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Genomics In The Journals: May 5, 2011

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – In Nature Medicine, researchers from Australia and the UK report that they have identified two new risk loci for a neurodegenerative eye disease called open angle glaucoma. The loci, which fall near the chromosome 1 gene TMCO1 and the CDKN2B-AS1 region of chromosome 9, were identified through a genome-wide association study involving 590 Australians with advanced open angle glaucoma and 3,956 unaffected controls and then validated in hundreds more controls and cases with severe open angle glaucoma, as well as two groups including individuals with less severe forms of the disease.

"[Open angle glaucoma] can be difficult to diagnose in the early stages, and these findings may be useful in the future to prioritize treatment effectively for individuals with possible but not definite early glaucoma (glaucoma suspects)," senior author Jamie Craig, from Flinders University in Adelaide, and co-authors wrote.

The two main Asian rice sub-species cultivated today share a lone origin of domestication, according to a targeted re-sequencing study in the online version of the Proceedings of the National Academy of Sciences. Researchers from New York, Stanford, Washington, and Purdue Universities sequenced 630 gene fragments from chromosomes 8, 10, and 12 in dozens of wild and domestic rice accessions. From SNP patterns in these sequences, they concluded that cultivated rice likely originated from a single source in China's Yangtze Valley, where domestication occurred between 8,200 and 13,500 years ago.

In the American Journal of Human Genetics, Spanish and French researchers outlined their strategy for finding a new mutation associated with an accelerated aging condition. The team sequenced protein-coding genes in individuals from two families affected by premature aging syndrome who did not carry mutations in known risk genes. The search yielded BANF1, a gene that was homozygously mutated in affected family members — a change that follow-up experiments suggest produces alterations to nuclear lamina and envelope structure.

"[T]his study underscores the importance of the nuclear lamina for human aging and demonstrates the utility of the new methods of genome sequencing to identify the genetic cause of rare and devastating diseases which have traditionally received limited attention," senior author Carlos López-Otín, from the University of Oviedo in Spain, said in a statement.

German researchers have found that levels of sFRP1, a gene that codes for a protein thought to influence Wnt signaling, are bumped up in triple-negative breast cancers — particularly in tumors that are more sensitive to neoadjuvant chemotherapy. The team found sFRP1 levels in triple-negative breast tumors that were nearly five times as high as in non-triple negative forms of the disease. Their subsequent experiments suggest that triple negative tumors expressing higher sFRP1 levels are also more sensitive to chemotherapy. On the other hand, curtailing the gene's expression with RNA interference decreases the chemosensitivity of a triple negative cancer cell line.

The work, which was presented at the IMPAKT Breast Cancer Conference in Brussels, is set to appear in a supplement to this month's issue of the Annals of Oncology.

By looking at genomic data for individual marine plankton cells, a team from the US and South Korea found evidence of varied interactions between the plankton and other microbes in the sea — findings they reported in Science. The group isolated three individual plankton cells from seawater by fluorescence-activated cell sorting, amplified genomes from each single cell, and sequenced them with the Roche 454 FLX Titanium platform.

The cells came from three different clades within the Picobiliphyta group, they found. One contained a slew of sequences from an uncharacterized single-stranded DNA virus in its genome, while the other two cells harbored DNA sequences that seem to have originated in large DNA viruses and marine bacteria in the Bacteroidetes phylum.

"Our single-cell sequencing approach opens novel opportunities to study protist, prokaryote, and viral interactions in situ, without cultivation artifacts," senior author Debashish Bhattacharya, an ecology, evolution, and natural resources researcher at Rutgers University, and co-authors noted, "and has biomedical applications; for example, in determining DNA differences between healthy and diseased cell."

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.