Topic:Bioinformatics
Bioinformatics in horses involves the application of computational tools and techniques to analyze and interpret biological data related to equine species. This interdisciplinary field integrates biology, computer science, and information technology to study genetic, genomic, and proteomic information in horses. Bioinformatics can be used to investigate genetic variations, understand disease mechanisms, and assist in the development of targeted therapies and breeding programs. Key areas of focus include genome sequencing, gene expression analysis, and the identification of genetic markers associated with specific traits or conditions. This page compiles peer-reviewed research studies and scholarly articles that explore the application and impact of bioinformatics on equine genetics, health, and breeding.
Cloning of a DNA repeat element from horse: DNA sequence and chromosomal localization. A DNA repeat element, revealed initially by digestion of horse DNA with TaqI, was cloned and characterized by Southern and in situ hybridization studies and nucleotide sequencing. The clone, e4/1, consisted of 32 tandem reiteration of a unit repeat of 21-22 bp, and produced multilocus DNA fingerprinting profiles that were useful for parentage analysis in horses. The tandem repeat element was shown by in situ hybridization to be localized in the centromeres of the acrocentric but not metacentric classes of horse chromosomes.
Beta-thiopropionyl cytochromes c modified at lysyl residues: preparation and characterization of the monosubstituted horse cytochromes c. beta-Thiopropionyl derivatives of horse cytochrome c singly modified at each of 18 different lysine epsilon-amino groups have been prepared using sulfosuccinimidyl-2-(biotinamido)ethyl-1,3-dithiopropionate and purified to homogeneity by high-pressure liquid chromatography. These derivatives were characterized by determination of: (i) the location of the modification; (ii) reduction potentials; (iii) visible and NMR spectra: and by (iv) measurement of electron transfer activity with cytochrome-c oxidase. No significant changes in structure were indicated, except for the ferric forms of the deri...
Partial sequence of the equine immunoglobulin epsilon heavy chain cDNA. In order to isolate a part of the immunoglobulin E (IgE) heavy chain cDNA of the horse, primers have been designed based upon well conserved sequences in humans, sheep and rats. The PCR resulted in a 500 bp fragment which hybridised with a human IgE constant region probe. The fragment was cloned and sequenced and its derived protein sequence compared with the corresponding sequences in humans, sheep and mice. Most amino acids common to these three species are also shared by the horse.
The DNA sequence of equine herpesvirus 2. The complete DNA sequence of equine herpesvirus 2 (EHV-2) strain 86/67 was determined. The genome is 184,427 bp in size and has a base composition of 57.5% G + C. Unusually for a herpesvirus, about a third of the sequence distributed in several large blocks appears not to encode proteins. The 79 open reading frames that were identified as probably polypeptide-coding are predicted to encode 77 distinct proteins. Amino acid sequence comparisons confirmed that EHV-2 is a gamma-herpesvirus that is genetically collinear with herpesvirus saimiri (HVS; a gamma 2-herpesvirus) and Epstein-Barr virus (E...
At least four MHC class I genes are transcribed in the horse: phylogenetic analysis suggests an unusual evolutionary history for the MHC in this species. Nineteen horse MHC class I specificities have been serologically identified previously at a single locus (ELA-A), and two other specificities appear to be coded at other loci. Biochemical studies indicate that there are at least two expressed loci. In order to establish the number of transcribed horse MHC class I genes, we made a cDNA library from a heterozygous animal (ELA-A3/A7), and screened for positive clones using a bovine class I probe. More than 200 class I clones were isolated in this way, and so far seven unique full length sequences have been identified. All of the sequences are pre...
Extensive mtDNA diversity in horses revealed by PCR-SSCP analysis. The hypervariable D-loop region of mitochondrial DNA (mtDNA) was amplified with the polymerase chain reaction using total horse DNA samples. Analysis of single strand conformation polymorphism (SSCP) of denatured amplification products was carried out by native polyacrylamide (8%) gel electrophoresis followed by silver staining. As many as 15 distinct SSCP variants were revealed when screening a total of 78 maternally unrelated horses representing five different breeds. All breeds showed a high degree of polymorphism and the estimated probability (PImt) that two maternally unrelated individual...
