," or BOINC. The team says that the strategy could offer a timesaving and cost-effective alternative to existing microscopy-based methods for characterizing the "connectome," the complex circuits and relationships between these brain cells.

A study in PLOS One outlines a method for peeking at gene expression profiles in non-model organisms that have not had their genomes sequenced. A Dutch team demonstrated the feasibility of this approach in Chironomus riparius, a midge species sometimes used for sediment ecotoxicity testing. The group sequenced complementary DNA from a range of the midge's developmental stages. Then, through a series of probe design and transcriptome assembly steps, it tracked down and tested thousands of probes targeting the organism's DNA and mRNA. "Our approach allowed the development of high-quality transcriptomics resources for C. riparius, and is applicable to any non-model organism, " University of Amsterdam researcher Martijs Jonker and his co-authors say. "It is expected, that these resources will advance ecotoxicity testing with C. riparius as whole-transcriptome gene-expression analysis are now possible with this species."

In PLOS Pathogens, meanwhile, the Wellcome Trust Sanger Institute's Gordon Dougan and his colleagues characterize microbial strains that show promise for treating chronic Clostridium difficile intestinal infections in mice, based on results from fecal transplant experiments. After successfully using fecal transplants from healthy mice to treat mice infected with a troublesome C. difficile strain called 027, the researchers sequenced the genomes of six bacterial strains that seemed to contribute to the fecal transplant's infection suppression effects. The study's authors also did phylogenetic analyses on the beneficial bugs — work that may set the stage for more standardized use of bacteria for treating certain infections. "Our results validate the microbiota as a viable therapeutic target," they write, "and open the way to rationally design bacteriotherapy to treat chronic C. difficile infections and potentially other forms of persistent dysbiosis."