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.
Xu S, Luosang J, Hua S, He J, Ciren A, Wang W, Tong X, Liang Y, Wang J, Zheng X.To investigate genetic mechanisms of high altitude adaptations of animals living in the Tibetan Plateau, three mitochondrial genomes (mt-genome) of Tibetan horses living in Naqu (4,500 m) of Tibetan, Zhongdian (3,300 m) and Deqin (3,100 m) of Yunnan province were sequenced. The structures and lengths of these three mt-genomes are similar to the Cheju horse, which is related to Tibetan horses, but little shorter than the Swedish horse. The pair-wise identity of these three horses on nucleotide level is more than 99.3%. When the gene encoding the mitochondrial protein of Tibetan horses was analy...
Casini A, Mastrobuoni G, Terenghi M, Gabbiani C, Monzani E, Moneti G, Casella L, Messori L.The interactions with protein targets of the ruthenium(III) complex imidazolium trans-[tetrachloro(dimethyl sulfoxide)(imidazole)ruthenate(III)], NAMI-A, an effective anticancer and antimetastatic agent now in clinical trials, deserve great attention as they are believed to be at the basis of the mechanism of action of this innovative molecule. Here, we report on the reactions of NAMI-A with two well-known model proteins, namely, hen egg white lysozyme and horse heart cytochrome c; these reactions were investigated by a variety of physicochemical methods, including optical spectroscopy, (1)H N...
Bruhn O, Regenhard P, Michalek M, Paul S, Gelhaus C, Jung S, Thaller G, Podschun R, Leippe M, Grötzinger J, Kalm E.Defensins are a predominant class of antimicrobial peptides, which act as endogenous antibiotics. Defensins are classified into three distinct sub-families: theta-, beta-, and alpha-defensins. Synthesis of alpha-defensin has been confirmed only in primates and glires to date and is presumably unique for a few tissues, including neutrophils and Paneth cells of the small intestine. Antimicrobial activities of these peptides were shown against a wide variety of microbes including bacteria, fungi, viruses and protozoan parasites. In the present study, we report the characterization of the equine a...
Slota E, Wnuk M, Bugno M, Pienkowska-Schelling A, Schelling C, Bratus A, Kotylak Z.Cytogenetic investigations of the nucleolar-organizing regions (NORs) show that there is variation in the transcriptional activity of rDNA in many organisms. As a consequence, genetic polymorphism of these regions has been detected. The aim of the present study was to evaluate the hypothetic genetic mechanisms determining the NORs polymorphism of the domestic horse chromosomes. Molecular cytogenetic analyses were carried out on Hucul horses and the following techniques were used: fluorescence in situ hybridization (FISH), telomere primed in situ synthesis (PRINS), in situ nick-translation with...
Coleman SJ, Gong G, Gaile DP, Chowdhary BP, Bailey E, Liu L, MacLeod JN.Loci for 9322 equine expressed sequence tags (ESTs) were predicted using the Comparative Mapping by Annotation and Sequence Similarity (Compass) strategy in order to evaluate the programme's ability to make accurate locus predictions in species with comparative gene maps. Using human genome sequence information from Build 35 (May 2004) and published marker information from the radiation hybrid (RH) maps for equine chromosomes (ECA) 17 and X, 162 ESTs were predicted to locations on ECA17 and 328 ESTs to locations on ECAX by selection of the 'top blast hit'. The locations of 30 ESTs were assesse...
Castagnasso EE, Kienast ME, García PP, Giovambattista G.Recently, the use of DNA markers has provided a more accurate method of identifying individuals and verifying parentage. In this report, we describe foal assignment in a farm bred jumping horses (Silla argentino). Ten mares were freely served by two stallions, resulting in nine foals. Weaning occurred without registration of the mare of each offspring, resulting in a failure to identify either the mare or the sire of each foal. Animals were typed using 12 microsatellite systems and four biochemical polymorphisms in order to determine the paternity/maternity of each foal. We used the CERVUS pro...
Morozova-Roche LA.Calcium-binding equine lysozyme (EL) combines the structural and folding properties of c-type lysozymes and alpha-lactalbumins, connecting these two most studied subfamilies. The structural insight into its native and partially folded states is particularly illuminating in revealing the general principles of protein folding, amyloid formation and its inhibition. Among lysozymes EL forms one of the most stable molten globules and shows the most uncooperative refolding kinetics. Its partially-folded states serve as precursors for calcium-dependent self-assembly into ring-shaped and linear amyloi...
