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      Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection

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          Abstract

          Background

          Previously, we identified a major quantitative trait locus (QTL) for host response to Porcine Respiratory and Reproductive Syndrome virus (PRRSV) infection in high linkage disequilibrium (LD) with SNP rs80800372 on Sus scrofa chromosome 4 (SSC4).

          Results

          Within this QTL, guanylate binding protein 5 ( GBP5) was differentially expressed (DE) (p < 0.05) in blood from AA versus AB rs80800372 genotyped pigs at 7,11, and 14 days post PRRSV infection. All variants within the GBP5 transcript in LD with rs80800372 exhibited allele specific expression (ASE) in AB individuals (p < 0.0001). A transcript re-assembly revealed three alternatively spliced transcripts for GBP5. An intronic SNP in GBP5, rs340943904, introduces a splice acceptor site that inserts five nucleotides into the transcript. Individuals homozygous for the unfavorable AA genotype predominantly produced this transcript, with a shifted reading frame and early stop codon that truncates the 88 C-terminal amino acids of the protein. RNA-seq analysis confirmed this SNP was associated with differential splicing by QTL genotype (p < 0.0001) and this was validated by quantitative capillary electrophoresis (p < 0.0001). The wild-type transcript was expressed at a higher level in AB versus AA individuals, whereas the five-nucleotide insertion transcript was the dominant form in AA individuals. Splicing and ASE results are consistent with the observed dominant nature of the favorable QTL allele. The rs340943904 SNP was also 100 % concordant with rs80800372 in a validation population that possessed an alternate form of the favorable B QTL haplotype.

          Conclusions

          GBP5 is known to play a role in inflammasome assembly during immune response. However, the role of GBP5 host genetic variation in viral immunity is novel. These findings demonstrate that rs340943904 is a strong candidate causal mutation for the SSC4 QTL that controls variation in host response to PRRSV.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s12864-015-1635-9) contains supplementary material, which is available to authorized users.

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          Most cited references 18

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          SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

          Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces generate reliable models without the need for complex software packages or downloading large databases. Here, we describe the latest version of the SWISS-MODEL expert system for protein structure modelling. The SWISS-MODEL template library provides annotation of quaternary structure and essential ligands and co-factors to allow for building of complete structural models, including their oligomeric structure. The improved SWISS-MODEL pipeline makes extensive use of model quality estimation for selection of the most suitable templates and provides estimates of the expected accuracy of the resulting models. The accuracy of the models generated by SWISS-MODEL is continuously evaluated by the CAMEO system. The new web site allows users to interactively search for templates, cluster them by sequence similarity, structurally compare alternative templates and select the ones to be used for model building. In cases where multiple alternative template structures are available for a protein of interest, a user-guided template selection step allows building models in different functional states. SWISS-MODEL is available at http://swissmodel.expasy.org/.
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            Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

            Motivation: High-throughput sequencing has made the analysis of new model organisms more affordable. Although assembling a new genome can still be costly and difficult, it is possible to use RNA-seq to sequence mRNA. In the absence of a known genome, it is necessary to assemble these sequences de novo, taking into account possible alternative isoforms and the dynamic range of expression values. Results: We present a software package named Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms. It achieves this by using an array of hash lengths, a dynamic filtering of noise, a robust resolution of alternative splicing events and the efficient merging of multiple assemblies. It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers. Availability and implementation: Oases is freely available under the GPL license at www.ebi.ac.uk/~zerbino/oases/ Contact: dzerbino@ucsc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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              Characterization of swine infertility and respiratory syndrome (SIRS) virus (isolate ATCC VR-2332).

              The characterization of an isolate of swine infertility and respiratory syndrome (SIRS) virus (ATCC VR-2332) is reported. A commercial cell line (CL2621) was used for the propagation of the virus for all assays. Laboratory studies indicate that this isolate is a fastidious, nonhemagglutinating, enveloped RNA virus. Cesium chloride-purified virions visualized by electron microscopy were spherical particles with an average diameter of 62 nm (range: 48-83 nm) and a 25-30 nm core surrounded by an envelope. Virus replication was restricted to the cytoplasm, as demonstrated by immunofluorescence. The virus did not react serologically with antisera to several common porcine viruses or with antisera to known viruses in the alphavirus, rubivirus, pestivirus, and ungrouped lactic dehydrogenase virus genera of the Togaviridae. However, convalescent sow sera and rabbit hyperimmune sera neutralized the SIRS virus at titers of 1:256 and 1:512, respectively. The virus was stable at 4 and -70 C, but was labile at 37 and 56 C. The properties of this isolate of SIRS virus resemble those of the family Togaviridae but do not match the described genera.
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                Author and article information

                Contributors
                jekoltes@iastate.edu
                ercfrtz@iastate.edu
                ceisley@iastate.edu
                Igseo.Choi@ARS.USDA.GOV
                bao1@ualberta.ca
                kommadat@ualberta.ca
                serao@iastate.edu
                nboddicker@genesus.com
                Sam.Abrams@ars.usda.gov
                schroyen@iastate.edu
                heri1008@iastate.edu
                cktuggle@iastate.edu
                plastow@ualberta.ca
                lguan@ualberta.ca
                stothard@ualberta.ca
                Joan.Lunney@ARS.USDA.GOV
                pliu@iastate.edu
                scarp@iastate.edu
                browland@vet.k-state.edu
                jdekkers@iastate.edu
                jreecy@iastate.edu
                Journal
                BMC Genomics
                BMC Genomics
                BMC Genomics
                BioMed Central (London )
                1471-2164
                28 May 2015
                28 May 2015
                2015
                : 16
                : 1
                Affiliations
                [ ]Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011 USA
                [ ]Department of Statistics, Iowa State University, 1121 Snedecor Hall, Ames, IA 50011 USA
                [ ]USDA-ARS, BARC, APDL, Building1040, Beltsville, MD 20705 USA
                [ ]Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5 Canada
                [ ]Genesus Inc, 101 2nd Street, Oakville, MB R0H 0Y0 Canada
                [ ]College of Veterinary Medicine, Kansas State University, K-231 Mosier Hall, Manhattan, KS 66506 USA
                Article
                1635
                10.1186/s12864-015-1635-9
                4446061
                © Koltes et al.; licensee BioMed Central. 2015

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                Categories
                Research Article
                Custom metadata
                © The Author(s) 2015

                Genetics

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