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.
Doube M, Firth EC, Boyde A.Combined backscattered electron scanning electron microscopy (BSE SEM) and confocal scanning laser microscopy (CSLM) have been used to put tissue mineralization data into the context of soft tissue histology and fluorescent label information. Mineralization density (Dm) and linear accretion rate (LAR) are quantifiable parameters associated with mineralizing fronts within calcified tissues. Quantitative BSE (qBSE) may be used to determine Dm, while CSLM may be used to detect label fluorescence from which LAR is calculated. Eighteen-month old Thoroughbred horses received single calcein injection...
Whan G, Runciman RJ, Hurtig M.Whole bone in vitro biomechanical compressive testing can be complicated by three factors: sample asymmetry, heterogeneous material properties, and unknown effective centroid location. Methods: The technique presented here facilitates the calculation of effective centroid position, modulus of elasticity and equivalent uniform strain magnitude for a cross section of bone from a simple whole bone compressive test. Simplification of section response to load is achieved through a combination of linear beam and simple planer geometry theory. The technique requires three longitudinal strain gauges b...
Rasmussen T, Brittain T, Berks BC, Watmough NJ, Thomson AJ.Nitrous oxide reductase (N2OR) catalyses the final step of bacterial denitrification, the two-electron reduction of nitrous oxide (N2O) to dinitrogen (N2). N2OR contains two metal centers; a binuclear copper center, CuA, that serves to receive electrons from soluble donors, and a tetranuclear copper-sulfide center, CuZ, at the active site. Stopped flow experiments at low ionic strengths reveal rapid electron transfer (kobs=150 s-1) between reduced horse heart (HH) cytochrome c and the CuA center in fully oxidized N2OR. When fully reduced N2OR was mixed with oxidized cytochrome c, a similar rat...
Kovaleva EG, Plapp BV.Binding of NAD+ to wild-type horse liver alcohol dehydrogenase is strongly pH-dependent and is limited by a unimolecular step, which may be related to a conformational change of the enzyme-NAD+ complex. Deprotonation during binding of NAD+ and inhibitors that trap the enzyme-NAD+ complex was examined by transient kinetics with pH indicators, and formation of complexes was monitored by absorbance and protein fluorescence. Reactions with pyrazole and trifluoroethanol had biphasic proton release, whereas reaction with caprate showed proton release followed by proton uptake. Proton release (200-55...
Fitzgibbon JE, Sagripanti JL.The development of a method in macroarray format for the identification of alphaviruses and orthopoxviruses in samples of concern in biodefense is reported. Capture oligonucleotides designed to bind generic members of the orthopox- or alphavirus families and a collection of additional oligonucleotides to bind specifically nucleic acids from five individual alphaviruses, including Venezuelan equine encephalitis, or DNA from each of four orthopoxviruses, including variola virus (VAR) were deposited onto nylon membranes. Hybridization of digoxigenin labeled PCR products to the macroarray produced...
Murata T, Yamashiro Y, Kondo T, Nakaichi M, Une S, Taura Y.Complementary DNA (cDNA) for bovine quaking gene (Bqk), equine quaking gene (Eqk) and porcine quaking gene (Pqk), which are homologous to mouse quaking gene (qkI), were isolated, and their nucleotide sequences were determined. cDNA sequences of Bqk, Eqk and Pqk showed very high homology to that of qkI at nucleotide level; 94.2, 95.7 and 95.6%, respectively. Deduced amino acid sequences for Bqk, Eqk and Pqk perfectly matched to that of qkI. These findings suggest that the quaking gene family is highly conserved during mammalian evolution, and that Bqk, Eqk and Pqk are likely to have important b...
Bi X, Li G, Doty SB, Camacho NP.The orientation of collagen molecules is an important determinant of their functionality in connective tissues. The objective of the current study is to establish a method to determine the alignment of collagen molecules in histological sections of cartilage by polarized Fourier transform infrared imaging spectroscopy (FT-IRIS), a method based on molecular vibrations. Methods: Polarized FT-IRIS data obtained from highly oriented tendon collagen were utilized to calibrate the derived spectral parameters. The ratio of the integrated areas of the collagen amide I/II absorbances was used as an ind...
