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Genomics in the Journals: May 8, 2014

NEW YORK (GenomeWeb) – In Nature Genetics, researchers from Memorial Sloan-Kettering Cancer Center and elsewhere took a closer look at PARK2 — an E3 ubiquitin ligase enzyme-coding gene found frequently deleted in cancers originating in many tissue types.

The team considered mutation patterns in genome sequence data for 4,934 tumors representing 11 cancer types. In that data set, PARK2 deletion was the fourth most frequent recurrent deletion, turning up in one form or another in up to 30 percent of tumors tested.

Nevertheless, the PARK2 deletions typically did not occur in tumors with certain cyclin oncogene amplifications, hinting that PARK2 codes for a component of a pathway that overlaps with those genes.

Additional follow-up analyses suggested that PARK2's gene product regulates proteins from both cell cycle regulation and tumor suppression pathways via interactions with cyclin CDK complexes and cyclins involved in the G1/S cell cycle transition, the study authors reported.

A flu virus recently found in Adélie penguins in the Antarctic belongs to an evolutionarily distant branch of the influenza A lineage compared to those contributing to most flu cases, according to a study in mBio.

Starting with blood and swab samples from hundreds of Adélie penguins in the Antarctic Peninsula, an international team led by investigators in Chile, Australia, and Singapore used real-time reverse transcriptase PCR, sequencing, phylogenetic analysis, and more to test viral cultures generated in hens' eggs using influenza A viruses from eight adult penguins and two chicks.

Of those, four viruses had their full genomes sequenced, though all of the isolates tested appeared to be avian H11N2 viruses. That flu subtype is genetically distinct from influenza A viruses described elsewhere, the study's authors explained, with most H11N2 gene segments apparently diverging from those in other present-day avian flu viruses between 49 and 80 years ago.

The viral ancestry appeared to come from several sources as well, with some segments sharing distant ancestry with South American avian flu viruses and others resembling avian or equine viruses circulating in North America.

University of Lyon researchers used existing metagenomic sequence data from dozens of environments to assess the prevalence of antibiotic resistance gene determinants in samples — work that they described in Current Biology.

Based on Roche 454 and Sanger metagenomic sequence data from 71 fecal, ocean, soil, and other environmental samples, the team determined that antibiotic resistance genes are more or less ubiquitous in the environments considered, though the diversity and nature of the resistance genes detected varied depending on the type of sample tested.

"While the environment is known to harbor antibiotic-resistant strains of bacteria, as proven by many preceding studies, we did not really know the extent of their abundance," first author Joseph Nesme, an environmental microbial genomics researcher from the University of Lyon, said in a statement. "The fact that we were able to detect antibiotic resistance genes at relatively important abundance in every environment tested is certainly our most striking result."

A Cell study by researchers in China, Denmark, the US, and elsewhere is providing new details about the timing and nature of polar bear evolution and adaptation, including the bears' ability to live on high fat dietary fare.

By sequencing the genomes of 79 present-day polar bears from Greenland and comparing them with 10 more newly sequenced brown bears from sites in the mainland US, islands off of Alaska, and a region in and around Scandinavia, the team assessed polar bears' evolutionary history and adaptations.

Notably, the researchers' results indicated that polar bears and brown bears diverged from one another sometime within the last 343,000 to 479,000 years. Since that polar bear speciation event, polar bears seem to have been particularly prone to amassing mutations in genes from cholesterol, fatty acid metabolism, and cardiovascular pathways, they noted, including the counterparts of human genes implicated in heart disease.

Of the top 16 genes showing signs of positive selection in the polar bear genome, for instance, nine have been linked to cardiomyopathy and/or vascular diseases in past studies, including the low-density lipoprotein component-coding gene APOB. Those and other polar bear features suggest that it may be possible to mine polar bear genetics and biology for clues to human diseases as well, the study's authors argued.

"The promise of comparative genomics is that we learn how other organisms deal with conditions that we also are exposed to," co-senior author Rasmus Nielsen, an integrative biology and statistics researcher at the University of California at Berkeley, said in a statement.

"For example, polar bears have adapted genetically to a high fat diet that many people now impose on themselves," Nielsen said. "If we learn a bit about the genes that allows them to deal with that, perhaps that will give us tools to modulate human physiology down the line."