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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

Latent HIV Found in White Blood Cells of Individuals on Long-Term Treatments

Researchers in Nature Microbiology find HIV genetic material in monocyte white blood cells and in macrophages that differentiated from them in individuals on HIV-suppressive treatment.

Seagull Microbiome Altered by Microplastic Exposure

The overall diversity and the composition at gut microbiome sites appear to coincide with microplastic exposure and ingestion in two wild bird species, according to a new Nature Ecology and Evolution study.

Study Traces Bladder Cancer Risk Contributors in Organ Transplant Recipients

In eLife, genome and transcriptome sequencing reveal mutation signatures, recurrent somatic mutations, and risky virus sequences in bladder cancers occurring in transplant recipients.

Genes Linked to White-Tailed Jackrabbits' Winter Coat Color Change

Climate change, the researchers noted in Science, may lead to camouflage mismatch and increase predation of white-tailed jackrabbits.