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This Week in Genome Biology: Oct 24, 2012

In the latest issue of Genome Biology, the University of British Columbia's Leonard Foster and his colleagues report on proteomic profiles of honey bees from colonies that are relatively resistant to the parasitic mite Varroa destructor, believed to be a contributor to colony-collapse disorder. The team used mass spectrometry-based analyses to track protein production by adult bees and bee larvae from several bee colonies, looking at which of the 1,200 or so proteins they assessed, if any, prompted hygienic bee behavior — the removal of V. destructor-compromised larvae — in colonies infested by the mite. "We have found a set of proteins which could be used to select colonies on their ability to resist Varroa mite infestation," Foster says in a press release, "and can be used to find individuals with increased hygienic behavior."

Researchers from the Harvard School of Public Health, the Broad Institute, and elsewhere used a combination of 16S ribosomal RNA gene sequencing and shotgun metagenomic sequencing to compare the gut microbiomes of hundreds of individuals with or without inflammatory bowel disease. The team used this data to assess gut microbial community components and microbial genes identified in intestinal biopsy and/or stool samples from 121 individuals with Crohn's disease, 75 individuals with ulcerative colitis, 27 healthy controls, and eight individuals whose IBD status was unknown. Findings from the study suggest that gut microbiomes from individuals with IBD are more apt to differ in their functional capabilities than in their composition. For instance, the researchers report, microbiomes from individuals with IBD displayed alterations affecting oxidative stress, carbohydrate metabolism, amino acid production, and nutrient transport pathways.

In a study in the early, online edition of Genome Biology, meanwhile, an international team led by investigators in Belgium describes tumor methylation markers that appear to correspond with survival for the childhood nervous system cancer neuroblastoma. The team tracked down the potentially prognostic biomarkers using multiple DNA methylation profiling methods in well-characterized neuroblastoma cell lines and 20 primary, pre-treatment neuroblastoma tumor samples. Dozens of candidate methylation markers were subsequently subjected to validation testing in a set of 89 more primary neuroblastoma tumors. The search led to "several novel prognostic DNA methylation markers," Ghent University medical genetics researcher Jo Vandesompele and colleagues say, "and provide a basis for the development of a DNA methylation-based prognostic classifier in neuroblastoma."

The Scan

Should've Been Spotted Sooner

Scientists tell the Guardian that SARS-CoV-2 testing issues at a UK lab should have been noticed earlier.

For Martian Fuel

Researchers have outlined a plan to produce rocket fuel on Mars that uses a combination of sunlight, carbon dioxide, frozen water, cyanobacteria, and engineered E. coli, according to Gizmodo.

To Boost Rapid Testing

The Washington Post writes that new US programs aim to boost the availability of rapid at-home SARS-CoV-2 tests.

PNAS Papers on Strawberry Evolution, Cell Cycle Regulators, False-Positive Triplex Gene Editing

In PNAS this week: strawberry pan-genome, cell cycle-related roles for MDM2 and MDMX, and more.