Taxon-specific probes for the cellulolytic genus Fibrobacter reveal abundant and novel equine-associated populations. A total of six 16S rRNA targeted oligonucleotide probes were used to quantify Fibrobacter abundance and diversity in the gastrointestinal contents of a pony. Approximately 12% of the total 16S rRNA extracted from cecal contents hybridized with a Fibrobacter genus-specific probe and a Fibrobacter succinogenes species-specific probe. However, no significant hybridization was observed with a probe for the species. Fibrobacter intestinalis or with three probes for F. succinogenes subspecies. This suggested the presence of a previously undescribed population of F. succinogenes-like organisms. Novel...
Delineating minimal protein domains and promoter elements for transcriptional activation by lentivirus Tat proteins. Lentivirus Tat proteins comprise a novel class of RNA-binding transcriptional activators that are essential for viral replication. In this study, we performed a series of protein fusion experiments to delineate the minimal protein domains and promoter elements required for Tat action. We show that a 15-amino-acid region of equine infectious anemia virus (EIAV) Tat protein, when fused to the GAL4 or LexA DNA binding domain, can activate transcription in appropriate promoter contexts. In the natural human immunodeficiency virus type 1 long terminal repeat, activation by Tat is dependent on multi...
Diaphyseal structural properties of equine long bones. We evaluated the single-cycle structural properties for axial compression, torsion, and 4-point bending with a central load applied to the caudal or lateral surface of a diaphyseal segment from the normal adult equine humerus, radius, third metacarpal bone, femur, tibia, and third metatarsal bone. Stiffness values were determined from load-deformation curves for each bone and test mode. Compressive stiffness ranged from a low of 2,690 N/mm for the humerus to a high of 5,670 N/mm for the femur. Torsional stiffness ranged from 558 N.m/rad for the third metacarpal bone to 2,080 N.m/rad for the fe...
Characterisation of a membrane receptor on ruminants and equine platelets and peripheral blood leukocytes similar to the human integrin receptor glycoprotein IIb/IIIa (CD41/61). This paper describes two anti-glycoprotein IIb/IIIa or CD41/61 murine monoclonal antibodies (Co.35E4 and Co.2oA1). The cellular distribution and apparent molecular weight of the antigen detected by these antibodies is consistent with their reaction with ruminant and equine glycoprotein IIb/IIIa. Biochemical analysis of the equine molecule using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) revealed bands of 24, 100 and 110 kDa under reducing conditions and 115 and 80 kDa under nonreducing conditions. Biochemical analysis of ruminant antigen revealed that the 24 kDa band...
Nucleotide sequence of exons 5 to 9 of the p53 tumour-suppressor gene of the donkey (Equus asinus). The evolutionary conserved region of the equine homologue of the p53 gene from the donkey genome was PCR amplified and cloned. The 1380 bp fragment consisted of exons 5 to 9 and the intervening introns. The exonic and intronic DNA sequences showed a variable but high level of homology with previously published human sequences. The aminoacid sequences corresponding to the evolutionary conserved domains II, III, and V were identical to the human regions, whilst domain IV was 96% homologous.
An algorithm to describe the oxygen equilibrium curve for the thoroughbred racehorse. An algorithm to describe the oxygen equilibrium curve (OEC) of the Thoroughbred horse was derived from raw oxygen equilibrium curve data obtained under standard conditions of temperature, pH and PCO2 (Smale and Butler, 1994). This algorithm was derived by a curve-fitting procedure based on the algorithm for human blood produced by Kelman (1966). The temperature, fixed acid and net CO2 coefficients were then incorporated in the algorithm to enable the accurate calculation of % saturation from any combination of PO2, temperature, pH and PCO2. The algorithm was checked using blood gas data obtain...
