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J G H Hickford

Publications and source records attributed to J G H Hickford.

13 recordsLinked to original sources
PubMed2006

Haplotype analysis of the DQA genes in sheep: evidence supporting recombination between the loci.

The ovine class II major histocompatibility complex mediates specific immune responses to exogenous antigens in sheep. A number of ovine class II loci have been identified, and most of them appear to be polymorphic. In this study we investigated the DQA1 locus of 520 sheep and the DQA2 locus of over 40,000 sheep, finding 12 sequences and 22 sequences, respectively, using DQA1- and DQA2-specific PCR primers. Among the DQA2 sequences, 2 groups of sequences can be found: those that share homology with the DQA2 sequences from closely related species and those that cluster with bovine DQA3 and DQA4 sequences and have been called DQA2-like in sheep. The occurrence of these DQA2-like sequences was once again confirmed to correspond with the absence of detectable DQA1 sequences, suggesting that they are found at the same location as DQA1. Within the sheep studied, 37 haplotypes could be detected, 23 being haplotypes of DQA1 and DQA2 sequences and with frequencies ranging from 0.38 to 9.27%, and 14 being haplotypes of DQA2 and DQA2-like sequences and with frequencies ranging from 0.03 to 14.53%. We discovered 12 DQA1-DQA2 combinations that were derived from 5 DQA1 alleles and 4 DQA2 alleles, and 8 DQA2-DQA2-like combinations from 5 DQA2 alleles and 2 DQA2-like sequences. The frequency of occurrence of recombined DQA1-DQA2 sequences and recombined DQA2-DQA2-like sequences is similar, once again suggesting the DQA2-like sequences are found at the DQA1 locus.

Alleles↗
PubMed2006

Polymorphism of the ovine calpastatin gene.

Calpastatin is a specific inhibitor of calpains and has been implicated in the regulation of beef tenderization. Variation in the ovine calpastatin gene (CAST) was investigated by amplification of a fragment containing the entire exon 6 using polymerase chain reaction (PCR), followed by single-strand conformational polymorphism (PCR-SSCP) analysis and DNA sequencing. Five novel SSCP patterns, representing five different sequences, were identified. Either one or two different sequences were detected in individual sheep and all the sequences identified shared high homology to the published ovine and bovine CAST sequences, suggesting that these sequences represent allelic variants of the ovine CAST gene. Sequence analysis revealed a non-synonymous amino acid variation in exon 6, which would result in a Gln/Leu substitution in Domain L of the mature protein. Considerable variation was detected in an intron region close to the acceptor splice site, with both sequence variation and length variation being observed in this region. Variation detected here might have an impact on both the function and expression of ovine calpastatin.

Alleles↗
PubMed2006

Polymorphism at the beta-adrenergic receptor (ADRB3) locus of Merino sheep and its association with lamb mortality.

Beta3-adrenergic receptors are predominantly found on the surface of adipocytes and are major mediators of the lipolytic and thermogenic effects of high catecholamine concentrations. Recently, variation in the ovine beta3-adrenergic receptor (ADRB3) gene has been reported to be associated with lamb survival. In this study, polymerase chain reaction-single strand conformational polymorphism analysis of part of the ADRB3 intron was used to genotype 4488 Merino lambs born at 10 farms throughout the South Island of New Zealand. Univariate and multivariate odds ratios for each allele revealed a significant association of the E allele with cdd survival and of the D allele with mortality. This variation at the ADRB3 locus may assist in the genetic selection for survival in Merino sheep.

Animals↗
PubMed2005

Convenient anaerobic techniques, science from the supermarket shelf.

We describe the application and evaluation of a widely available commercial jar as an anaerobic container suitable for the growth of a wide variety of anaerobes. A system for generating stable anaerobiosis was developed by combining standard anaerobic environment generators with Click-Clack jars produced by Click-Clack Ltd. This system was simple, reliable, and reduced capital outlay on anaerobic jars by at least an order of magnitude.

Bacteria, Anaerobic↗
PubMed2005

Technical note: determination of alleles of the ovine PRNP gene using PCR-single-strand conformational polymorphism analysis.

Susceptibility to scrapie in sheep is linked to variation at codons 136, 154, and 171 in the host prion protein gene (PRNP). A number of techniques are available for detecting these polymorphisms, but none allow for a rapid and accurate determination of genotype. Here we describe PCR coupled with single-strand conformational polymorphism (SSCP) analysis, which allows for the accurate identification of ovine PRNP alleles. A gene region including codons 136 to 171 was amplified by PCR, and the amplimers were then denatured and subjected to electrophoresis in a nondenaturing polyacrylamide gel. Nine unique SSCP patterns, representing nine different alleles of the ovine PRNP gene, could be resolved. A new polymorphism (I/T) at codon 142 also was detected. The profiles produced by SSCP allowed for the accurate differentiation of PRNP alleles and could be employed to genotype PRNP in sheep.

Alleles↗
PubMed2005

Polymorphism of the DQA2 gene in goats.