Hebenbrock M, Düe M, Holzhausen H, Sass A, Stadler P, Ellendorff F.Global Positioning Systems (GPS) are considered suitable to monitor the position and velocity of horses during cross-country competition or in training. Furthermore, simultaneous recording of life data such as heart rate could be useful to assess the horse's condition during exercise. To test the suitability and reliability of a commercially available GPS system with integrated heart rate recording system and with built in GSM for data transmission, the Fidelak Equipilot Type EP-2003-15/G-2.11 (EP-15/G) was evaluated first for reliability of pulse recording from a pulse generator within the ph...
Steinbach F, Stark R, Ibrahim S, Gawad EA, Ludwig H, Walter J, Commandeur U, Mauel S.The myeloid cell system comprises of monocytes, macrophages (MPhi), dendritic cells (DC), Kupffer cells, osteoclasts or microglia and is also known as the mononuclear phagocytic system (MPS). Essential cytokines to differentiate or activate these cells include GM-CSF or IL-4. Important markers for characterization include CD1, CD14, CD68, CD163 and CD206. All these markers, however, were not cloned or further characterized in equids by use of monoclonal antibodies earlier. To overcome this problem with the present study, two approaches were used. First, we cloned equine cytokines and markers, ...
Zabek T, Nogaj A, Radko A, Nogaj J, Słota E.Genetic variation of endangered Biłgoraj horses and two common Polish horse breeds was compared with the use of 12 microsatellite loci (AHT4, AHT5, ASB2, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, HTG10, VHL20). Lower allelic diversity was detected in all investigated populations in comparison to other studies. Large differences in the frequencies of microsatellite alleles between Biłgoraj horses and two other horse breeds were discovered. In all polymorphic loci all investigated breeds were in the Hardy-Weinberg equilibrium. Mean Fis values and the results of a test for the presence of a rec...
Elsheikha HM, Lacher DW, Mansfield LS.Phylogenetic analyses based on sequences of the nuclear-encoded small subunit rRNA (ssurRNA) gene were performed to examine the origin, phylogeny, and biogeographic relationships of Sarcocystis neurona isolates from opossums and horses from the State of Michigan, USA, in relation to other cyst-forming coccidia. A total of 31 taxa representing all recognized subfamilies and genera of Sarcocystidae were included in the analyses with clonal isolates of two opossum and two horse S. neurona. Phylogenies obtained by the four tree-building methods were consistent with the classical taxonomy based on ...
Perelygin AA, Lear TL, Zharkikh AA, Brinton MA.Mammalian 2'-5' oligoadenylate (2-5A) synthetases are important mediators of the antiviral activity of interferons. Both human and mouse 2-5A synthetase gene families encode four forms of enzymes: small, medium, large and ubiquitin-like. In this study, the structures of four equine OAS genes were determined using DNA sequences derived from fifteen cDNA and four BAC clones. Composition of the equine OAS gene family is more similar to that of the human OAS family than the mouse Oas family. Two OAS-containing bovine BAC clones were identified in GenBank. Both equine and bovine BAC clones were phy...
Tschetter JR, Blikslager AT, Little D, Howard RD, Woody SL, Beex LM, Crisman MV.Colic is a serious disease syndrome in horses. Much of the mortality is associated with ischaemic-injured intestine during strangulating obstruction, yet there is limited understanding of the associated molecular events. Identification of differentially expressed genes during ischaemic injury should expand our understanding of colic and may lead to novel targeted therapeutic approaches in the future. Objective: To isolate and identify differentially expressed genes in equine jejunum following a 2 h ischaemic event compared to normally perfused jejunum. Methods: Suppressive subtractive hybridis...
Hunter DJ, Macmaster R, Roszak AW, Riboldi-Tunnicliffe A, Griffiths IR, Freer AA.Equine P2 protein has been isolated from horse spinal cord and its structure determined to 2.1 A. Since equine myelin is a viable alternative to bovine tissue for large-scale preparations, characterization of the proteins from equine spinal cord myelin has been initiated. There is an unusually high amount of P2 protein in equine CNS myelin compared with other species. The structure was determined by molecular replacement and subsequently refined to an R value of 0.187 (Rfree=0.233). The structure contains a molecule of the detergent LDAO and HEPES buffer in the binding cavity and is otherwise ...
