Lesions of the biliary system in Atlantic salmon (Salmo salar L.)

Gallbladders with mucosal outpouchings (diverticula) were found in a population of Atlantic salmon farmed in sea water. Soft tissue calcification affected the skin, skeletal muscle and gut, as identified by histological observations. In addition, inflammation of muscle and intestinal tissue and lymphocytic and fibrous reaction were present in the liver. The general fish population was characterized by poor growth and unspecified mortalities. Here we describe the observed lesions and discuss them in the light of the general health status of the population.Lesions of the biliary system in Atlantic salmon (Salmo salar L.)publishedVersio

rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

A dramatic exception to the general pattern of single-copy genes in bacterial and archaeal genomes is the presence of 1–15 copies of each ribosomal RNA encoding gene. The original version of the Ribosomal RNA Database (rrnDB) cataloged estimates of the number of 16S rRNA-encoding genes; the database now includes the number of genes encoding each of the rRNAs (5S, 16S and 23S), an internally transcribed spacer region, and the number of tRNA genes. The rrnDB has been used largely by microbiologists to predict the relative rate at which microbial populations respond to favorable growth conditions, and to interpret 16S rRNA-based surveys of microbial communities. To expand the functionality of the rrnDB (http://ribosome.mmg.msu.edu/rrndb/index.php), the search engine has been redesigned to allow database searches based on 16S rRNA gene copy number, specific organisms or taxonomic subsets of organisms. The revamped database also computes average gene copy numbers for any collection of entries selected. Curation tools now permit rapid updates, resulting in an expansion of the database to include data for 785 bacterial and 69 archaeal strains. The rrnDB continues to serve as the authoritative, curated source that documents the phylogenetic distribution of rRNA and tRNA genes in microbial genomes

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

In situ enrichment of ocean crust microbes on igneous minerals and glasses using an osmotic flow-through device

Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 12 (2011): Q06007, doi:10.1029/2010GC003424.The Integrated Ocean Drilling Program (IODP) Hole 1301A on the eastern flank of Juan de Fuca Ridge was used in the first long-term deployment of microbial enrichment flow cells using osmotically driven pumps in a subseafloor borehole. Three novel osmotically driven colonization systems with unidirectional flow were deployed in the borehole and incubated for 4 years to determine the microbial colonization preferences for 12 minerals and glasses present in igneous rocks. Following recovery of the colonization systems, we measured cell density on the minerals and glasses by fluorescent staining and direct counting and found some significant differences between mineral samples. We also determined the abundance of mesophilic and thermophilic culturable organotrophs grown on marine R2A medium and identified isolates by partial 16S or 18S rDNA sequencing. We found that nine distinct phylotypes of culturable mesophilic oligotrophs were present on the minerals and glasses and that eight of the nine can reduce nitrate and oxidize iron. Fe(II)-rich olivine minerals had the highest density of total countable cells and culturable organotrophic mesophiles, as well as the only culturable organotrophic thermophiles. These results suggest that olivine (a common igneous mineral) in seawater-recharged ocean crust is capable of supporting microbial communities, that iron oxidation and nitrate reduction may be important physiological characteristics of ocean crust microbes, and that heterogeneously distributed minerals in marine igneous rocks likely influence the distribution of microbial communities in the ocean crust.The subseafloor flow cell enrichment chambers were funded by a small grant from the Ocean Drilling Program. This work was also funded by NASA grant NNX08AO22G, NSF OCE 0727119 to C.G.W., NSF OCE 0452333 to S.M.S., and OCE‐0550713 and OCE‐0727952 to A.T.F., PSU, and OSU

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

Narcolepsy risk loci outline role of T cell autoimmunity and infectious triggers in narcolepsy

Narcolepsy has genetic and environmental risk factors, but the specific genetic risk loci and interaction with environmental triggers are not well understood. Here, the authors identify genetic loci for narcolepsy, suggesting infection as a trigger and dendritic and helper T cell involvement. Narcolepsy type 1 (NT1) is caused by a loss of hypocretin/orexin transmission. Risk factors include pandemic 2009 H1N1 influenza A infection and immunization with Pandemrix (R). Here, we dissect disease mechanisms and interactions with environmental triggers in a multi-ethnic sample of 6,073 cases and 84,856 controls. We fine-mapped GWAS signals within HLA (DQ0602, DQB1*03:01 and DPB1*04:02) and discovered seven novel associations (CD207, NAB1, IKZF4-ERBB3, CTSC, DENND1B, SIRPG, PRF1). Significant signals at TRA and DQB1*06:02 loci were found in 245 vaccination-related cases, who also shared polygenic risk. T cell receptor associations in NT1 modulated TRAJ*24, TRAJ*28 and TRBV*4-2 chain-usage. Partitioned heritability and immune cell enrichment analyses found genetic signals to be driven by dendritic and helper T cells. Lastly comorbidity analysis using data from FinnGen, suggests shared effects between NT1 and other autoimmune diseases. NT1 genetic variants shape autoimmunity and response to environmental triggers, including influenza A infection and immunization with Pandemrix (R)

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