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Genomics In The Journals: Jul 19, 2012

NEW YORK (GenomeWeb News) – The nature and abundance of microbes living in elderly individuals' intestines can provide information about their broader health, according to a study online in Nature. Researchers from Ireland and the UK used 16S sequencing and other analyses to assess microbial community composition in fecal samples from 78 elderly Irish individuals between the ages of 64 and 102 years old who had not taken antibiotics recently. They also tested more than a dozen younger adults, who were 36 years old, on average. Overall, the team saw more variation between the gut microbiomes of the elderly individuals, which varied by diet and living situation. In particular, individuals living in the community typically had more diverse gut microbial communities than those living in long-term care facilities. Frail individuals and those with inflammation or fecal metabolite patterns pointing to poor health showed a similar shift away from the gut microbiome features found in those living in the community.

Based on these findings, University College Cork researcher Paul O'Toole, the study's senior author, and his colleagues argued that "microbiota profiling, potentially coupled with metabolomics, offers the potential for biomarker-based identification of individuals at risk for, or undergoing, less-health aging."


Methylation patterns at birth could offer clues for understanding and influencing an individual's health in the future, according to a Genome Research study by a team based in Australia, Finland, and the US. The researchers tracked down shared and distinct methylation features in twins at birth, looking at tens of thousands of methylation sites in umbilical cord tissue, cord blood, and placental tissue from 22 pairs of identical twins and a dozen non-identical twin pairs. Methylation patterns where typically more similar for identical than for non-identical twins, researchers reported. Within each set of twins, individuals shared more methylation signatures at specific sites in the genome that were rich in cytosine and guanine bases, known as CpG islands, than they did at spots falling further from these islands. Likewise, methylation at CpG island sites was more apt to be influenced by inherited genetic factors. Overall, though, much of the methylation that the team detected appeared to be influenced by non-heritable factors, particularly environmental exposures in the womb. And with findings from the study linking weight at birth to methylation status at several metabolism, growth, and cardiovascular-related genes, its authors argued that epigenetic profiles established before birth could be important for predicting complex disease risk over an individual's lifetime.

"This has potential to identify and track disease risk early in life," co-senior author Richard Saffery, a pediatrics and epigenetics researcher at Murdoch Childrens Research Institute in Australia, said in a statement, "or even to modify risk through specific environmental or dietary interventions."


A study in the New England Journal of Medicine highlights the distinct genetic features behind two syndromes classified as antineutrophil cytoplasmic antibody-associated vasculitis, which includes conditions characterized by inflammation-related damage to small blood vessels. A large international team led by investigators in the UK did a genome-wide association study involving 1,233 individuals from the UK with ANCA-associated vasculitis, along with almost 6,000 unaffected controls. After testing candidate variants detected in the discovery stage of the study in thousands more cases and controls, researchers were left with four variants showing genome-wide significant ties to ANC-associated vasculitis. Three of these fell in and around major histocompatibilty complex component coding regions, while one turned up in a non-MHC related gene called SERPINA1. A SNP in PRTN3 that was tested based on that gene's suspected role in vasculitis was also significantly associated with the condition. Meanwhile, a closer look at the variants implicated in two forms of ANCA-associated vasulitis — granulomatosis with polyagniitis and microscopic polyangiitis — pointed to distinct genetic underpinnings for the two syndromes.


Investigators from the University of California at Berkeley used whole-genome sequencing and transcriptome studies in fruit flies to explore sex chromosome evolution — work that they describe in Science. Because sex chromosomes have evolved several times within species from the Drosophila genus, investigators were able to compare older and younger X and Y chromosomes using sequences from two fly species: D. pseudoobscura and D. miranda. The latter species experienced a bout of sex chromosome evolution just a million or so years ago — a relatively recent event in evolutionary terms. Results of the study highlight the rapid gene loss that tends to occur on the Y chromosome once it makes the switch from an autosome to a sex chromosome. Genes that do stick around on the Y chromosome seem to evolve quickly and become "masculinized," the team explained, showing expression that's specific male tissues and/or contributing to functions that benefit males. On the other hand, they found clues that sex-specific influences over X chromosome evolution can shift with time, with some genes from burgeoning X chromosomes showing elevated expression in male-specific tissues and genes from more mature X chromosomes showing relatively little expression in these tissues.


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

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