Variation in the caprine DQA2 gene was investigated using PCR-single-strand conformational polymorphism (SSCP) and DNA sequencing. Eleven DQA2 alleles were defined by SSCP patterns from 23 goats. All the caprine alleles shared high sequence homology to ovine DQA2 sequences, and exhibited a pattern of polymorphism similar to DQA2 alleles from sheep and cattle but different from caprine DQA1 sequences. Thirty-eight AA positions in the alpha1 domain of caprine DQA2 molecules were polymorphic, and a high degree of polymorphism was observed in the putative antigen-binding region, with 74% of the positions being polymorphic. Phylogenetic analysis of caprine, ovine, and bovine DQA sequences revealed that the caprine DQA2 sequences identified here grouped with ovine DQA2, bovine DQA2, DQA3, and DQA4 sequences but are separate from the group of caprine DQA1 alleles. Nine of the caprine DQA2 sequences were more similar to ovine DQA2 alleles, whereas the remaining two were more closely related to ovine DQA2-like and bovine DQA3 alleles. This finding suggests that the caprine DQA2 sequences may represent two loci, which probably arose by either gene duplication or gene conversion events. Allelic lineages were evident for both DQA2 and DQA2-like loci, supporting the trans-species mode of evolution of major histocompatibilitly complex genes. The high level of polymorphism and similarity between caprine and ovine DQA2 alleles suggests that the DQA2 gene may play an important role in immune responses to shared pathogens.

Alleles↗
PubMed2004

Allelic polymorphism in the ovine DQA1 gene.

Variation in the ovine DQA1 gene was investigated by amplification of exon 2 using PCR, followed by single-strand conformational polymorphism (SSCP) analysis, cloning, and DNA sequencing. Fourteen novel SSCP patterns, representing 14 different sequences, were identified. Eight of these 14 sequences were identical to published DQA1 sequences from sheep, whereas the remaining six were novel but similar to the published DQA1 sequences from sheep and cattle. These six new sequences exhibited conserved region and variable region patterns similar to the published sheep DQA1 sequences, but were different than the published DQA2 sequences from sheep. All of these 14 putative sheep DQA1 sequences fulfilled the criteria used by the established bovine leukocyte antigens major histocompatibility complex nomenclature committee for assignment as new alleles. Comparison of the available DQA1 sequences from sheep and cattle revealed several clusters of ovine DQA1 sequences, and some sheep alleles were more similar to cattle alleles than other sheep alleles. The occurrence of trans-species polymorphism suggests the action of balancing selection at the DQA1 locus. Twenty-four percent of the nucleotide positions showed variation within exon 2, and this variation seems to have arisen largely by point mutation and gene conversion. The nonsynonymous and synonymous substitution rates were similar in both the putative antigen-binding site codons and the putative nonantigen-binding site codons. The extensive polymorphism reported in this article is consistent with polymorphism reported at the bovine DQA1 locus.

Alleles↗
PubMed2004

Diversity of the ovine DQA2 gene.

Variation in the ovine DQA2 gene was investigated in approximately 2,000 sheep from six breeds. Fragments of DNA containing the ovine DQA2 exon 2 were amplified using PCR. Single-strand conformational polymorphism analysis and DNA sequence analysis were employed to detect genetic variation. Twenty-three nucleic acid sequences, encoding 22 DQA2 amino acid sequences, were identified. This increases the number of alleles identified from 10 to 23. In some cases, three or four unique sequences were isolated from individual sheep, suggesting that these DQA2 sequences may represent two loci. Phylogenetic tree analysis revealed that 5 of these 23 sequences were more closely related to cattle DQA3 or DQA4 sequences than to other sheep DQA2 sequences. These sequences clustered together and were called DQA2-like to differentiate them from other DQA2 sequences. There was no evidence of DQA5-like sequences in sheep. Information theory-based analysis indicated that some of the DQA2-like sequences had low information content at splice sites, suggesting that these alleles may have low functional activity. Allelic lineages were observed not only at the DQA2 locus, but also at the DQA2-like locus, supporting the trans-species mode of evolution of MHC genes. Comparison of the allelic sequences suggests that polymorphism seems to have arisen largely by point mutation and gene conversion, and a recent gene conversion event seems to have occurred between the DQA2 and DQA2-like loci. The high level of sequence polymorphism detected and varied number of loci demonstrate the extensive diversity of the ovine DQA2 gene.

Alleles↗
PubMed2003

Polymorphism at the ovine beta3-adrenergic receptor locus: associations with birth weight, growth rate, carcass composition and cold survival.

The beta3-adrenergic receptors (ADRB3s) are predominantly found on the surface of adipocytes and are the major mediators of the lipolytic and thermogenic effects of high catecholamine concentrations. Polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) analysis of part of the ovine beta3-adrenergic receptor gene (ADRB3) intron was used to screen 12 large Merino half-sib families for sequence variation. Six different alleles that segregated in a Mendelian fashion were observed. The genetic basis for the allelic differences were identified by sequencing the ADRB3 (coding and non-coding regions) from animals that were homozygous for each of the alleles. Five sire lines (two Merino x Merino, two Merino x Coopworth, one Dorset Down x Coopworth) provided phenotypic and genotypic data used to ascertain the effects of allelic variation at the ADRB3 locus on birth weight, weaning weight, growth rate (up until weaning), carcass composition at 63 days post-weaning and cold survival. Statistical analyses within each half-sib family showed that in some sire lines (S13, S15, and S17) the inheritance of a particular allele was associated with increased birth weights and/or increased growth rates up until weaning. The inheritance of a particular sire allele was associated with fatter carcasses in sire line S16. Chi-squared analysis revealed the association of the E allele with cold survival and the D allele with cold-related mortality in sire line S14. Such associations support the hypothesis that ADRB3s are involved in energy homeostasis. With more research, the variation detected at the ADRB3 locus may assist in the genetic selection for desirable animal production traits.

Acclimatization↗