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.
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 ...
Registration of myometrial activity using multiple site electromyography in cyclic mares. A method for interpreting and analysing electromyographic (EMG) data of myometrial electrical activity was established. This method was used to study EMG activity in the uterus during the various stages of the oestrus cycle in mares. Recordings were analysed from four pairs of electrodes that were surgically implanted in the myometrium of four reproductively sound mares. The electrodes were placed at the tip, middle and base of the left horn and in the uterine body. Electrical activity was monitored by a polygraph. Data were transformed to a digitized form and statistically analysed. Myometria...
Comparative studies of the Spi1 proteins of three equine alpha-1-proteinase inhibitor haplotypes following isolation by affinity chromatography. 1. Antiproteinase deficiency can result in excessive proteinase-induced tissue damage. The major anti-elastase (Spi1) protein of equine alpha 1-proteinase inhibitor (alpha 1-PI) was isolated from the plasma/serum of three common haplotypes (I, L and U). 2. The N-terminal amino acid sequences of the three inhibitors were identical, but were only approx 65-77% homologous with two other published equine Spi1 sequences. 3. All three inhibitors complexed quickly and irreversibly with equine leucocyte proteinase 2A (kass = 2 x 10(7) M-1 sec-1). They were also efficient inhibitors of chymase (rat mas...
Silent blood chimaerism in a mare confirmed by DNA marker analysis of hair bulbs. Microsatellite DNA markers in a mare's hair bulbs not concordant with markers in her blood confirmed the hypothesis of chimaerism which had been proposed to explain the apparent parentage exclusion of the mare from her suckling foal. Parentage analysis for this foal based on genetic markers not originating from blood cells of its dam supported a parentage verification conclusion.
Synteny mapping in the horse using horse-mouse heterohybridomas. In a study of 35 horse-mouse heterohybridoma cell lines, synteny in the horse was found between LDHB, PEPB and IGF1 and between NP, MPI and IDH2. A synteny between ADA and PEPC was also indicated. The loci for horse immunoglobulin light chain (IgL) genes and for LDHA were independent.
[Ganglioside GM3 from horse erythrocytes: structure and effect on cell proliferation]. An increase of the mouse fibroblast proliferation by ganglioside GM3 from equine erythrocytes is described. The structure of GM3 has been established on the basis of chemical methods, enzymatic degradation, GC-MS, as well as plasma desorption mass spectrometry and HPLC of 9-anthrylmethyl esters of gangliosides to characterize the long-chain base composition. The oligosaccharide moiety includes an N-glycolylneuraminic acid residue, whereas the main components of the lipid moiety are 20:1 sphingosine and 24:0 fatty acids.
DNA sequence analysis of serologically detected ELA class II haplotypes at the equine DQ beta locus. The genetic diversity at the ELA DQ beta locus was investigated using polymerase chain reaction and DNA sequencing. Based upon serological methods 16 class II homozygous animals were selected and their genomic DNA was used. A DQ beta gene from an equine cDNA library was also sequenced. Our methodology and the similarity between the genomic and the cDNA sequences suggest that the studied locus is expressed on equine lymphocytes. In the predicted amino acid sequence the most extensive variation is located at residues 56-60. The pattern of these five amino acids is strongly correlated to the sero...
The cDNA sequence of horse transferrin. The cDNA sequence of horse transferrin was determined by sequencing clones isolated from a horse liver cDNA library and clones obtained by PCR. The 2305 bp horse transferrin cDNA sequence included part of the 5' untranslated region and extended to the poly(A) tail. It had 80% sequence identity with the human transferrin cDNA, and encoded a protein of 706 residues, including a signal sequence of 19 amino acids. The horse transferrin sequence had the duplicated structure and conserved iron binding and cysteine residues which are characteristic of the transferrin family.
Proto-oncogene of genomic DNA, related to the human epidermal growth factor receptor (EGFR) gene, from clinically normal domestic animals. Genomic DNAs of cattle, horses, pigs, dogs, cats and chickens were surveyed using Southern blot hybridization analysis, with a human EGFR cDNA fragment. Several bands with different numbers and molecular weights were observed under the condition of low stringency in the individual animal species. The bands showing DNA polymorphism were observed among bovine genomic PstI-digested DNAs from 4 individuals and EcoRI-digested genomic DNAs from 4 chickens. These results may provide basic data which are useful for analysis of tumorigenetic mechanisms in domestic animals.
Structural features of the trans-activation response RNA element of equine infectious anemia virus. A 25-nucleotide RNA with the sequence of the trans-activation response (TAR) element of equine infectious anemia virus (EIAV) was analyzed by biochemical methods and by one- and two-dimensional NMR spectroscopy. NMR, nuclease probing, and polyacrylamide gel migration rates show that the RNA consists of an A-helical stem capped by two non-Watson-Crick U-G base pairs and a compact four-nucleotide loop. The loop is stabilized by base stacking, with loop nucleotides C12 and C15 stacked upon U11 and G16, respectively. Near the 5' end of the molecule, the stem contains a bulge at nucleotide C2, most...