Estimation of material properties in the equine metacarpus with use of quantitative computed tomography. The purpose of this study was to investigate the relationships between data obtained from quantitative computed tomography and mechanical properties in the equine metacarpus, as measured in vitro in bone specimens. Three hundred and fifty-five bone specimens from the metacarpi of 10 horses were machined into right cylinders aligned with the long axis of the bone. A computed tomographic scan of the specimens, along with a Cann-Genant K2HPO4 calibration standard, was obtained. The specimens then were compressed to failure, and the elastic modulus, yield stress, yield strain, strain energy densit...
The complete mitochondrial DNA sequence of the horse, Equus caballus: extensive heteroplasmy of the control region. The sequence of the mitochondrial (mt) DNA of the horse (Equus caballus) was determined. The length of the sequence presented is 16,660 bp. This figure, however, is not absolute due to pronounced heteroplasmy caused by variable numbers of the motif GTGCACCT in the control region of different molecules. Boundaries of the 13 peptide-coding genes were determined by the presence of start and stop codons, and by analogy with other eutherian mtDNAs. Three genes (COIII, NADH3 and NADH4) were not terminated by a stop codon. Comparison among the peptide-coding genes of the horse and eight other mammals...
Further characterisation of forms of haemosiderin in iron-overloaded tissues. The biochemical and biophysical properties of isolated haemosiderins have been compared to that of another iron-containing protein, termed prehaemosiderin, which sediments through chaotropic potassium iodide only after 20 h of ultracentrifugation, in contrast to that of haemosiderin which is recovered after 2 h of ultracentrifugation. The iron/protein ratio and iron/phosphate ratio were less that that of the corresponding haemosiderin, while the elemental composition was also reduced in many of the prehaemosiderin samples. Mossbauer spectroscopy and electron diffraction identified the predomin...
[The metabolism of foreign substances in the horse with reference to other animal species]. In this paper, the metabolism of xenobiotics in the horse, including differences to other species, is discussed. The most important metabolic reactions of phase I (oxidation, reduction and hydrolysis of substrates), as well as of phase II (conjugation of substrates with glucuronic acid, sulphuric acid, acetic acid, alkyl groups, amino acids, amino acid derivatives, glutathione etc.), are discussed and enzymes involved in the metabolic reactions are considered.
Polymorphic sequence in the D-loop region of equine mitochondrial DNA. The D-loop regions in equine mitochondrial DNA were cloned from three thoroughbred horses by polymerase chain reaction (PCR). The total number of bases in the D-loop region were 1114 bp, 1115 bp and 1146 bp. The equine D-loop region is A/T rich like many other mammalian D-loops. The large central conserved sequence block and small conserved sequence blocks 1, 2 and 3, that are common to other mammals, were observed. Between conserved sequence blocks 1 and 2 there were tandem repeats of an 8 bp equine-specific sequence TGTGCACC, and the number of tandem repeats differed among individual horses....
Molecular dynamics simulation of equine infectious anemia virus Tat protein in water and in 40% trifluoroethanol. Two molecular dynamics (MD) simulations were performed in order to increase the understanding of the dependence of protein conformation on solvent environment. The protein used for these simulations is the transcriptional activator of the equine infectious anemia virus (EIAV-Tat). The structure of this protein has been determined by nuclear magnetic resonance (NMR) in aqueous solution (Willbold et al., Science 264, 1584 (1994)) and in 40% (v/v) trifluoroethanol (TFE) (Sticht et al., Eur. J. Biochem., submitted) showing considerable differences in the stability of the secondary structure elemen...
