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Genomics In The Journals: 2011.07.28

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – Researchers from Japan and Australia report in Nature that they have sequenced the genome of the scleractinian coral Acropora digitifera — a feat that they say will help gauge how coral reef communities may react to changing ocean conditions such as acidification and temperature shifts.

Once they'd sequenced the coral's 420 million base genome to about 151 times coverage with the Roche 454 GS-FLX and Illumina GAIIx, the researchers analyzed its gene content and compared it to the sea anemone genome. They found that while A. digitifera has nearly 23,700 protein-coding genes, it lacks the genetic wherewithal to make its own cysteine, suggesting it gets the amino acids from symbiotic dinoflagellate species. On the other hand, the coral genome contains several genes involved in innate immunity and calcification, they noted, as well as genes predicted to help it survive harsh sunlight.

In the early, online edition of the Proceedings of the National Academy of Science, a team from the University of Wisconsin, the Great Lakes Bioenergy Research Center, Michigan State University, and the US Department of Energy Joint Genome Institute sequenced the genomes of two yeast species — Spathaspora passalidarum and Candida tenuis — to about 44 and 27 times coverage, respectively. The bark beetle-associated fungi can ferment xylose, a five-carbon sugar found in the plant material that some hope to use as a biofuel substrate.

Through comparative genomic analyses of S. passalidarum, C. tenuis and several other fungi, the investigators found genes used to turn xylose into ethanol by the species that are the most naturally adept at this conversion. Transplanting 10 of these genes into engineered yeast strains enhanced their xylose use, too, the team reported.

"This research has provided us with a great genomic toolset," first author Dana Wohlbach, a post-doctoral researcher at the University of Wisconsin at Madison, said in a statement. "We're excited to explore new ways to increase yeast's ability to consume xylose and improve ethanol production for cellulosic biofuels."

Researchers led by Charis Eng of the Genomic Medicine Institute at the Cleveland Clinic conducted genome-wide mapping to identify three genes — MSR1, ASCC1, and CTHRC1 — that they said are associated with Barrett esophagus/esophageal adenocarcinoma. The researchers used the Affymetrix GeneChip Human Mapping 100K SNP set to genotype 21 concordant-affected sibling pairs (42 individuals with BE/EAC) and 11 discordant sibling pairs (11 with BE/EAC and 11 without BE/EAC). According to their results, published in the July 27 issue of the Journal of the American Medical Association, mutational analyses of 12 priority candidates genes in the BE/EAC cases found mutations in MSR1, ASCC1, and CTHRC1 in 13 of 116 patients.

"These 3 genes together accounted for 11 percent of our cases, reflecting what is normally considered a moderate-to high-penetrance genetic load for a disease," the researchers wrote. "Nonetheless, future independent studies are needed to replicate our data in other patient populations to confirm the conclusions."

Following on a published study last week in The Lancet Infectious Diseases evaluating the performance of Cepheid's Xpert MTB/RIF molecular test in pediatric tuberculosis cases, this week two separate studies have been published in PLoS Medicine evaluating the test in populations with high HIV rates.

In the first study, led by Stephen Lawn from the Desmond Tutu HIV Centre at the University of Cape Town in South Africa, researchers compared the diagnostic accuracy of Xpert MTB/RIF with several other tests, including liquid culture, in HIV-infected patients. Nearly a fifth of the patients had culture-positive TB, and Xpert MTB/RIF identified three-quarters of these patients. The Cepheid test also had a low false-positive rate and was able to detect all cases of smear-positive, culture-positive TB but only 43.4 percent of smear-negative, culture-positive cases from a single sputum sample.

In addition, the test correctly identified rifampicin resistance in all four patients who had multidrug-resistant TB, but it incorrectly identified resistance in three patients with drug-sensitive TB.

"In this population of individuals at high risk of TB, intensive screening using the Xpert MTB/RIF assay increased case detection by 45 percent compared with smear microscopy, strongly supporting replacement of microscopy for this indication," the researchers wrote. "However, despite the ability of the assay to rapidly detect rifampicin-resistant disease, the specificity for drug resistant TB was sub-optimal."

In the second study, Lesley Scott from the University of the Witwatersrand in Johannesburg, South Africa, and collaborators compared the performance of the Cepheid test with smear microscopy, liquid culture, and two other nucleic acid amplification tests (MTBDRplus and LightCycler MTB) in 311 adults suspected of having TB. Their results suggest that the Xpert MTB/RIF test may provide a more accurate rapid diagnosis of TB than smear microscopy and other currently available tests, including molecular tests, in regions where HIV and TB are endemic.

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