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.
[Differentiation of domestic horse and Przewalskis horse using various DNA sequences]. The electrophoretic mobility of seven erythrocyte enzymes and spectra of fragments amplified by RAPD-PCR with primers UBC-85 and UBC-126 were comparatively analyzed in domestic horse and Przewalski's horse. All tested genetic markers were classified into two groups differing in their involvement in differentiation of the two closely related horse species. Markers from different groups differed neither in their type (a polymorphic protein or an amplification product) nor in their biochemical role (for enzymes).
Evidence that commercial calf and horse sera can contain substantial amounts of trans-10,cis-12 conjugated linoleic acid. We analyzed fetal calf, newborn calf, horse, and adult cow sera for conjugated linoleic acid (CLA). All sera samples contained CLA, but the amounts varied. The predominant isomer was cis-9,trans-11 CLA but some samples appeared to contain substantial amounts of an isomer with the retention time of trans-10,cis-12 CLA.
[Population genetic parameters of aboriginal Yakut horses as related to modern breeds of the domestic horse Equus caballus L]. This study was the first to analyze the polymorphic characteristics of a wide range of biochemical markers in aboriginal Yakut horses. A total of 124 alleles, including 48 alleles of seven blood-group loci and 76 alleles of ten loci for enzymes and other proteins, were studied. For these polymorphic systems, a computer analysis of the genetic distances between 85 horse breeds of different origin from all parts of the world was performed. The low level of hereditary variation in the Yakut horses confirmed that this breed is old and has long been an isolated population. Phylogenetic analysis dem...
Construction of a horse BAC library and cytogenetical assignment of 20 type I and type II markers. A horse BAC library was constructed with about 40,000 clones and mean insert size of 110 kb representing a 1.5 genome equivalent coverage and a probability of finding a single sequence of 0.75. It was characterized by PCR screening of about 130 sequences of horse microsatellites and exonic gene sequences retrieved from databases. BACs containing 8 microsatellites and 12 genes were subsequently localized by fluorescent in situ hybridization (FISH) on chromosomes. Two linkage groups were newly assigned to chromosomes: LG2 to ECA3 and LG5 to ECA24, and five linkage groups were also oriented--LG3,...
Diversity among isolates of Actinobacillus equuli and related organisms as revealed by ribotyping. The objective of this work was to examine the diversity within Australian isolates of Actinobacillus equuli and related organisms by the genotypic method of ribotyping. Methods: Ribotyping, performed using the enzyme HaeIII, was used to examine the diversity in 12 field isolates of A equuli (five being capable of fermenting L-arabinose), one field isolate of Pasteurella caballi and two unclassifiable field isolates. Isolates were obtained from Australian horses, except for three isolates of A equuli (one L-arabinose positive and two L-arabinose negative) which were obtained from horses and a p...
Articular Cartilage Optical Properties in the Spectral Range 300-850 nm. Measurements of absolute total reflectance were recorded from weight-bearing (n=9) and nonweight-bearing (n=9) equine articular cartilage specimens from 300 to 850 nm using a spectrophotometer with integrating sphere attachment. Following correction of measured spectra for interfacial reflections and edge losses, Kubelka-Munk theory was applied to estimate absorption and scattering coefficient, one-dimensional light intensity distribution, and light penetration depth. Kubelka-Munk absorption coefficients ranged from ∼7 cm-1 at 330 nm to ∼1 cm-1 at 850 nm. A localized absorption peak wa...
Report of the Second Equine Leucocyte Antigen Workshop, Squaw valley, California, July 1995. The final assignment of antibody clusters for leucocyte antigens and immunoglobulins, as described in detail in Sections 3 and 4, is summarized in Table 4. Together with other mAbs developed outside of ELAW II (Table 9) this pool of reagents represent a powerful array of tools for the study of equine immunity. The Second Equine Leucocyte Antigen Workshop made considerable advances in pursuing the objectives of establishing the specificities of mAbs and achieving consensus on the nomenclature for equine leucocyte and immunoglobulin molecules. Of equal importance, several productive collaboratio...
CLoning of equine interleukin 1 alpha and equine interleukin 1 beta and determination of their full-length cDNA sequences. To clone equine interleukin 1 alpha (IL-1 alpha) and equine interleukin 1 beta (IL-1 beta) and determine their full-length cDNA sequences. Methods: The mRNA isolated from lipopolysaccharide-stimulated cultured equine monocytes was reverse transcribed, and a cDNA library was constructed in a lambda phage. The cDNA library was screened by means of plaque hybridization with radiolabeled human IL-1 alpha and IL-1 beta cDNA probes. The cDNA nucleotide sequences for equine IL-1 alpha and equine IL-1 beta were determined by use of the dideoxy chain termination technique. The cDNA sequences were analy...