Gilger BC, Reeves KA, Salmon JH.To measure the ocular surface area, scleral thickness, and the aqueous and vitreous humor volumes in the canine and equine eye. Animals studied Fourteen canine and 16 equine cadaver eyes. Methods: Eyes were measured either fresh or following fixation in formalin. Ocular surface area was calculated using the fluid displacement method. Globes were hemisected and aqueous and vitreous humor were collected and quantitated. Scleral thickness was measured by digital caliper, by image projection, and by ultrasonic biomicroscopy (UBM). Results: Mean +/- standard deviation (SD) scleral surface areas in ...
Lopes MS, Mendonça D, Cymbron T, Valera M, da Costa-Ferreira J, Machado Ada C.The analysis of mitochondrial D-loop sequences (408 bp) from 145 Lusitano founder mares yielded a total of 27 different haplotypes. The distribution of these mtDNA sequences was quite unequal, with the three most frequent ones representing 56.5% of all the Lusitano founder mares and 14 haplotypes (51.9%) being rare variants found only once in the sampling. Four main haplotype clusters were present in the Lusitano breed. The comparison of these sequences with other equine haplotypes shows that they fall in groups shared with other horse breeds. These data support the hypothesis of multiple dome...
Keyser-Tracqui C, Blandin-Frappin P, Francfort HP, Ricaut FX, Lepetz S, Crubézy E, Samashev Z, Ludes B.Sequence polymorphism of the mitochondrial DNA D-loop was used to determine the genetic diversity of horses recovered from a Scythian princely tomb dating from the beginning of the 3rd century BC. Eight haplotypes were found among the 13 ancient horse samples tested. Phylogenetical analysis showed that these ancient horse's sequences, along with two Yakut ones, were distributed throughout the tree defined by modern horses' sequences and are closely related to them. No clear geographical affiliation of the specimens studied was thus determined. Our work, among others, supports the very ancient ...
van der Harst MR, van de Lest CH, Degroot J, Kiers GH, Brama PA, van Weeren PR.A detailed and comprehensive insight into the normal maturation process of the different tissues that make up functional units of the locomotor system such as joints is necessary to understand the influence of early training on musculoskeletal tissues. Objective: To study simultaneously the maturation process in the entire composite structure that makes up the bearing surface of a joint (cartilage, subchondral and trabecular bone) in terms of biochemical changes in the tissues of juvenile horses at 2 differently loaded sites of the metacarpophalangeal joint, compared to a group of mature horse...
Díaz S, Giovambattista G, Peral-García P.Sequence information was obtained on the variation of the ELA-DRB upstream regulatory region (URR) after polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) cloning and sequencing of approximately 220 bp upstream of the first exon of horse DRB genes. The sequence of the proximal URR of equine DRB is composed of highly conserved sequence motifs, showing the presence of the W, X, Y, CAAT and TATA conserved boxes of major histocompatibility complex (MHC) class II promoters. Five different polymorphic horse DRB promoter sequences were detected in five horse breeds. The res...
Dahlgren LA, Nixon AJ.To define a portion of the nucleotide sequences of each of the 6 insulin-like growth factor (IGF) binding proteins (IGFBPs) in horses and describe patterns of messenger RNA (mRNA) and protein expression for IGFBPs in normal equine tendons. Methods: 7 horses. Methods: Total RNA was extracted from the tensile region of normal superficial digital flexor tendons and reverse transcribed into complimentary DNA (cDNA). The cDNA was amplified via PCR, and products representing portions of each IGFBP were cloned and sequenced. Nucleotide sequences were used to deduce the amino acid sequences, and both ...
