Polarisation of Major Histocompatibility Complex II Host Genotype with Pathogenesis of European Brown Hare Syndrome Virus.

A study was conducted in order to determine the occurrence of European Brown Hare Syndrome virus (EBHSV) in Denmark and possible relation between disease pathogenesis and Major Histocompatibility Complex (MHC) host genotype. Liver samples were examined from 170 brown hares (hunted, found sick or dead), collected between 2004 and 2009. Macroscopical and histopathological findings consistent with EBHS were detected in 24 (14.1%) hares; 35 (20.6%) had liver lesions not typical of the syndrome, 50 (29.4%) had lesions in other tissues and 61 (35.9%) had no lesions. Sixty five (38.2%) of 170 samples were found to be EBHSV-positive (RT-PCR, VP60 gene). In order to investigate associations between viral pathogenesis and host genotype, variation within the exon 2 DQA gene of MHC was assessed. DQA exon 2 analysis revealed the occurrence of seven different alleles in Denmark. Consistent with other populations examined so far in Europe, observed heterozygosity of DQA (H o = 0.1180) was lower than expected (H e = 0.5835). The overall variation for both nucleotide and amino acid differences (2.9% and 14.9%, respectively) were lower in Denmark than those assessed in other European countries (8.3% and 16.9%, respectively). Within the peptide binding region codons the number of nonsynonymous substitutions (dN) was much higher than synonymous substitutions (dS), which would be expected for MHC alleles under balancing selection. Allele frequencies did not significantly differ between EBHSV-positive and -negative hares. However, allele Leeu-DQA*30 was detected in significantly higher (P = 0.000006) frequency among the positive hares found dead with severe histopathological lesions than among those found sick or apparently healthy. In contrast, the latter group was characterized by a higher frequency of the allele Leeu-DQA*14 as well as the proportion of heterozygous individuals (P = 0.000006 and P = 0.027). These data reveal a polarisation between EBHSV pathogenesis and MHC class II genotype within the European brown hare in Denmark

Hexavalent Chromium Reduction under Fermentative Conditions with Lactate Stimulated Native Microbial Communities

This work conducted by ENIGMA- Ecosystems and Networks Integrated with Genes and Molecular Assemblies (http://enigma.lbl.gov), a Scientific Focus Area Program at Lawrence Berkeley National Laboratory. The submitted manuscript has been authored by a contractor of the U.S. Government under contract DE-AC05-00OR22725. Accordingly, the U.S. Government retains a nonexclusive, royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for U.S. Government purposes.Conceived and designed the experiments: ACS JJM MP TJP SDB AVP DAE. Performed the experiments: ACS JJM ZKY. Analyzed the data: ACS JJM TY JDVN JZ DAE. Contributed reagents/materials/analysis tools: DAE TCH APA. Wrote the paper: ACS JJM DAE.Microbial reduction of toxic hexavalent chromium (Cr(VI)) in-situ is a plausible bioremediation strategy in electron-acceptor limited environments. However, higher Cr(VI) may impose stress on syntrophic communities and impact community structure and function. The study objectives were to understand the impacts of Cr(VI) concentrations on community structure and on the Cr(VI)-reduction potential of groundwater communities at Hanford, WA. Steady state continuous flow bioreactors were used to grow native communities enriched with lactate (30 mM) and continuously amended with Cr(VI) at 0.0 (No-Cr), 0.1 (Low-Cr) and 3.0 (High-Cr) mg/L. Microbial growth, metabolites, Cr(VI), 16S rRNA gene sequences and GeoChip based functional gene composition were monitored for 15 weeks. Temporal trends and differences in growth, metabolite profiles, and community composition were observed, largely between Low-Cr and High-Cr bioreactors. In both High-Cr and Low-Cr bioreactors, Cr(VI) levels were below detection from week 1 until week 15. With lactate enrichment, native bacterial diversity substantially decreased as Pelosinus spp., and Sporotalea spp., became the dominant groups, but did not significantly differ between Cr concentrations. The Archaea diversity also substantially decreased after lactate enrichment from Methanosaeta (35%), Methanosarcina (17%) and others, to mostly Methanosarcina spp. (95%). Methane production was lower in High-Cr reactors suggesting some inhibition of methanogens. Several key functional genes were distinct in Low-Cr bioreactors compared to High-Cr. Among the Cr resistant microbes, Burkholderia vietnamiensis, Comamonas testosterone and Ralstonia pickettii proliferated in Cr amended bioreactors. In-situ fermentative conditions facilitated Cr(VI) reduction, and as a result 3.0 mg/L Cr(VI) did not impact the overall bacterial community structure.Yeshttp://www.plosone.org/static/editorial#pee

Groups of Danish brown hares individuals according to the presence of EBHSV and the variation in exon 2 DQA gene.

<p>Numbers (N) and percentages of Danish brown hares assessed for the four groups defined in this study: EBHSV negative (EBHSV⁻), EBHSV positive (EBHSV⁺), susceptible (EBHSV⁺ Dead), resistant (EBHSV⁺ not Dead).</p

Percentages indicating the occurrence of the homogygous and heterozygous <i>DQA</i> genotypes.

<p>Percentages indicating the occurrence of the homogygous and heterozygous <i>DQA</i> genotypes in the four groups of <i>Lepus europaeus</i> sampled in Denmark. Bars indicate the occurrence of each genotype in non affected or affected animals. Pies above bars indicate the occurrence of each genotype among the affected <i>L. europeaus</i> individuals in susceptible animals found dead with lesions typical to the EBHS in various organs or resistant not dead animals.</p

Phylogenetic tree of the EBHSV isolates.

<p>Phylogenetic tree resulting from the Bayesian analysis, clustering the seven Danish isolates identified in this study combined with sequences available from the EMBL database. The topology of the clusters was similar for the NJ tree. Numbers on branches at the internodes of the clusters correspond to posterior probabilities from the Bayesian analysis. At the end of the branches the designation and origin of the EBHS viruses studied. Probabilities below 50% are omitted.</p

DQA alleles (residues 8–76) of <i>Lepus europaeus.</i>

<p>DQA alleles (residues 8–76) of <i>Lepus europaeus.</i> Polymorphic residues are in bold. Residues contributing to the formation of binding pockets P1, P6 and P9 are indicated. Shaded residues are putative TCR contacts. Crosses indicate residues with hydrogen bonds to the peptide. The boxed area determines αβ pairing.</p

UPGMA phylogenetic tree of the eight <i>Lepus europaeus</i> DQA exon 2 alleles.

<p>UPGMA phylogenetic tree resulting from the analysis of the eight <i>Lepus europaeus</i> DQA exon 2 alleles identified in this study, together with sequences assessed in the study of Koutsogiannouli et al. 2009 available from GenBank. Numbers indicate the percentage bootstrap support (10000 replicates). The evolutionary distances were computed using the maximum composite likelihood method and are in the units of the number of base substitutions per site. The populations in which each allele was present are given abbreviated in parentheses. (The neighbour-joining tree produced similar results with comparable bootstrap values).</p

Location map of EBHSV positive <i>Lepus europaeus</i> individuals.

<p>Location map of the 65 <i>Lepus europaeus</i> individuals sampled throughout Denmark that were affected by the virus of the European Brown Hare Syndrome (EBHSV).</p