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This Week in PLOS: Sep 3, 2012

Investigators in Switzerland report their study of the establishment of a gut microbiome in infants in PLOS One. Using a combination of culturing, 16S rRNA gene sequencing, qPCR analysis, and Sanger sequencing, they examined the bacterial makeup of feces from seven healthy, vaginally delivered, breast-fed babies. The researchers found that there were more anaerobic bacteria than facultative anaerobic bacteria in all samples, with high levels of Bifidobacterium and Bacteroides. Bacteroides, the investigators note, is more commonly found in adults. "The presence of Bacteroidetes as pioneer bacteria in the majority of neonates studied demonstrates that adult-type strict anaerobes may reach adult-like population densities already within the first week of life," they write. "Consequently the switch from facultative to strict anaerobes may occur earlier than previously assumed."

Over in PLOS Genetics, Mayo Clinic researchers write that whole-chromosome instability is not a barrier to reprogramming cells to pluripotency. In two mouse lines that commonly experience improper chromosome segregation, the researchers found that the cells could be reprogrammed "to pluripotency with normal efficiency." They add that "furthermore, our data reveal that W-CIN that exists at the somatic cell level can become dormant upon reprogramming, indicating that testing of both iPSCs and the iPSC-founding cells for chromosome number instability will be necessary for the safe application of iPSC technology in regenerative medicine."

Finally in PLOS Neglected Tropical Diseases, researchers in China present their transcriptome analysis of the parasite Trichinella sparilis. They examined the T. sparilis transcriptome at three developmental stages, identifying genes involved in parasite development and host-parasite interaction. "Approximately 65% of genes in T. spiralis genome were identified and a large number of functionally interesting genes were discovered and analyzed in the three developmental stages of the parasite through high throughput RNA sequencing techniques," the authors say. "More than 45% of the protein-coding genes showed evidence of transcription from both sense and antisense strands."

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.