Luo Y, Uboh CE, Soma LR, Guan F, Rudy JA, Tsang DS.This method describes the simultaneous separation, identification, quantification and confirmation of betamethasone (BTM) and dexamethasone (DXM) in equine plasma by liquid chromatography (LC) integrated with multidimensional tandem mass spectrometry. Analytes were directly extracted from equine plasma by methyl tert-butyl ether (MTBE). The residues were reconstituted with sample solvent. LC separation of the analytes was performed on a Hypercarb column using acetonitrile/water/formic acid (95:5:0.5, v/v/v) as the mobile phase. Sample screening, quantification and confirmation were performed i...
Abbott Y, O'Mahony R, Leonard N, Quinn PJ, van der Reijden T, Dijkshoorn L, Fanning S.A complete gene cassette contained in a class 1 integron from a multidrug-resistant (MDR) isolate of Acinetobacter baumannii cultured from a horse was characterized by molecular methods. Methods: Template genomic DNA purified from the A. baumannii isolate was investigated by PCR. A gene cassette-associated amplicon was detected and completely characterized. Results: A 2.6 kbp DNA fragment containing four gene cassettes was amplified from the MDR A. baumannii isolate. Sequence analysis showed it was similar to sequences recently reported in Klebsiella pneumoniae, Serratia marcescens and an Esch...
Keegan KG, Arafat S, Skubic M, Wilson DA, Kramer J, Messer NM, Johnson PJ, O'Brien DP, Johnson G.Subjective neurological evaluation in horses is prone to bias. An objective method of spinal ataxia detection is not subject to these limitations and could be of use in equine practice and research. Objective: Kinematic data in the walking horse can differentiate normal and spinal ataxic horses. Methods: Twelve normal and 12 spinal ataxic horses were evaluated by kinematic analysis walking on a treadmill. Each body position signal was reduced to a scalar measure of uncertainty then fuzzy clustered into normal or ataxic groups. Correct classification percentage (CCP) was then calculated using m...
Cappelli K, Porceddu A, Verini-Supplizi A, Capomaccio S, Marchis FD, Falcinelli M, Gaiti A, Silvestrelli M.The identification of differentially expressed genes is a fundamental prerequisite for understanding the molecular regulation of most physiological and pathological processes. Among the procedures employed to compare mRNA populations, those that are gel-based appear to hold great promise and are considered excellent tools for studying gene expression in species, such as the equine one, for which little genomic information is available. In the present study, we evaluated two techniques for studying mRNA profiles in horse tissue, one referred to the cDNA-amplified fragment length polymorphism (A...
Kimura J, Hirano Y, Takemoto S, Nambo Y, Ishinazaka T, Himeno R, Mishima T, Tsumagari S, Yokota H.The equine ovary has a very unique structure in terms of its extreme large size, the presence of the ovulation fossa and the inverted location of its cortex and medulla. In the previous study, it was recognized that the application of three-dimensional internal structure microscopy (3D-ISM) to observe the mare ovary is very effective. Three-dimensional reconstruction of serially sliced images made by 3D-ISM was successful in this study with the aid of the sophisticated image processing technique. The rotation of the reconstructed ovary has been carried out with and without the application of t...
Norman SE, Eager RA, Waran NK, Jeffery L, Schroter RC, Marlin DJ.Analysis of heart rate variability (HRV) is a non-invasive technique useful for investigating autonomic function in both humans and animals. It has been used for research into both behaviour and physiology. Commercial systems for human HRV analysis are expensive and may not have sufficient flexibility for appropriate analysis in animals. Some heart rate monitors have the facility to provide inter-beat interval (IBI), but verification following collection is not possible as only IBIs are recorded, and not the raw electrocardiogram (ECG) signal. Computer-based data acquisition and analysis syste...
Paulis M, Moralli D, Bensi M, De Carli L, Raimondi E.Tigger elements are human DNA transposons homologous to the pogo element of Drosophila melanogaster. They contain an open reading frame for a transposase very similar to the major mammalian centromere protein CENP-B. We found in the horse genome a DNA element ( Ecatig3) sharing 88% homology with human Tigger3. The presence of Tigger elements in the horse genome confirms previous data that date these elements before the divergence between Perissodactyla and Primates (80-90 Myr ago). Copy number evaluation indicates that the horse element is much more abundant than its human counterpart. Souther...