Objectivity of two methods of differentiating fibre types and repeatability of measurements by application of the TEMA image analysis system. The objectivity of two of the most widely used methods for differentiation of fibre types, i.e. 1) the myosin ATP-ase method (Brooke and Kaiser, 1970a,b) and 2) the combined method, by which the myosin ATP-ase reaction is used to differentiate between fast and slow twitch fibres and NADH-tetrazolium reductase activity is used to identify the subgroups of fast twitch fibres (Ashmore and Doerr, 1970, Peter et al., 1972), was assessed in muscle samples from horses, calves and pigs. We also assessed the objectivity of the alpha-amylase-PAS preparation for the visualisation of capillaries (Andersen...
Application of probability techniques to the objective interpretation of veterinary clinical biochemistry data. Methods for the interpretation of veterinary clinical biochemistry have not developed as rapidly as biochemical technology. However, the results of clinical biochemistry tests are only of value when they are interpreted appropriately. A retrospective study was undertaken to investigate the equine biochemistry data which had been stored in a veterinary hospital database. By applying percentile analysis and Bayesian probability methods to the clinical biochemistry and corresponding diagnosis data, a novel method for the interpretation of clinical biochemistry data has been developed. The method ...
A microtiter plate assay for the determination of uronic acids. The amount of uronic acid residues in samples containing glycosaminoglycans or pectin is an important parameter in the quantitative and structural analysis of these complex carbohydrates. This paper describes a method to determine the content of uronic acids in biological samples, using conventional polystyrene microtiter plates and microtiter plate-reading equipment with standard interference filters (i.e., 540 or 492 nm). This assay is a modification of a commonly used procedure, viz. hydrolysis of uronic acid containing carbohydrate polymers in 80% sulfuric acid containing tetraborate ions ...
Equus caballus gelsolin–cDNA sequence and protein structural implications. We have generated and characterized the cDNA from equine smooth muscle that encodes gelsolin, an actin-modulating protein. Overlapping cDNA clones synthesized by the reverse transcriptase/polymerase chain reaction and clones isolated from a horse genomic library provided the complete primary structure for the intracellular isoform of gelsolin, while cDNA complemented with protein sequence data produced the full-length primary transcript of the gelsolin isoform found circulating in equine plasma. The deduced amino acid sequences of the intracellular and secreted versions of equine gelsolin infe...
Zoo-FISH with microdissected arm specific paints for HSA2, 5, 6, 16, and 19 refines known homology with pig and horse chromosomes. Microdissected arm specific paints (ASPs) for human (HSA) chromosomes (Chrs) 2, 5, 6, 16, and 19 were used as probes on pig (SSC) and horse (ECA) metaphase chromosomes. Regions homologous to individual human arms were delineated in the two species studied. Of the ten ASPs used, HSA6 and 16 ASPs showed complete synteny conservation of individual arms as single blocks/ arms both in pig and horse. A similar trend was, in general, also observed for HSA19 ASPs. However, contrary to these observations, synteny conservation of individual arms of HSA2 and HSA5 was not observed in pig and horse. The ar...
Characterization, genetic and physical mapping analysis of 36 horse plasmid and cosmid-derived microsatellites. Thirty-six new horse microsatellites (11 from plasmid libraries and 25 from a cosmid library) were isolated and characterized on a panel of four horse breeds. Thirty were found to be polymorphic with heterozygosity levels ranging between 0.20 and 0.87. Twenty-two of the cosmids were physically mapped to R-banded single horse Chromosomes (Chrs) 1, 3, 4, 9, 11, 12, 13, 15, 18, 19, 21, 22, 23 and three to pericentromeric regions. Furthermore, linkage analysis between a selection of 42 DNA markers, including those presented in this study, and 16 conventional markers of the horse hemotype was perfo...
A myoglobin variant with a polar substitution in a conserved hydrophobic cluster in the heme binding pocket. Well-ordered internal amino acids can contribute significantly to the stability of proteins. To investigate the importance of the hydrophobic packing interface between helices G and H in the proximal heme pocket of horse heart myoglobin, the highly conserved amino acid, Leu104, was substituted with asparagine, a polar amino acid of similar size. The Leu104Asn mutant protein and its recombinant wild-type horse heart myoglobin counterpart were expressed from synthetic genes in Escherichia coli. Thermal denaturation of these two recombinant myoglobins, as studied by measurement of circular dichro...
Muscarinic signaling pathway for calcium release and calcium-activated chloride current in smooth muscle. We investigated the muscarinic activation of Ca(2+)-activated Cl- currents [ICl(Ca)] in voltage-clamped equine tracheal myocytes. The threshold of cytosolic free Ca2+ concentration ([Ca2+]i) required for activation of ICl(Ca) was 202 +/- 22 nM, and full activation of the current occurred at 771 +/- 31 nM. Hexahydro-sila-difenidol (M3 antagonist) inhibited the methacholine-induced phasic [Ca2+]i increase and ICl(Ca) in a concentration-dependent manner, whereas methoctramine (M2 antagonist) only slightly attenuated the [Ca2+]i increase and ICl(Ca) (14.8 and 21.4%, respectively), consistent with ...
