About: Evolution of the Bovine TLR Gene Family and Member Associations with Mycobacterium avium Subspecies paratuberculosis Infection

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About: Evolution of the Bovine TLR Gene Family and Member Associations with Mycobacterium avium Subspecies paratuberculosis Infection Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Evolution of the Bovine TLR Gene Family and Member Associations with Mycobacterium avium Subspecies paratuberculosis Infection
Creator	Vikram, Meenu Dowd, Scot Schnabel, Robert Seabury, Christopher Taylor, Jeremy Womack, James Bhattarai, Eric Fisher, Colleen Osterstock, Jason Schukken, Ynte Seabury, Paul Whitlock, Robert
source	Medline; PMC
abstract	Members of the Toll-like receptor (TLR) gene family occupy key roles in the mammalian innate immune system by functioning as sentries for the detection of invading pathogens, thereafter provoking host innate immune responses. We utilized a custom next-generation sequencing approach and allele-specific genotyping assays to detect and validate 280 biallelic variants across all 10 bovine TLR genes, including 71 nonsynonymous single nucleotide polymorphisms (SNPs) and one putative nonsense SNP. Bayesian haplotype reconstructions and median joining networks revealed haplotype sharing between Bos taurus taurus and Bos taurus indicus breeds at every locus, and specialized beef and dairy breeds could not be differentiated despite an average polymorphism density of 1 marker/158 bp. Collectively, 160 tagSNPs and two tag insertion-deletion mutations (indels) were sufficient to predict 100% of the variation at 280 variable sites for both Bos subspecies and their hybrids, whereas 118 tagSNPs and 1 tagIndel predictively captured 100% of the variation at 235 variable sites for B. t. taurus. Polyphen and SIFT analyses of amino acid (AA) replacements encoded by bovine TLR SNPs indicated that up to 32% of the AA substitutions were expected to impact protein function. Classical and newly developed tests of diversity provide strong support for balancing selection operating on TLR3 and TLR8, and purifying selection acting on TLR10. An investigation of the persistence and continuity of linkage disequilibrium (r(2)≥0.50) between adjacent variable sites also supported the presence of selection acting on TLR3 and TLR8. A case-control study employing validated variants from bovine TLR genes recognizing bacterial ligands revealed six SNPs potentially eliciting small effects on susceptibility to Mycobacterium avium spp paratuberculosis infection in dairy cattle. The results of this study will broadly impact domestic cattle research by providing the necessary foundation to explore several avenues of bovine translational genomics, and the potential for marker-assisted vaccination.
has issue date	2011-11-30(xsd:dateTime)
bibo:doi	10.1371/journal.pone.0027744
bibo:pmid	22164200
has license	cc-by
sha1sum (hex)	6737b541bf9d5d5bbb80cc1dd06456f93dbcda72
schema:url	https://doi.org/10.1371/journal.pone.0027744
resource representing a document's title	Evolution of the Bovine TLR Gene Family and Member Associations with Mycobacterium avium Subspecies paratuberculosis Infection
has PubMed Central identifier	PMC3227585
has PubMed identifier	22164200
schema:publication	PLoS One
resource representing a document's body	covid:6737b541bf9d5d5bbb80cc1dd06456f93dbcda72#body_text
is schema:about of	named entity 'TLR GENE FAMILY' named entity 'polymorphism' named entity 'SNP' named entity 'Bos taurus indicus' named entity 'TLR' named entity 'Associations' named entity 'indels' named entity 'detection' named entity 'infection' named entity 'Subspecies' named entity 'Member' named entity 'FOUNDATION' covid:arg/6737b541bf9d5d5bbb80cc1dd06456f93dbcda72 named entity 'CASE-CONTROL STUDY' named entity 'OPERATING' named entity 'BEEF' named entity 'VARIATION' named entity 'ACROSS' named entity 'PERSISTENCE' named entity 'SPECIALIZED' named entity 'JOINING' named entity 'BREEDS' named entity 'BOS TAURUS' named entity 'INDICATED' named entity 'TAG' named entity 'PATHOGENS' named entity 'EVOLUTION' named entity 'LIGANDS' named entity 'PROVIDING' named entity 'SPECIFIC' named entity 'NEWLY' named entity 'KEY' named entity 'HOST' named entity 'UP TO' named entity 'IMMUNE RESPONSES' named entity 'PROTEIN FUNCTION' named entity 'BACTERIAL' named entity 'CUSTOM' named entity 'DENSITY' named entity 'VARIABLE' named entity 'POTENTIAL' named entity 'THEIR' named entity 'GENOTYPING' named entity 'NETWORKS' named entity 'FUNCTIONING' named entity 'RESEARCH' named entity 'NONSENSE' named entity 'IMPACT' named entity 'NEXT-GENERATION SEQUENCING' named entity 'PRESENCE OF' named entity '240' named entity 'ROLES' named entity 'ASSOCIATIONS' named entity '118' named entity '100%' named entity 'HYBRIDS' named entity 'SUBSPECIES' named entity 'CLASSICAL' named entity 'REVEALED' named entity 'SIFT' named entity 'TLR8' named entity 'DETECTION' named entity 'SNPS' named entity 'BOVINE' named entity 'EVOLUTION' named entity 'AMINO ACID' named entity 'MYCOBACTERIUM AVIUM' named entity 'MEMBER' named entity 'BOVINE' named entity 'EXPECTED'

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