Talluri TR, Kumaresan A, Paul N, Sinha MK, Ebenezer Samuel King JP, Elango K, Sharma A, Raval K, Legha RA, Pal Y.Seminal plasma proteins and pathways associated with sperm motility have not been elucidated in stallions. Therefore, in the current study, using the high throughput LC/MS-MS approach, we profiled stallion seminal plasma proteins and identified the proteins and pathways associated with sperm motility. Seminal plasma from six stallions producing semen with contrasting sperm motility ( = 3 each high-and low-motile group) was utilized for proteomic analysis. We identified a total of 1687 proteins in stallion seminal plasma, of which 1627 and 1496 proteins were expressed in high- (HM) and low-...
Freitag GP, de Lima LGF, Jacomini JA, Kozicki LE, Ribeiro LB.This study proposes a standardized image analysis method for assessing horse conformation. A total of 34 adult American Quarter Horses (mean age = 6.7 ± 2.9 years, body weight = 489 ± 44 kg) were used. Reference angular measurements were performed using a digital goniometer, and reference linear measurements were determined using a standard measuring tape. For image analysis, photographs from the animal's left profile were taken at a distance of 3 m using eight markers to facilitate visualization. Images were processed using ImageJ software. Reference and estimated values showed great ac...
Weber KS, Wagener K, Blanco M, Bauersachs S, Bollwein H.Subfertility is a major problem in modern horse breeding. Especially, mares without clinical signs of reproductive diseases, without known uterine pathogens and no evidence of inflammation but not becoming pregnant after several breeding attempts are challenging for veterinarians. To obtain new insights into the cause of these fertility problems and aiming at improving diagnosis of subfertile mares, a comparative analysis of the intrauterine transcriptome in subfertile and fertile mares was performed. Uterine cytobrush samples were collected during estrus from 57 mares without clinical signs o...
Albert R, Vásárhelyi G, Bodó G, Kenyeres A, Wolf E, Papp T, Terdik T, Módis L, Felszeghy S.One of the most promising applications for the restoration of small or moderately sized focal articular lesions is mosaicplasty (MP). Although recurrent hemarthrosis is a rare complication after MP, recently, various strategies have been designed to find an effective filling material to prevent postoperative bleeding from the donor site. The porous biodegradable polymer Polyactive (PA; a polyethylene glycol terephthalate - polybutylene terephthalate copolymer) represents a promising solution in this respect. A histological evaluation of the longterm PA-filled donor sites obtained from 10 exper...
Wagner ML, Raudsepp T, Goh G, Agarwala R, Schaffer AA, Dranchak PK, Brinkmeyer-Langford C, Skow LC, Chowdhary BP, Mickelson JR.A comparative approach that utilizes information from more densely mapped or sequenced genomes is a proven and efficient means to increase our knowledge of the structure of the horse genome. Human chromosome 2 (HSA2), the second largest human chromosome, comprising 243 Mb, and containing 1246 known genes, corresponds to all or parts of three equine chromosomes. This report describes the assignment of 140 new markers (78 genes and 62 microsatellites) to the equine radiation hybrid (RH) map, and the anchoring of 24 of these markers to horse chromosomes by FISH. The updated equine RH maps for ECA...
Ganeshpurkar A, Singh R, Kumar D, Gutti G, Sardana D, Shivhare S, Singh RB, Kumar A, Singh SK.Machine learning (ML), an emerging field in drug design, has the potential to predict toxicity, shape-based analysis of inhibitors, scoring function (SF) etc. In the present study, a homology model, docking protocol, and a dedicated SF have been developed to identify the inhibitors of horse butyrylcholinesterase (BChE) enzyme. Horse BChE enzyme has homology with human BChE and is a substitute for the screening of inhibitors. The developed homology model was validated and the active site residues were identified from Cavityplus to generate grid box for docking. The validation of docking invol...
BMC research notesApril 16, 2013
Volume 6 152 doi: 10.1186/1756-0500-6-152
Christensen MB, Sørensen JC, Jacobsen S, Kjelgaard-Hansen M.Serum amyloid A (SAA) is useful as a diagnostic marker of systemic inflammation in horses, but only heterologous assays based on non-equine calibration and standardization are available for measurements of equine SAA. More accurate measurements could be obtained using purified species-specific SAA in native conformation for assay calibration and standardization. Further knowledge about the biochemical properties of SAA would facilitate a future production of native species-specific calibration material Therefore, the aim of the study was an investigation of the solubility and potentials for pu...