Models of the three-dimensional structures of echidna, horse, and pigeon lysozymes: calcium-binding lysozymes and their relationship with alpha-lactalbumins. Similarities in amino acid sequences, three-dimensional structures, and the exon-intron patterns of their genes have indicated that c-type lysozymes and alpha-lactalbumins are homologous proteins, i.e., descended by divergent evolution from a common ancestor. Like the alpha-lactalbumins, echidna milk, horse milk, and pigeon eggwhite lysozymes all bind Ca(II). Models of their three-dimensional structures, based on their amino acid sequences and the known crystal structures of domestic hen eggwhite and human lysozymes and baboon and human alpha-lactalbumins, have been built. The several structur...
Sequence of a cDNA encoding horse growth hormone. A cDNA encoding horse growth hormone (ecGH) was isolated and sequenced. The coding sequence resembles a typical mammalian GH pre-protein and contains a 3' untranslated region of 101 nucleotides carrying two contiguous polyadenylation signals.
Cloning and sequencing of the equine testicular follitropin receptor. To investigate the possibility that specific structural determinants within the equine follitropin receptor (eFSHR) are critical to the enhanced specificity of this receptor compared to other FSHRs, we used the RACE-PCR technique to clone the eFSHR from equine testis. Sequence analysis revealed that the eFSHR is highly homologous to other mammal FSHRs, but it presents 10 unique amino acid residue replacements in the extracellular domain. Furthermore, a potential N-glycosylation site was detected at a position not encountered in other receptors. Northern blot analysis identified three transcrip...
Studies on glycoprotein-derived carbohydrates. This research focuses on the study of glycoproteins, specifically investigating their carbohydrate chains and their various functions in living organisms. The article highlights the challenges in isolating specific carbohydrate chains […]
Polymorphism in the coding sequence of the horse transferrin gene. Transferrin, the iron transport protein of the blood, is highly polymorphic in many species, including the horse. A number of sequence polymorphisms that distinguish several of the variants of horse transferrin are reported here. Previous studies indicated that exons 12 and 15 were likely to be polymorphic. Sequencing regions of exons 12 and 15 from D and R variants revealed 10 nucleotide substitutions that encoded six amino acid replacements. The F1, F2, H2, and * variants were identical to D, and the O variant was almost identical to R, in the regions studied. The data indicated that the hor...
Molecular cloning of an equine satellite-type DNA sequence and its chromosomal localization. We have molecularly cloned portions of equine satellite-type DNA and investigated the organization of the DNA sequence of the cloned segments. Sequence analysis and dot-blot analysis, using the cloned sequence (ES200) as a probe, indicate that the satellite-type DNA sequence consists mainly of 221-bp tandem repeats and represents 3.7-11% of the equine genome. Southern blot analysis further shows that (1) no sequences homologous to ES200 exist in the human, swine, and bovine genomes and that (2) the fragment pattern of the satellite-type DNA produced by ApaI cleavage shows a slight difference a...
Characterization of horse (Equus caballus) T-cell receptor beta chain genes. Genes encoding the horse (Equus caballus) T-cell receptor beta chain (TCRB) were cloned and characterized. Of 33 cDNA clones isolated from the mesenteric lymph node, 30 had functionally rearranged gene segments, and three contained germline sequences. Sixteen unique variable segments (TCRBV), 14 joining genes (TCRBJ), and two constant region genes (TCRBC) were identified. Horse TCRBV were grouped into nine families based on similarity to human sequences. TCRBV2 and TCRBV12 were the most commonly represented horse families. Analysis of predicted protein structure revealed the presence of conser...
Morphometric study of the recurrent laryngeal nerve in young ‘normal’ horses. Quantitative measurements were made on cross-sectional preparations of the distal part of the recurrent laryngeal nerve (RLN) from nine young mixed-breed horses to establish reference values for the total number of myelinated fibres, mean fibre diameter and percentage of thickest fibres (over 9.5 microns) and to delineate diameter distribution curves. The total number of myelinated fibres, mean fibre diameter and percentage of thickest fibres for the left RLN were significantly lower than those of the right RLN (P < 0.005). The distribution of fibres was unimodal. The fibre diameter ranged ...