Microbial colonization and alteration of basaltic glass

International audienceMicroorganisms have been reported to be associated with the alteration of the glassy margin of seafloor pillow basalts (Thorseth et al., 2001, 2003; Lysnes et al., 2004). The amount of iron and other biological important elements present in basalts and the vast abundance of basaltic glass in the earth's crust, make glass alteration an important process in global element cycling. To gain further insight into microbial communities associated with glass alteration, five microcosm experiments mimicking seafloor conditions were inoculated with seafloor basalt and incubated for one year. Mineral precipitations, microbial attachment to the glass and glass alteration were visualized by scanning electron microscopy (SEM), and the bacterial community composition was fingerprinted by PCR and denaturing gradient gel electrophoresis (DGGE) in combination with sequencing. SEM analysis revealed a microbial community with low morphological diversity of mainly biofilm associated and prosthecate microorganisms. Approximately 30 nm thick alteration rims developed on the glass in all microcosms after one year of incubation; this however was also seen in non inoculated controls. Calcium carbonate precipitates showed parallel, columnar and filamentous crystallization habits in the microcosms as well as in the sterile controls. DGGE analysis showed an alteration in bacterial community profiles in the five different microcosms, as a response to the different energy and redox regimes and time. In all microcosms a reduction in number of DGGE bands, in combination with an increase in cell abundance were recorded during the experiment. Sequence analysis showed that the microcosms were dominated by four groups of organisms with phylogenetic affiliation to four taxa: The Rhodospirillaceae, a family containing phototrophic marine organisms, in which some members are capable of heterotrophic growth in darkness and N2 fixation; the family Hyphomicrobiaceae, a group of prosthecate oligotrophic organisms; the genus Rhizobium, N2 fixating heterotrophs; and the genus Sphingomonas, which are known as bio-film producing oligotrophs. Although no bioalteration of glass could be confirmed from our experiments, oligotrophic surface adhering bacteria such as the Sphingomonas sp. and Hyphomicrobium sp. may nevertheless be important for bioalteration in nature, due to their firm attachment to glass surfaces, and their potential for biofilm production

Gene Expression Profiling of Soft and Firm Atlantic Salmon Fillet

Texture of salmon fillets is an important quality trait for consumer acceptance as well as for the suitability for processing. In the present work we measured fillet firmness in a population of farmed Atlantic salmon with known pedigree and investigated the relationship between this trait and gene expression. Transcriptomic analyses performed with a 21 K oligonucleotide microarray revealed strong correlations between firmness and a large number of genes. Highly similar expression profiles were observed in several functional groups. Positive regression was found between firmness and genes encoding proteasome components (41 genes) and mitochondrial proteins (129 genes), proteins involved in stress responses (12 genes), and lipid metabolism (30 genes). Coefficients of determination (R2) were in the range of 0.64–0.74. A weaker though highly significant negative regression was seen in sugar metabolism (26 genes, R2 = 0.66) and myofiber proteins (42 genes, R2 = 0.54). Among individual genes that showed a strong association with firmness, there were extracellular matrix proteins (negative correlation), immune genes, and intracellular proteases (positive correlation). Several genes can be regarded as candidate markers of flesh quality (coiled-coil transcriptional coactivator b, AMP deaminase 3, and oligopeptide transporter 15) though their functional roles are unclear. To conclude, fillet firmness of Atlantic salmon depends largely on metabolic properties of the skeletal muscle; where aerobic metabolism using lipids as fuel, and the rapid removal of damaged proteins, appear to play a major role

Effect of dietary digestible energy content on expression of genes of lipid metabolism and LC-PUFA biosynthesis in liver of Atlantic salmon (Salmo salar L.)

The relationship between lipid and digestible energy content of the feed and growth performance has been exploited with great effect in Atlantic salmon (Salmo salar). The precise metabolic consequences of so-called "high-energy" feeds have not been fully defined, but increased and altered tissue lipid deposition patterns impacting on carcass and product quality have been reported. Recent studies on global gene expression have shown that dietary lipid and digestible energy content can have significant effects on gene expression in salmonids. In addition, we recently showed that functional feeds with reduced digestible energy significantly improved outcomes in response to inflammatory disease in salmon. The present study aimed to elucidate and clarify the effects of dietary digestible energy content (22, 20 and 18 MJ/kg; HE, ME and LE diets, respectively) on lipid and fatty acid metabolism in salmon fed diets containing graded amounts of lipid. Specifically the effects on liver lipid and fatty acid compositions, and on the hepatic expression of genes of lipid and fatty acid metabolism were determined. Final weight and weight gain were significantly higher, and FCR lower, in fish fed the HE diet. Crude lipid content was significantly lower in fish fed the LE diet compared to fish fed the two higher energy contents. Significantly lower total lipid and triacylglycerol levels were recorded in liver of fish fed the LE diet compared to fish fed the higher energy diets. Liver lipids in salmon fed the LE diet had generally significantly higher proportions of saturated fatty acids and long-chain polyunsaturated fatty acids (LC-PUFA), and lower monounsaturated fatty acids, C18 and n - 6 PUFA. Consistent with this, salmon fed the LE diet showed increased liver expression of both Δ6 and Δ5 fatty acyl desaturases in comparison to fish fed the diets with higher energy levels. Fatty acid synthase expression showed a clear upward trend as dietary energy decreased, and sterol regulatory element binding protein 2 and liver X receptor showed reciprocal trends that were consistent with the level of dietary cholesterol that reflects digestible energy content. Although not statistically significant, these trends were biologically logical, significant and relevant. Expression of genes of fatty acid oxidation was less consistent. Overall, reduced dietary digestible energy/lipid content alone, without major changes in dietary fatty acid composition, altered the expression of key genes of lipid and fatty acid metabolism resulting in general up-regulation of biosynthetic pathways

HLA-DPB1 and HLA Class I Confer Risk of and Protection from Narcolepsy

Correction: AMERICAN JOURNAL OF HUMAN GENETICS Volume: 96 Issue: 5 Pages: 852-852 DOI: 10.1016/j.ajhg.2015.04.001 Published:MAY 7 2015Peer reviewe

Common variants in P2RY11 are associated with narcolepsy.