Enzyme immunoassay for measuring 25-hydroxyvitamin D3 in serum. We developed a rapid, competitive enzyme immunoassay (EIA) for measuring 25-hydroxyvitamin D3 [25(OH)D3] in serum. The EIA was based upon 25(OH)D3-3-hemisuccinate covalently coupled to secondary amino groups grafted onto the polystyrene surface of microtiter wells. Optimal coupling conditions were established, and we found that inclusion of 40 mumol/L chloramine T, an agent not previously described for use in coupling to these plates, resulted in both more reproducible coupling as well as more than a twofold increase in the coupling efficiency. Before EIA, 25(OH)D3 was extracted from the serum...
Cloning, sequencing and in vitro functional expression of recombinant donkey follicle-stimulating hormone receptor: a new insight into the binding specificity of gonadotrophin receptors. Among all mammalian FSH receptors (FSH-R; including donkey (dk) FSH-R), only horse (hs) FSH-R does not bind hsLH/chorionic gonadotrophin (CG). In order to delineate the structural origin of hsFSH-R specificity precisely, we have cloned dkFSH-R cDNA from donkey testis mRNA by RT-PCR. Transiently expressed dkFSH-R endowed COS-7 cells with both hsLH/CG- and FSH-binding activity, as well as FSH-induced cAMP production. The deduced dkFSH-R amino acid sequence shares 96% identity with the hsFSH-R: notably, in the hormone-binding domain, the specificity of hsFSH-R may be ascribed to only four diverge...
Characterization and mutational studies of equine infectious anemia virus dUTPase. The macrophage tropic lentivirus, equine infectious anemia virus (EIAV), encodes a dUTPase in the pol gene that is required for efficient replication in macrophages. Two naturally occurring variants of the enzyme were expressed as recombinant proteins in Escherichia coli; metal chelate affinity chromatography was used to purify histidine-tagged recombinant enzymes to greater than 80% homogeneity in a single chromatographic step. Biochemical and enzymatic analyses of these preparations suggest that this method yields dUTPase that is suitable for detailed mutational analysis. Specific activities...
Low-molecular-weight displacers for high-resolution protein separations. The resolving power of displacement chromatography using low-molecular-weight displacers was investigated using a model mixture containing bovine and horse heart cytochrome c. The linear and nonlinear adsorption behavior of these two proteins was examined in cation-exchange chromatography and shown to be quite similar. Furthermore, an analysis of the dynamic affinity of these proteins indicated extremely similar affinities under displacement conditions. Despite the extreme similarities in the adsorption behavior, displacement chromatography using a protected amino acid displacer resulted in ex...
Ground reaction forces in horses, assessed from hoof wall deformation using artificial neural networks. An artificial neural network (ANN) was developed to investigate whether hoof wall deformation could be used to determine ground reaction forces (GRF) in horses. The ANN was taught this relationship under certain conditions and was able to generalise this knowledge to conditions for which it was not trained before. To acquire data to train and test the ANN, a horse was equipped with strain gauges attached to the dorsal, lateral and medial parts of the hoof to assess hoof wall deformation. A force plate was used to measure the GRFs. Both hoof wall deformation and GRF were recorded simultaneously...
Molten globule state of equine beta-lactoglobulin. The acid-unfolded state of equine beta-lactoglobulin was characterized by means of circular dichroism, nuclear magnetic resonance, analytical gel-filtration chromatography, and analytical centrifugation. The acid-unfolded state of equine beta-lactoglobulin has a substantial secondary structure as shown by the far-ultraviolet circular dichroism spectrum but lacks persistent tertiary packing of the side chains as indicated by the near-ultraviolet circular dichroism and nuclear magnetic resonance spectra. It is nearly as compact as the native conformation as shown by the gel filtration and sedime...
Partial cloning of prohibitin cDNA from canine, feline, bovine, equine, and rabbit liver mRNA by RT-PCR. Prohibitin is the protein which has an inhibitory function in cell growth, and its gene is suggested to be one of putative tumor suppressor genes. In this report, we described a partial cloning of prohibitin cDNAs from canine, feline, bovine, equine, and rabbit liver mRNAs by RT-PCR, and their homology analysis. The sequences of these RT-PCR products were compared with each other as well as those reported for human and rat. The homology in this region of prohibitin cDNA was approximately 90%, and the amino acid sequence of each RT-PCR product shared more than 95% identity. Therefore, it is con...