Stock KF, Distl O, Hoeschele I.Requirements for successful implementation of multivariate animal threshold models including phenotypic and genotypic information are not known yet. Here simulated horse data were used to investigate the properties of multivariate estimators of genetic parameters for categorical, continuous and molecular genetic data in the context of important radiological health traits using mixed linear-threshold animal models via Gibbs sampling. The simulated pedigree comprised 7 generations and 40000 animals per generation. Additive genetic values, residuals and fixed effects for one continuous trait and ...
Kang J, Lee MS, Watowich SJ, Gorenstein DG.A phosphorothioate RNA aptamer (thioaptamer) targeting the capsid protein of Venezuelan equine encephalitis virus (VEEV) was isolated by in vitro combinatorial selection. The selected thioaptamer had a strong binding affinity (approximately 7nM) and high specificity for the target protein. For the binding to the protein, the overall tertiary structure of the thioaptamer is required. We introduce two theoretical methods to examine the effect of phosphorothioate modification on the enhancement of binding affinity and one experimental method to examine the nature of the multiple bands of thioapta...
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...
Mucher E, Jayr L, Rossignol F, Amiot F, Gidrol X, Barrey E.Progress could be achieved by using microarrays to understand metabolic adaptations and disorders in equine muscle in response to exercise. Objective: To test the feasibility of using mouse cDNA microarrays to analyse gene expression profile in normal equine muscles. Methods: Muscular biopsies of dorsal gluteus medius and longissimus lumborum were done in 4 healthy Standardbreds. Total RNA was extracted from the muscle samples. The concentration and quality of RNA were measured before and after amplification. Gene expression profiles were measured using mouse cDNA microarrays including 15,264 ...
Miclo L, Girardet JM, Egito AS, Mollé D, Martin P, Gaillard JL.Highly phosphorylated casein with a low molecular mass was isolated from Haflinger mare's milk by RP-HPLC. It accounts for 4.0% of the casein content. Its mass was determined by LC-ESI-MS before and after treatment by alkaline phosphatase. The molecular mass found for the apo-form (10,591 +/- 2 Da) is in agreement with its primary structure, which was established by ESI-MS/MS from tryptic peptides. It appeared that this short protein (94 amino acid residues) is an internally truncated form of the full-length equine beta-casein (226 residues). This low-Mr variant of equine beta-casein displays ...
Green RD, Qureshi MA, Long JA, Burfening PJ, Hamernik DL.Agricultural animal research has been immensely successful over the past century in developing technology and methodologies that have dramatically enhanced production efficiency of the beef, dairy, swine, poultry, sheep, and aquaculture industries. In the past two decades, molecular biology has changed the face of agricultural animal research, primarily in the arena of genomics and the relatively new offshoot areas of functional genomics, proteomics, transcriptomics, metabolomics and metagenomics. Publication of genetic and physical genome maps in the past 15 years has given rise to the possib...
Nakagawa K, Yamada Y, Fujiwara K, Ikeguchi M.Equine beta-lactoglobulin forms a compact intermediate at an acidic pH (A state). It also forms an expanded and helical conformation at low temperatures (C state). The structure of a single disulfide mutant C66A/C160A is similar to the A state in the presence of salts, while it is similar to the C state at low anion concentrations. We have investigated the temperature-dependent change in the secondary structure using circular dichroism and proline scanning mutagenesis. At low anion concentrations, the helical content increased linearly as temperature decreased. In the presence of salts, the A ...
Schneeweiss W, Stanek C, Wagner M, Hein I.The potential of five different commercial DNA isolation methods to remove real-time PCR inhibitors from the synovial fluid of horses, cattle and pigs was investigated. All kits with the exception of one included a silica column-based purification of the DNA. With the fifth kit, DNA purification is achieved by removing contaminating macromolecules by a desalting process. We used a recently developed method based on comparison of the real-time PCR signal of an artificial target incorporated into each PCR reaction in the presence of the isolated DNA from the sample, and in control samples contai...
