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John C Schwartz, John A Hammond
The leukocyte receptor complex (LRC) encodes numerous immunoglobulin (Ig)-like receptors involved in innate immunity. These include the killer-cell Ig-like receptors (KIR) and the leukocyte Ig-like receptors (LILR) which can be polymorphic and vary greatly in number between species. Using the recent long-read genome assembly, Sscrofa11.1, we have characterized the porcine LRC on chromosome 6. We identified a ~ 197-kb region containing numerous LILR genes that were missing in previous assemblies. Out of 17 such LILR genes and fragments, six encode functional proteins, of which three are inhibitory and three are activating, while the majority of pseudogenes had the potential to encode activating receptors...
June 21, 2018: Immunogenetics
Mohammad Saeed
Parkinson's disease (PD) is a common, disabling neurodegenerative disorder with significant genetic underpinnings. Multiple genome-wide association studies (GWAS) have been conducted with identification of several PD loci. However, these only explain about 25% of PD genetic risk indicating that additional loci of modest effect remain to be discovered. Association clustering methods such as gene-based tests are more powerful than single-variant analysis for identifying modest genetic effects. Combined with the locus-based algorithm, OASIS, the most significant association signals can be homed in...
June 19, 2018: Immunogenetics
James Robinson, Lisbeth A Guethlein, Giuseppe Maccari, Jeroen Blokhuis, Benjamin N Bimber, Natasja G de Groot, Nicholas D Sanderson, Laurent Abi-Rached, Lutz Walter, Ronald E Bontrop, John A Hammond, Steven G E Marsh, Peter Parham
The increasing number of Killer Immunoglobulin-like Receptor (KIR) sequences available for non-human primate species and cattle has prompted development of a centralized database, guidelines for a standardized nomenclature, and minimum requirements for database submission. The guidelines and nomenclature are based on those used for human KIR and incorporate modifications made for inclusion of non-human species in the companion IPD-NHKIR database. Included in this first release are the rhesus macaque (Macaca mulatta), chimpanzee (Pan troglodytes), orangutan (Pongo abelii and Pongo pygmaeus), and cattle (Bos taurus)...
June 4, 2018: Immunogenetics
Lydia Siebert, Margaret E Staton, Susan Headrick, Mark Lewis, Barbara Gillespie, Charles Young, Raul A Almeida, Stephen P Oliver, Gina M Pighetti
Mastitis is a detrimental disease in the dairy industry that decreases milk quality and costs upwards of $2 billion annually. Often, mastitis results from bacteria entering the gland through the teat opening. Streptococcus uberis is responsible for a high percentage of subclinical and clinical mastitis. Following an intramammary experimental challenge with S. uberis on Holstein cows (n = 40), milk samples were collected and somatic cell counts (SCC) were determined by the Dairy Herd Improvement Association Laboratory...
June 3, 2018: Immunogenetics
Vanessa Meyer, Liza Bornman
Caudal-type homeobox protein 2 (CDX-2) is an intestine-specific transcription factor (TF), with a polymorphic binding site (Cdx-2, rs11568820, A/G) in the vitamin D receptor gene (VDR). The molecular mechanism underlying Cdx-2 association with conditions like osteoporosis, which depends on intestinal VDR expression and calcium absorption, is believed to be due to higher affinity of CDX-2 for the ancestral A allele compared to the G allele. However, it is unclear why the polymorphism is associated with diseases like tuberculosis, which is dependent on VDR expression in immune cells that do not express CDX-2...
May 28, 2018: Immunogenetics
R S Fraser, J S Lumsden, B N Lillie
Infectious diseases are a significant issue in animal production systems, including both the dairy and beef cattle industries. Understanding and defining the genetics of infectious disease susceptibility in cattle is an important step in the mitigation of their impact. Collagenous lectins are soluble pattern recognition receptors that form an important part of the innate immune system, which serves as the first line of host defense against pathogens. Polymorphisms in the collagenous lectin genes have been shown in previous studies to contribute to infectious disease susceptibility, and in cattle, mutations in two collagenous lectin genes (MBL1 and MBL2) are associated with mastitis...
May 10, 2018: Immunogenetics
Michael Halagan, Danielli Cristina Oliveira, Martin Maiers, Raquel A Fabreti-Oliveira, Maria Elisa Hue Moraes, Jeane Eliete Laguila Visentainer, Noemi Farah Pereira, Matilde Romero, Juliana Fernandes Cardoso, Luís Cristóvão Porto
The Registries of Bone Marrow Donors around the world include more than 30 million volunteer donors from 57 different countries, and were responsible for over 17,000 hematopoietic stem cell transplants in 2016. The Brazilian Bone Marrow Volunteer Donor Registry (REDOME) was established in 1993 and is the third largest registry in the world with more than 4.3 million donors. We characterized HLA allele and haplotypes frequencies from REDOME comparing them with the donor self-reported race group classification...