Cristoni S, Bernardi LR, Biunno I, Guidugli F.A new approach, based on the use of atmospheric pressure chemical ionization ion trap mass spectrometry (APCI-ITMS), but without a corona discharge, was investigated for application to creating and monitoring protein ions. It must be emphasized that APCI is not usually used in protein analysis. In order to verify the applicability of the proposed method to the analysis of proteins, two standard proteins (horse cytochrome c and horse myoglobin) were analyzed. A mixture of the two proteins was also analyzed showing that this novel approach, based on the use of APCI, can be used in the analysis o...
Sakagami M, Hirota K, Awata T, Yasue H.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...
Xie T, Zhang S, Shen W, Zhang G, Guo R, Zhang W, Cao Y, Pan Q, Liu F, Sun Y, Liu S.Twinning trait in donkeys is an important manifestation of high fecundity, but few reports are available elucidating its genetic mechanism. To explore the genetic mechanism underlying the twin colt trait in Dezhou donkeys, DNA from 21 female Dezhou donkeys that had birthed single or twin colts were collected for whole-genome resequencing. FST, θπ and Tajima’s D were used to detect the selective sweeps between single and twin colt fecundity in the Dezhou donkey groups. Another set of 20 female Dezhou donkeys with single or multiple follicles during estrus were selected to compare concentrat...
Tachibana Y, Sakurai T, Bai H, Shiota K, Nambo Y, Nagaoka K, Imakawa K.Extensive studies have been conducted to characterize the unique phenomena of equine pregnancy. Most studies have focused on embryo transmigration when the embryo is covered with a mucin-like glycoprotein capsule and on the characterization of the chorionic girdle and chorionic gonadotropin (CG) secretion. However, the events preceding and following capsule disappearance have not been well studied. In this study, the mRNA expression in conceptus membranes at days 19, 21, and 25 (day 0 = day of ovulation) was analyzed by RNA-seq (SOLiD3), and transcript levels on these three days and day 13...
Tozaki T, Inoue S, Mashima S, Ohta M, Miura N, Tomita M.Microsatellites are useful tools for the construction of a linkage map and parentage testing of equines, but only a limited number of equine microsatellites have been elucidated. Thus, we constructed the equine genomic library enriched for DNA fragments containing (CAG)n repeats. The enriched method includes hybridization-capture of repeat regions using biotin-conjugated oligonucleotides, nucleotide substrate-biased polymerase reaction with the oligonucleotides and subsequent PCR amplification, because these procedures are useful for the cloning of less abundant trinucleotide microsatellites. ...
Nam GH, Ahn K, Bae JH, Han K, Lee CE, Park KD, Lee SH, Cho BW, Kim HS.Muscle glycogen Phosphorylase (PYGM) has been shown to catalyze the degradation of glycogen to glucose-1-phosphate. The PYGM gene can contribute to providing energy to the body by disassembling the glycogen in muscle. Here, we analyzed the genomic structure and expression of the PYGM gene in the thoroughbred horse. The PYGM gene, containing several transposable elements (MIRs, LINEs, and MERs), was highly conserved in mammalian genomes. In order to understand the expression of the horse PYGM gene, we performed quantitative RT-PCR using 11 thoroughbred horse tissue samples. The horse PYGM gene ...
Liu C, Lei H, Ran X, Wang J.The Guizhou pony (GZP) is an indigenous species of equid found in the mountains of the Guizhou province in southwest China. We selected four regions of the equine leukocyte antigen (ELA), including , , and and used them to assess the diversity of the major histocompatibility complex (MHC) class II gene using direct sequencing technology. had the lowest / ratio (0.560) compared with the other three loci, indicating that was conserved and could be conserved after undergoing selective processes. Nine , five , nine and seven codons were under significant positive selection at the antigen b...