Nakagawa K, Tokushima A, Fujiwara K, Ikeguchi M.The secondary structure in the molten globule state (an equilibrium analogue of a burst-phase folding intermediate) of equine beta-lactoglobulin was investigated by changes in the circular dichroic spectrum induced by a series of site-directed proline substitutions. The results challenge the structural picture obtained from previous hydrogen/deuterium exchange experiments. A stable non-native alpha-helix was found to exist in the region corresponding to the eighth strand (H strand) in the native structure, where the backbone amide protons are the most strongly protected from exchange. Therefor...
Kuehn R, Kaczensky P, Lkhagvasuren D, Pietsch S, Walzer C.Recent studies suggest that Asiatic wild asses (Equus hemionus) are being increasingly poached in a commercial fashion. Part of the meat is believed to reach the meat markets in the capital Ulaanbaatar. To test this hypothesis, we collected 500 meat samples between February and May 2006. To differentiate between domestic horse (Equus caballus) and wild ass meat, we developed a restriction fragment length polymorphism (RFLP) assay based on the polymerase chain reaction (PCR). We amplified and sequenced a cytochrome b fragment (335 bp) and carried out a multialignment of the generated sequences ...
Cappelli K, Verini-Supplizi A, Capomaccio S, Silvestrelli M.The knowledge of molecular mechanisms of stress response in athlete horses can allow us to plan an appropriate and high-grade training to obtain better performance and to preserve horse welfare. It is well known that excessive muscular exercise can lead to a number of responses which may be associated with modification of the mRNA levels for a number of metabolic genes such as those involved in the immune response. In the present study cDNA-AFLP technique was applied to Arab endurance horses under stressing conditions to visualise variations of transcriptional profiles; 49 transcript derived f...
de Val N, Herschbach H, Potier N, Dorsselaer AV, Crichton RR.An essential difference between eukaryotic ferritins and bacterioferritins is that the latter contain naturally, in vivo haem as Fe-protoporphyrin IX. This haem is located in a hydrophobic pocket along the 2-fold symmetry axes and is liganded by two Met 52. However, in in vivo studies, a cofactor has been isolated in horse spleen apoferritin similar to protoporphyrin IX; in in vitro experiments, it has been shown that horse spleen apoferritin is able to interact with haem. Studies of haemin (Fe(III)-PPIX) incorporation into horse spleen apoferritin have been carried out, which show that the me...
Brunberg E, Andersson L, Cothran G, Sandberg K, Mikko S, Lindgren G.The Silver coat color, also called Silver dapple, in the horse is characterized by dilution of the black pigment in the hair. This phenotype shows an autosomal dominant inheritance. The effect of the mutation is most visible in the long hairs of the mane and tail, which are diluted to a mixture of white and gray hairs. Herein we describe the identification of the responsible gene and a missense mutation associated with the Silver phenotype. Results: Segregation data on the Silver locus (Z) were obtained within one half-sib family that consisted of a heterozygous Silver colored stallion with 34...
Levy R, Forsyth CM, LaPorte SL, Geren IN, Smith LA, Marks JD.Botulinum neurotoxin (BoNT), the most poisonous substance known, causes naturally occurring human disease (botulism) and is one of the top six biothreat agents. Botulism is treated with polyclonal antibodies produced in horses that are associated with a high incidence of systemic reactions. Human monoclonal antibodies (mAbs) are under development as a safer therapy. Identifying neutralizing epitopes on BoNTs is an important step in generating neutralizing mAbs, and has implications for vaccine development. Here, we show that the three domains of BoNT serotype A (BoNT/A) can be displayed on the...
McGahern A, Bower MA, Edwards CJ, Brophy PO, Sulimova G, Zakharov I, Vizuete-Forster M, Levine M, Li S, MacHugh DE, Hill EW.Equine mitochondrial DNA (mtDNA) phylogeny reconstruction reveals a complex pattern of variation unlike that seen in other large domesticates. It is likely that this pattern reflects a process of multiple and repeated, although not necessarily independent, domestication events. Until now, no clear geographic affiliation of clades has been apparent. In this study, amova analyses have revealed a significant non-random distribution of the diversity among equine populations when seven newly sequenced Eurasian populations were examined in the context of previously published sequences. The associati...