April 26, 2018: Immunogenetics
Roxanne Collin, Kathy Doyon, Victor Mullins-Dansereau, Martin Karam, Geneviève Chabot-Roy, Erin E Hillhouse, Alexandre Orthwein, Sylvie Lesage
Several immune regulatory cell types participate in the protection against autoimmune diseases such as autoimmune diabetes. Of these immunoregulatory cells, we and others have shown that peripheral CD4- CD8- double negative (DN) T cells can induce antigen-specific immune tolerance. Particularly, we have described that diabetes-prone mice exhibit a lower number of peripheral DN T cells compared to diabetes-resistant mice. Identifying the molecular pathways that influence the size of the DN T cell pool in peripheral lymphoid organs may thus be of interest for maintaining antigen-specific immune tolerance...
April 25, 2018: Immunogenetics
Alexander A Celik, Gwendolin S Simper, Wiebke Hiemisch, Rainer Blasczyk, Christina Bade-Döding
HLA-G is known for its strictly restricted tissue distribution. HLA-G expression could be detected in immune privileged organs and many tumor entities such as leukemia, multiple myeloma, and non-Hodgkin and Hodgkin's lymphoma. This functional variability from mediation of immune tolerance to facilitation of tumor immune evasion strategies might translate to a differential NK cell inhibition between immune-privileged organs and tumor cells. The biophysical invariability of the HLA-G heavy chain and its contrary diversity in immunity implicates a strong influence of the bound peptides on the pHLA-G structure...
March 30, 2018: Immunogenetics
Rebecca A Morgan, Julie A Karl, Hailey E Bussan, Katelyn E Heimbruch, David H O'Connor, Dawn M Dudley
Baboons are valuable models for complex human diseases due to their genetic and physiologic similarities to humans. Deep sequencing methods to characterize full-length major histocompatibility complex (MHC) class I (MHC-I) alleles in different nonhuman primate populations were used to identify novel MHC-I alleles in baboons. We combined data from Illumina MiSeq sequencing and Roche/454 sequencing to characterize novel full-length MHC-I transcripts in a cohort of olive and hybrid olive/yellow baboons from the Southwest National Primate Research Center (SNPRC)...
March 28, 2018: Immunogenetics
R Sadeghi, Mohammad Moradi-Shahrbabak, S R Miraei Ashtiani, D C Miller, Douglas F Antczak
Previous research on the equine major histocompatibility complex (MHC) demonstrated strong correlations between haplotypes defined by polymorphic intra-MHC microsatellites and haplotypes defined using classical serology. Here, we estimated MHC diversity in a sample of 124 Arabian horses from an endangered strain native to Iran (Persian Asil Arabians), using a validated 10-marker microsatellite panel. In a group of 66 horses related as parent-offspring pairs or half-sibling groups, we defined 51 MHC haplotypes, 49 of which were new...
May 2018: Immunogenetics
Katrina M Morris, Haylee J Weaver, Denis O'Meally, Marion Desclozeaux, Amber Gillett, Adam Polkinghorne
Bandicoots are omnivorous marsupials of the order Peramelemorphia. Conservation concerns and their unique biological characteristics suggest peramelomorphs are worthy research subjects, but knowledge of their genetics and immunology has lagged behind that of other high-profile marsupials. Here, we characterise the transcriptome of the long-nose bandicoot (Perameles nasuta), the first high-throughput data set from any peramelomorph. We investigate the immune gene repertoire of the bandicoot, with a focus on key immune gene families, and compare to previously characterised marsupial and mammalian species...
May 2018: Immunogenetics
Yoram Louzoun, Idan Alter, Loren Gragert, Mark Albrecht, Martin Maiers
Regardless of sampling depth, accurate genotype imputation is limited in regions of high polymorphism which often have a heavy-tailed haplotype frequency distribution. Many rare haplotypes are thus unobserved. Statistical methods to improve imputation by extending reference haplotype distributions using linkage disequilibrium patterns that relate allele and haplotype frequencies have not yet been explored. In the field of unrelated stem cell transplantation, imputation of highly polymorphic human leukocyte antigen (HLA) genes has an important application in identifying the best-matched stem cell donor when searching large registries totaling over 28,000,000 donors worldwide...