Li B, He X, Zhao Y, Bai D, Shiraigo W, Zhao Q, Manglai D.Studies on the molecular genetics of horse skin pigmentation have typically focused on very few genes and proteins. In this study, we used Illumina sequencing to determine the global gene expression profiles in horses with white-colored coats and those with black-colored coats, with the goal of identifying novel genes that could regulate horse coat color. Results: Genes encoding ribosomal-associated proteins were highly expressed in horse skin. We found a total of 231 unigenes that were differentially expressed between horses with white coats and horses with black coats; 119 were down-regulate...
Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Takahashi Y, Nagata SI.Thoroughbreds are some of the most famous racehorses worldwide and are currently animals of high economic value. To understand genomic variability in Thoroughbreds, we identified genome-wide insertions and deletions (INDELs) and obtained their allele frequencies in this study. INDELs were obtained from whole-genome sequencing data of 101 Thoroughbred racehorses by mapping sequence reads to the horse reference genome. By integrating individual data, 1,453,349 and 113,047 INDELs were identified in the autosomal (1-31) and X chromosomes, respectively, while 18 INDELs were identified on the mitoch...
Meghoufel A, Cloutier G, Crevier-Denoix N, de Guise JA.The hypothesis is that an imaging technique based on decompression and segmentation of B-scan images with morphological operators can provide a measurement of the integrity of equine tendons. Methods: Two complementary approaches were used: (i) Simulation of B-scan images to better understand the relationship between image properties and their underlying biological structural contents and (ii) extraction and quantification from B-scan images of tendon structures identified in step (i) to diagnose the status of the superficial digital flexor tendon (SDFT) by using the proposed imaging technique...
Gläser KE, Sun Q, Wells MT, Nixon AJ.No large scale equine microarray is available commercially to allow genomic and transcriptional profiling of the majority of genes that would define the genetic basis of equine disease. Objective: To generate a whole transcript target labelled GeneChip to interrogate the equine transcriptome and validate chip performance using RNA samples derived from organs, articular cells and normal cartilage. Methods: Equine mRNA and selected equine gene sequences derived from perfect cross-hybridisation of equine RNA on human microarray GeneChips, were used to design a custom equine gene microarray. Seque...
Ivanetich KM, Hsu PH, Wunderlich KM, Messenger E, Walkup WG, Scott TM, Lukasik J, Davis J.Criteria for sub-typing of microbial organisms by DNA sequencing proposed by Olive and Bean were applied to several genes in Escherichia coli to identify targets for the development of microbial source tracking assays. Based on the aforementioned criteria, the icd (isocitrate dehydrogenase), and putP (proline permease) genes were excluded as potential targets due to their high rates of horizontal gene transfer; the rrs (16S rRNA) gene was excluded as a target due to the presence of multiple gene copies, with different sequences in a single genome. Based on the above criteria, the mdh (malate d...
Hanson PD, Markel MD, Vanderby R.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...
Liu X, Zhang Y, Pu Y, Ma Y, Jiang L.Transposable elements (TEs) are diverse, abundant, and complicated in genomes. They not only can drive the genome evolution process but can also act as special resources for adaptation. However, little is known about the evolutionary processes that shaped horses. In this work, 126 horse assemblages involved in most horse breeds in China were used to investigate the patterns of TE variation for the first time. By using RepeatMasker and melt software, we found that the horse-specific short interspersed repetitive elements family, equine repetitive elements (ERE1), exhibited polymorphisms in hors...
Reeben M, Koho NM, Raekallio M, Hyyppä S, Pösö AR.Transport of lactate across membranes is facilitated by proton-monocarboxylate transporters (MCT). The most widely distributed isoform is MCT1, which needs an ancillary protein CD147. Studies on erythrocytes have shown that high activity of MCT1 is inherited as the dominant allele and that activity is regulated through CD147. Mutations of human MCT1 have been described that appear to impair lactate transport in muscles and cause exertional rhabdomyolysis. There are no reports of this potential relationship in the horse. Objective: To obtain sequences of equine MCT1 and CD147 to examine differe...
