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Genomics in the Journals Aug 21, 2014

NEW YORK (GenomeWeb) – In Nature Genetics, an American- and Finnish-led team described the apparent effects of an EGLN1 mutation that's been linked to high-altitude adaptations in the absence of increased hemoglobin levels in individuals from Tibet.

Through targeted gene sequencing on 26 individuals of Tibetan ancestry in the US and more than 100 control individuals of Asian or European ancestry, the researchers determined that the Tibetans tended to share a missense mutation in EGLN1, a gene previously implicated in high-altitude adaptation.

That gene codes for a prolyl hydroxylase 2 enzyme, they explained, which appears to contribute to the degradation of the hypoxia-inducible factors that would normally trigger new blood cell formation and other physiological responses to low oxygen conditions.

The team's follow-up analyses — which included EGLN1 genotype frequencies for dozens of additional Tibetan individuals from India, China, and Tibet — indicated that the EGLN1 mutation and a related variant are shared by most Tibetans but are found at far lower frequency in other populations.

"These findings help us understand the unique aspects of Tibetan adaptation to high altitudes, and to better understand human evolution," the University of Utah's Josef Prchal, a co-corresponding author on the study, said in a statement.


A paper in mBio pointed to genetic factors that bolster the fitness of the plague-causing pathogen Yersinia pestis during deep tissue infection.

University of Massachusetts Medical School researchers used a combination of transposon mutagenesis and high-throughput sequencing to systematically assess the consequences of introducing insertion mutations into virulent Y. pestis genotypes.

When the team looked at the mutations that altered Y. pestis growth patterns in rich nutrient media or after intravenous injections into mouse tissue, it found fitness effects when introducing mutations to most of the genes previously implicated in Y. pestis virulence.

The study's authors also tracked down new fitness factors using the transposon mutagenesis sequencing (Tn-seq) method, including dozens of genes involved in Y. pestis metabolism or nutrient acquisition.

"Our findings suggest that diverse nutrient limitations in deep tissue play a more important role in controlling bacterial infection than has heretofore been appreciated," they wrote. "Because much is known about Y. pestis pathogenesis, this study also serves as a test case that assesses the ability of Tn-seq to detect virulence genes."


With the help of small subunit ribosomal RNA gene sequencing, a team from the US and Italy that included investigators working on the Whillans Ice Stream Sub-glacial Access Research Drilling (WISSARD) project characterized a microbial community found below a West Antarctica ice sheet.

As they reported in Nature, the researchers used a hot water drilling system to bore through the ice sheet and collect samples from a sub-glacial lake below. Along with their measurements of sample temperature and geochemical composition, they were able to identify microbes from Sub-glacial Lake Whillans and begin discerning their metabolic capabilities.

For example, the team determined that archaea were particularly common in microbial communities hidden away under the West Antarctic ice sheet. Together with bacteria, these archaea contributed to metabolic communities with functions ranging from carbon dioxide fixation from ammonia to methane-based energy production.

"We were able to prove unequivocally to the world that Antarctica is not a dead continent," co-author John Priscu, a land resources and environmental science researcher at Montana State University, said in a statement.


In Cancer Cell, members of the Cancer Genome Atlas described the suite of somatic alterations they detected in a rare form of kidney cancer called chromophobe renal cell carcinoma.

The team did array-based copy number, methylation, and gene expression profiling — together with exome sequencing, mitochondrial DNA sequencing, and/or whole-genome sequencing — to assess matched tumor and normal samples from 66 individuals with chromophobe renal cell carcinoma.

From this integrated genomic analysis, the investigators saw signs that altered mitochondrial function may contribute to the development and progression of chromophobe renal cell carcinoma. Their data also revealed recurrent rearrangements impacting promoter sequences for TERT, a gene coding for a telomerase complex component.

The latter alterations appear to bump up TERT expression, the study authors explained, potentially contributing to cancer cell immortalization in a subset of chromophobe renal cell carcinoma cases.

"[W]ith many cancer cells, telomerase levels are really high … which allows the cell to never die," co-senior author Chad Creighton, a researcher with Baylor College of Medicine's Human Genome Sequencing Center, said in a statement, noting that the TERT-related rearrangements were picked up thanks to the availability of whole-genome sequencing data for many of the chromophobe renal cell carcinoma tumors.


A Science study by researchers in the US, Japan, and Ireland suggests the hummingbird's penchant for sugary flavors stems from an evolutionary adaptation that turned an ancestral taste receptor capable of perceiving both sweet and savory flavors into a taste perception system centered on sweets.

Using whole-genome sequences for 10 bird species with different dietary preferences, the team searched for a set of G protein-coupled taste receptors known as T1Rs that are present in other vertebrates.

In three bird species — the chicken, Anna's hummingbird, and a related insect-eater called the chimney swift — investigators went on to clone identified T1Rs and track their expression in oral tissue.

Their analysis revealed a lack of the vertebrate sweet receptor sub-unit called T1R2 in the hummingbirds. Instead, the researchers found evidence that the hummingbird taste perception system involves ancestral umami receptors based on the T1R1 and T1R3 sub-units that were repurposed for sugar sensing in hummingbirds since their split from the insectivorous swift birds.

"We propose that changing taste receptor function enabled hummingbirds to perceive and use nectar," Harvard Medical School's Stephen Liberles, senior author on the study, and his colleagues wrote, "facilitating the massive radiation of hummingbird species."

The Scan

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J&J CSO to Step Down

The Wall Street Journal reports that Paul Stoffels will be stepping down as chief scientific officer at Johnson & Johnson by the end of the year.

Science Papers Present Proteo-Genomic Map of Human Health, Brain Tumor Target, Tool to Infer CNVs

In Science this week: gene-protein-disease map, epigenomic and transcriptomic approach highlights potential therapeutic target for gliomas, and more