May 2018: Immunogenetics
Jörg B Hans, Linda Vigilant
In comparison to humans and chimpanzees, gorillas show low diversity at MHC class I genes (Gogo), as reflected by an overall reduced level of allelic variation as well as the absence of a functionally important sequence motif that interacts with killer cell immunoglobulin-like receptors (KIR). Here, we use recently generated large-scale genomic sequence data for a reassessment of allelic diversity at Gogo-C, the gorilla orthologue of HLA-C. Through the combination of long-range amplifications and long-read sequencing technology, we obtained, among the 35 gorillas reanalyzed, three novel full-length genomic sequences including a coding region sequence that has not been previously described...
May 2018: Immunogenetics
Yinan Wang, Shixiong Cheng, Yaqing Chang, Kaiquan Li, Yang Chen, Yi Wang
In this study, a homolog of the TLR11 family gene from the sea urchin Strongylocentrotus intermedius (denoted as SiTLR11) was cloned and characterized. The full-length cDNA of SiTLR11 was 2096-bp long, which included 43 bp of 5' untranslated region (UTR), 238 bp of 3' UTR, and a putative open reading frame of 1815 bp encoding a polypeptide of 604 amino acid residues. Representative domains such as leucine-rich repeat (LRR) (residues 108-249) and a cytoplasmic Toll-interleukin-1 receptor (TIR) (residues 429-571) domains were detected in the predicted amino acid sequence of SiTLR11...
May 2018: Immunogenetics
John C Schwartz, Rebecca L Philp, Derek M Bickhart, Timothy P L Smith, John A Hammond
The domestic goat (Capra hircus) is an important ruminant species both as a source of antibody-based reagents for research and biomedical applications and as an economically important animal for agriculture, particularly for developing nations that maintain most of the global goat population. Characterization of the loci encoding the goat immune repertoire would be highly beneficial for both vaccine and immune reagent development. However, in goat and other species whose reference genomes were generated using short-read sequencing technologies, the immune loci are poorly assembled as a result of their repetitive nature...
May 2018: Immunogenetics
Fany Blanc, Françoise Créchet, Nicolas Bruneau, Guillaume Piton, Jean-Jacques Leplat, Fabrice Andréoletti, Giorgia Egidy, Silvia Vincent-Naulleau, Emmanuelle Bourneuf
The cluster of differentiation 4 (CD4) molecule functions as a co-receptor for MHC class II binding to TCR in T helper cells. A CD4 epitope deficiency was identified in the swine MeLiM (melanoblastoma-bearing Libechov minipig) strain, a model for spontaneous cutaneous melanoma development and regression. Extensive sequencing revealed a high genetic variability of CD4 and the existence of several haplotypes segregating in MeLiM. Forty polymorphisms were identified in the coding sequence, out of which 20 correspond to non-synonymous variants and 10 are located in the 3'UTR of CD4 transcripts...
April 2018: Immunogenetics
Xiao-Dong Lian, Xi-He Zhang, Zheng-Xi Dai, Yong-Tang Zheng
The northern pig-tailed macaque (Macaca leonina) has been considered as an independent species from the pig-tailed macaque group. We have previously reported that this species macaque has the potential to be a useful animal model in HIV/AIDS pathogenesis and vaccine studies due to its susceptibility to HIV-1. To develop this animal into a potential HIV/AIDS model, we have studied the classical MHC genes of this animal. In this study, the non-classical MHC genes Malo-DM and Malo-DO alleles were first characterized by sequencing and cloning in 12 unrelated northern pig-tailed macaques...
April 2018: Immunogenetics
Jiro Miyamae, Shingo Suzuki, Fumihiko Katakura, Sae Uno, Mizuki Tanaka, Masaharu Okano, Taro Matsumoto, Jerzy K Kulski, Tadaaki Moritomo, Takashi Shiina
The current information on the polymorphism variation and haplotype structure of the domestic dog leukocyte antigen (DLA) genes is limited in comparison to other experimental animals. In this paper, to better elucidate the degree and types of polymorphisms and genetic differences for DLA-88, DLA-12 and DLA-64, we genotyped four families of 38 beagles and another 404 unrelated dogs representing 49 breeds by RT-PCR based Sanger sequencing. We also sequenced and analyzed the genomic organization of the DLA-88 and DLA-12 gene segments to better define these two-gene DLA haplotypes more precisely...
April 2018: Immunogenetics
Jolyon Martin, Hannes Ponstingl, Marie-Paule Lefranc, Joy Archer, David Sargan, Allan Bradley
Dogs are an excellent model for human disease. For example, the treatment of canine lymphoma has been predictive of the human response to that treatment. However, an incomplete picture of canine (Canis lupus familiaris) immunoglobulin (IG) and T cell receptor (TR)-or antigen receptor (AR)-gene loci has restricted their utility. This work advances the annotation of the canine AR loci and looks into breed-specific features of the loci. Bioinformatic analysis of unbiased RNA sequence data was used to complete the annotation of the canine AR genes...
April 2018: Immunogenetics
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