Bao W, Yu J, He Y, Liu M, Yang X.The intestinal flora has a variety of physiological functions involved in the regulation of host metabolism, immunity and endocrinology, and plays an important role in maintaining the health of the host. In this study, we used high-throughput sequencing technology to analyze the intestinal bacterial diversity and their gene functions in three equine species of the genus Shetland Pony (SP), Mongolian Wild Ass (MA), and Plain Zebra (PZ) in captivity in two wildlife parks in Inner Mongolia Autonomous Region, China. The results showed that only the SP intestinal bacterial abundance index (Chao1) w...
Premont A, Saadeh K, Edling C, Lewis R, Marr CM, Jeevaratnam K.Understanding cardiomyocyte ion channel expression is crucial to understanding normal cardiac electrophysiology and underlying mechanisms of cardiac pathologies particularly arrhythmias. Hitherto, equine cardiac ion channel expression has rarely been investigated. Therefore, we aim to predict equine cardiac ion channel gene expression. Raw RNAseq data from normal horses from 9 datasets was retrieved from ArrayExpress and European Nucleotide Archive and reanalysed. The normalised (FPKM) read counts for a gene in a mix of tissue were hypothesised to be the average of the expected expression in e...
Guo X, Aoyama M, Sugita S.Three optic nerves (L1, R2, R3) 12-18 mm behind the eyeball of the horse (Thoroughbred) were investigated quantitatively under light and electron microscopes. Thin sections at the thickness of 0.35 microm were cut, stained by toluidine blue and observed under the light microscope. The areas of the optic nerve and the axon bundles were 20.03 +/- 1.04 and 16.59 +/- 0.79 mm2 (mean +/- SD, n=3), respectively. The axon numbers for optic nerve L1, R2 and R3, estimated from light micrographs, were about 481 x 10(3), 543 x 10(3), and 494 x 10(3), respectively. Axons of optic nerve L1 were also counted...
Foury A, Mach N, Ruet A, Lansade L, Moisan MP.The improvement of horse welfare through housing conditions has become a real issue in recent years and have highlighted the detrimental effect of individual housing of horses on their health and behaviour. In this new study, we analysed the blood transcriptome of 45 sport horses housed individually that were previously examined for their behaviour and gut microbiota. We performed differential and regression analyses of gene expression, followed by downstream bioinformatic analyses, to unveil the molecular pathways related to the behavioural changes associated with welfare impairment in these ...
Mei M, Chen R, Gao X, Cao Y, Weng W, Duan Y, Tan X, Liu Z.Meat fraud and adulteration incidents occur frequently in almost all regions of the globe, especially with the increase in the world's population. To ensure the authenticity of meat products, we developed a 10-plex xMAP assay to simultaneously detect ten animal materials: bovine, caprine, poultry, swine, donkey, deer, horse, dog, fox and mink. Results: This method was investigated by analyzing DNA extracts from raw muscle, muscle mixtures, meat products and animal feeds. Our results indicated that the species of interest can be identified, differentiated and detected down to 1 g kg in bina...
Leiberich M, Marais HJ, Naidoo V.The plight of the white rhinoceros () and the increasing need of treatment options for injured poaching victims led to the necessity to expand the knowledge on applicable drugs in this endangered species. With very little information available on drug pharmacokinetics in rhino, veterinarians have to rely on information generated from other species. The horse being a closely related species, has served as the model for dose extrapolations. However, from recent research on enrofloxacin and carprofen, the white rhino showed considerable differences in the pharmacokinetic properties of these drugs...
Pimentel F, McManus C, Soares K, Caetano AR, de Faria DA, Paiva SR, Ianella P.Optimization of DNA collection for National gene bank and conservation programs requires information on spatial and genetic distribution of animals countrywide. The relationship between genetic and geographic distances were examined in 8 Brazilian horse breeds (Baixadeiro, Crioulo, Campeiro, Lavradeiro, Marajoara, Mangalarga Marchador, Pantaneiro and Puruca) using Single Nucleotide Polymorphism markers and collection point locations. Mantel correlations, Genetic Landscape Shape Interpolation, Allelic Aggregation Index Analyses and Spatial autocorrelation tests indicated a nonrandom distributio...