Growing evidence supports the hypothesis that narcolepsy with cataplexy is an autoimmune disease. We here report genome-wide association analyses for narcolepsy with replication and fine mapping across three ethnic groups (3,406 individuals of European ancestry, 2,414 Asians and 302 African Americans). We identify a SNP in the 3' untranslated region of P2RY11, the purinergic receptor subtype P2Y₁₁ gene, which is associated with narcolepsy (rs2305795, combined P = 6.1 × 10⁻¹⁰, odds ratio = 1.28, 95% CI 1.19-1.39, n = 5689). The disease-associated allele is correlated with reduced expression of P2RY11 in CD8(+) T lymphocytes (339% reduced, P = 0.003) and natural killer (NK) cells (P = 0.031), but not in other peripheral blood mononuclear cell types. The low expression variant is also associated with reduced P2RY11-mediated resistance to ATP-induced cell death in T lymphocytes (P = 0.0007) and natural killer cells (P = 0.001). These results identify P2RY11 as an important regulator of immune-cell survival, with possible implications in narcolepsy and other autoimmune diseases.journal articleresearch support, n.i.h., extramuralresearch support, non-u.s. gov'tresearch support, u.s. gov't, p.h.s.2011 Jan2010 12 19importedErratum in : Nat Genet. 2011 Oct;43(10):1040

First Investigation of the Microbiology of the Deepest Layer of Ocean Crust

We would like to thank Frederick (Rick) Colwell for input on molecular analyses in low biomass environments, Donna Blackman, Benoît Ildefonse, Adélie Delacour, and Gretchen Früh-Green for discussions regarding geological and geochemical aspects of this manuscript, and the Integrated Ocean Drilling Program Expeditions 304/305 Science Party. We would also like to thank Captain Alex Simpson and the entire crew of the JOIDES Resolution.Conceived and designed the experiments: OUM MRF SJG. Performed the experiments: OUM TN MR JDVN AM. Analyzed the data: OUM TN MR JDVN AM. Contributed reagents/materials/analysis tools: TN MR JZ MRF SJG. Wrote the paper: OUM.The gabbroic layer comprises the majority of ocean crust. Opportunities to sample this expansive crustal environment are rare because of the technological demands of deep ocean drilling; thus, gabbroic microbial communities have not yet been studied. During the Integrated Ocean Drilling Program Expeditions 304 and 305, igneous rock samples were collected from 0.45-1391.01 meters below seafloor at Hole 1309D, located on the Atlantis Massif (30 °N, 42 °W). Microbial diversity in the rocks was analyzed by denaturing gradient gel electrophoresis and sequencing (Expedition 304), and terminal restriction fragment length polymorphism, cloning and sequencing, and functional gene microarray analysis (Expedition 305). The gabbroic microbial community was relatively depauperate, consisting of a low diversity of proteobacterial lineages closely related to Bacteria from hydrocarbon-dominated environments and to known hydrocarbon degraders, and there was little evidence of Archaea. Functional gene diversity in the gabbroic samples was analyzed with a microarray for metabolic genes (“GeoChip”), producing further evidence of genomic potential for hydrocarbon degradation - genes for aerobic methane and toluene oxidation. Genes coding for anaerobic respirations, such as nitrate reduction, sulfate reduction, and metal reduction, as well as genes for carbon fixation, nitrogen fixation, and ammonium-oxidation, were also present. Our results suggest that the gabbroic layer hosts a microbial community that can degrade hydrocarbons and fix carbon and nitrogen, and has the potential to employ a diversity of non-oxygen electron acceptors. This rare glimpse of the gabbroic ecosystem provides further support for the recent finding of hydrocarbons in deep ocean gabbro from Hole 1309D. It has been hypothesized that these hydrocarbons might originate abiotically from serpentinization reactions that are occurring deep in the Earth's crust, raising the possibility that the lithic microbial community reported here might utilize carbon sources produced independently of the surface biosphere.Yeshttp://www.plosone.org/static/editorial#pee

Common variants in P2RY11 are associated with narcolepsy.

l e t t e r s Growing evidence supports the hypothesis that narcolepsy with cataplexy is an autoimmune disease. We here report genomewide association analyses for narcolepsy with replication and fine mapping across three ethnic groups (3,406 individuals of European ancestry, 2,414 Asians and 302 African Americans). We identify a SNP in the 3′ untranslated region of P2RY11, the purinergic receptor subtype P2Y 11 gene, which is associated with narcolepsy (rs2305795, combined P = 6.1 × 10 −10 , odds ratio = 1.28, 95% CI 1.19-1.39, n = 5689). The diseaseassociated allele is correlated with reduced expression of P2RY11 in CD8 + T lymphocytes (339% reduced, P = 0.003) and natural killer (NK) cells (P = 0.031), but not in other peripheral blood mononuclear cell types. The low expression variant is also associated with reduced P2RY11-mediated resistance to ATP-induced cell death in T lymphocytes (P = 0.0007) and natural killer cells (P = 0.001). These results identify P2RY11 as an important regulator of immune-cell survival, with possible implications in narcolepsy and other autoimmune diseases