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Genomics In The Journals: Mar 29, 2012

NEW YORK (GenomeWeb News) – A comparative genomics study in PLoS Pathogens illustrates the way seemingly minor genetic changes can dramatically influence the virulence of protozoan parasites.

An international team led by investigators in the UK and Saudi Arabia did genome and transcriptome sequencing on a pathogen called Neospora caninum that can spread from dogs to a limited number of host animals, including cattle, and Toxoplasma gondii, a parasite that can spread from cats to humans and a broad range of other vertebrates.

Comparisons between the parasite sequences indicated that Toxoplasma's infectious edge may be due to the presence of ROP18, a gene that helps it elude proteins in some host immune systems. The same gene seems to have been turned into a pseudogene in Neospora in the 28 million years or so since the parasites diverged from one another. On the other hand, Neospora has far more genes coding for cell surface antigen proteins, researchers found, though many appear to be inactive.

"Collectively, our results indicate that the ecological niches occupied by both parasites are influenced by subtle, adaptive, genetic changes," University of Liverpool researcher Jonathan Wastling, co-senior author on the study, said in a statement. "This project is an excellent example of how humans and animal medicine can learn from each other to provide better outcomes for both."

A meta-analysis appearing in Nature Genetics has uncovered nine new loci influencing rheumatoid arthritis risk in the Japanese population.

Researchers participating in the Genetics and Allied research in Rheumatic diseases Networking, or GARNET, consortium brought together GWAS data on 4,074 Japanese individuals with rheumatoid arthritis and more than four times as many unaffected controls from the same population, identifying four known and three previously unidentified loci. Replication testing in another 5,277 cases and 21,684 controls verified these associations, while the team's combined analysis of discovery and replication group data uncovered six more new loci.

Through comparisons with data from published meta-analyses done in European populations, meanwhile, investigators found a set of 14 rheumatoid arthritis risk loci that are shared between European and Japanese populations, including two identified through the Japanese meta-analysis.

In Proceedings of the National Academy of Sciences, researchers from the University of Michigan, Baylor College of Medicine, and Case Western Reserve University describe the ribosomal RNA sequencing strategy that they used to track bacterial community composition in the airways of cystic fibrosis patients over several years.

From 16S rRNA hyper-variable sequence patterns found in sputum samples collected from half a dozen men with cystic fibrosis over eight or nine years, the team concluded that bacterial communities tend to maintain their density but become less diverse as lung disease progresses in cystic fibrosis, particularly after antibiotic use. Even so, the overall bacterial communities present in the samples generally varied more between patients than it did within any one individual.

Genetic variants in and around HLA class II immune coding loci in the genome influence susceptibility to a disfiguring leg swelling disease seen in some individuals' exposure to minerals in volcanic red clay soil, according to a New England Journal of Medicine study.

An international research team did a genome-wide association study involving 194 individuals from southern Ethiopia with the condition, a form of elephantiasis known as podoconiosis, or endemic nonfilarial elephantiasis. When they compared patterns in the genome with those found in 203 unaffected individuals from the same population, researchers detected several HLA class II region variants.

Through follow-up analyses in 200 trios, along with 94 cases and as many controls, the team found an association in the HLA-DQA1 area that reached genome-wide significance, along with several other variants near HLA-DQA1, HLA-DQB1, and HLA-DRB1 with suggestive associations. Variants in the region appear to elevate podoconiosis risk by two to three times, consistent with the notion that risk for the disease is related to inflammation and immune function.

"It confirms what we had expected, that there is an immunological basis to the disease," co-author Melanie Newport, an infectious diseases and global health researcher at Brighton and Sussex Medical School, said in a statement. "Although this is still early days for identifying potential treatments, it suggests that drugs that target immune responses may be useful."

She and her colleagues have kicked off a program called Footwork to marshal public and private efforts towards podoconiosis prevention and treatment. They also plan to partner with other organizations that are tackling other neglected tropical diseases and/or foot diseases.

By applying a pattern recognition strategy called fuzzy cluster analysis, researchers from the University of California at San Diego, Virginia Commonwealth University, and elsewhere have come up a map of the surface of the human brain cortex based on a dozen different genetic clusters — work that they describe in Science. To create their genetics-based brain atlas, researchers relied on brain imaging information for 406 twins enrolled in a longitudinal study through the Vietnam Era Twin Registry, including both identical twins, who have nearly identical genomes, and non-identical twins, who are as closely related genetically as typical siblings.

"Using the twin design, which compares monozygotic and dizygotic twins, we then estimated genetic correlations between different points on the cortical surface," UCSD researchers William Kremen and Anders Dale, co-senior authors of the study, and their colleagues explained. "These genetic correlations represent shared genetic influences on relative areal expansion between cortical regions."

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

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.