Genomic location and characterisation of nonclassical MHC class I genes in cattle.
ABSTRACT The cattle major histocompatibility complex (MHC) region contains a variable number of classical class I genes encoding polymorphic, ubiquitously expressed molecules with a role in antigen presentation. Class I cDNA sequences have previously been reported that are thought to derive from putative nonclassical class I genes. We have located four nonclassical class I genes within the cattle genome; three are close to the MIC genes, and one is close to the classical class I genes. The genomic position relative to anchor genes is very similar to the arrangement reported in the pig MHC region. We have designed gene-specific oligonucleotide primers with which to investigate the presence of these genes in distinct and well-defined MHC haplotypes and to assess transcription in different cell types. Analysis and comparison of all sequences allows an assessment of allelic variation in each case. Partial characterisation gives an indication of the possible role and likely importance of each of these genes.
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ABSTRACT: Artificial breeding is an important project to protect, recover and reintroduce endangered species. Knowledge of the population’s genetic diversity at functional loci is important for the establishment of effective captive breeding programs. The major histocompatibility complex (MHC) genes are ideal candidate genetic markers to inform planned breeding, due to their high levels of polymorphism and importance in the main immune coding region of the vertebrate genome. In this study, we constructed BAC-based contigs and isolated six functional MHC class I genes from the giant panda (Ailuropoda melanoleuca), which we designated Aime-C, Aime-F, Aime-I, Aime-K, Aime-L and Aime-1906. Analyses of the tissue expression patterns and full-length cDNA sequences of these class I genes revealed that Aime-C, -F, -I and -L could be considered classical class I loci, due to their extensive expression patterns and normal exonic structures. In contrast, Aime-K and -1906 appeared to be nonclassical genes based on their tissue-specific expression patterns and the presence of an abnormal exon 7 in both genes. We established techniques for genotyping exons 2 and 3 of the classical loci using locus-specific single strand conformation polymorphism (SSCP) and sequence analysis. In the Chengdu captive population, we identified one monomorphic locus (Aime-F) and three polymorphic loci with different numbers of alleles (4/4/4 exon 2 alleles at Aime-C/I/L and 6/5/5 exon 3 alleles at Aime-C/I/L). The distributions of the Aime-C, -I and -L alleles among members of different families were in good agreement with the known pedigree relationships, suggesting that the genotyping results are reliable. Therefore, the MHC-I genotyping techniques established in this study may provide a powerful tool for the future design of scientific breeding or release/reintroduction programs.Chinese Science Bulletin 06/2012; 58(18). · 1.37 Impact Factor
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ABSTRACT: Variation in the major histocompatibility complex (MHC) class I of the European bison was characterized in a sample of 99 individuals using both classical cloning/Sanger sequencing and 454 pyrosequencing. Three common (frequencies: 0.348, 0.328, and 0.283) haplotypes contain 1-3 classical class I loci. A variable and difficult to estimate precisely number of nonclassical transcribed loci, pseudogenes, and/or gene fragments were also found. The presence of additional 2 rare haplotypes (frequency of 0.020 each), observed only in heterozygotes, was inferred. The overall organization of MHC I appears similar to the cattle system, but genetic variation is much lower with only 7 classical class I alleles, approximately one-tenth of the number known in cattle and a quarter known in the American bison. An extensive transspecific polymorphism was found. MHC I is in a strong linkage disequilibrium with previously studied MHC II DRB3 gene. The most likely explanation for the low variation is a drastic bottleneck at the beginning of the 20th century. Genotype frequencies conformed to Hardy-Weinberg expectations, and no signatures of selection in contemporary populations but strong signatures of historical positive selection in sequences of classical alleles were found. A quick and reliable method of MHC I genotyping was developed.The Journal of heredity 04/2012; 103(3):349-59. · 1.97 Impact Factor
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ABSTRACT: LUCID is the luminosity monitor of the LHC accelerator for the ATLAS experiment. Thanks to an intrinsically fast response and to its custom readout electronics, LUCID estimates the number of interactions per LHC bunch crossing and provides an interaction trigger to the experiment. The performance of LUCID is evaluated in the full luminosity range of LHC (up to 1034 cm-1s-1) by means of a PYTHIA simulation of inelastic pp collisions at s=7TeV and a full GEANT4 simulation of the detector.Nuclear Physics B - Proceedings Supplements 06/2011; 215(1):232-234. · 0.88 Impact Factor