Weston MC, Cunningham FM, Collins ME.CCL11 (also known as eotaxin) is a very potent and selective mediator of eosinophil migration which exerts its effects through its receptor, CCR3. In this study we report the cloning of an equine CCR3 cDNA sequence and investigation of the localization of CCR3 mRNA expression in horse tissues. Equine CCR3 displayed high levels of sequence identity with CCR3 sequences in other species. RT-PCR analysis revealed the expression of CCR3 in colon, lung and spleen of normal horses. In situ hybridisation experiments indicated that expression of CCR3 mRNA in colon was predominantly in eosinophils and t...
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...
Marletta D, Tupac-Yupanqui I, Bordonaro S, García D, Guastella AM, Criscione A, Cañón J, Dunner S.The distribution of genetic diversity and the genetic relationships among western Mediterranean horse breeds were investigated using microsatellite markers. The examined sample included seven Spanish and three Italian local horse breeds and populations, plus a Spanish Thoroughbred outgroup. The total number of animals examined was 682 (on average 62 animals per breed; range 20-122). The microsatellite marker set analysed provided 128 alleles (10.7 alleles per locus). Within-breed genetic diversity was always high (>0.70), with breeds contributing about 8% of the total genetic variability. T...
Russo AT, White MA, Watowich SJ.Alphavirus replication and propagation is dependent on the protease activity of the viral nsP2 protein, which cleaves the nsP1234 polyprotein replication complex into functional components. Thus, nsP2 is an attractive target for drug discovery efforts to combat highly pathogenic alphaviruses. Unfortunately, antiviral development has been hampered by a lack of structural information for the nsP2 protease. Here, we report the crystal structure of the nsP2 protease (nsP2pro) from Venezuelan equine encephalitis alphavirus determined at 2.45 A resolution. The protease structure consists of two dist...
Li JL, Shi YF, Bu RQ, Mang L.Restriction endonucleases, namely BamH I, Taq I, Hae III, Rsa I and Hinc II, were used to analyze the polymorphism of partial mtDNA Cytb gene sequences from 256 horses 6 types (Thoroughbred, Sanhe, Wuzhumuqin, Xinihe, Wushen and Pony) including the imported breed, cultivated breed and local breed. The products of endonuclease digestion were run on 8% non-denaturing polyacrylamide gel electrophoresis and detected by silver staining. Results indicated BamH I and Taq I polymorphism. In all 7 restriction patterns were defected that could be sorted into 3 haplotypes, of which haplotypes I and III w...
Tiwari M, Sodhi M, Verma P, Vivek P, Kataria RS, Niranjan SK, Bharti VK, Masharing N, Gujar G, Chanda D, Mukesh M.The identification of appropriate references genes is an integral component of any gene expression-based study for getting accuracy and reliability in data interpretation. In this study, we evaluated the expression stability of 10 candidate reference genes (GAPDH, RPL4, EEF1A1, RPS9, HPRT1, UXT, RPS23, B2M, RPS15, ACTB) in peripheral blood mononuclear cells of livestock species that are adapted to high altitude hypoxia conditions of Leh-Ladakh. A total of 37 PBMCs samples from six native livestock species of Leh-Ladakh region such as Ladakhi cattle, Ladakhi yak, Ladakhi donkey, Chanthangi goat...
Bronstein A, Marx A.Comparison of myoglobin structures reveals that protein isolated from horse heart consistently adopts an alternate turn conformation in comparison to its homologues. Analysis of hundreds of high-resolution structures discounts crystallization conditions or the surrounding amino acid protein environment as explaining this difference, that is also not captured by the AlphaFold prediction. Rather, a water molecule is identified as stabilizing the conformation in the horse heart structure, which immediately reverts to the whale conformation in molecular dynamics simulations excluding that structur...
Głażewska I, Prusak B, Gralak B.The goal of this study was to demonstrate the usefulness of pedigree data in studies of mitochondrial DNA diversity in dogs and horses. Pedigree information allows for precisely choosing animals with distinct haplotypes for analysis, makes it possible to find rare haplotypes present exclusively in single individuals and helps to evaluate haplotype frequencies at the present and in the past. Estimating founder contributions to gene pools enables evaluating the parts of gene pools observed with the help of mtDNA analysis. An important aspect is also the financial benefits: using pedigree data, r...
Kun TJ, Wictum EJ, Penedo MCT.Degraded biological samples are a challenge for testing laboratories. Genotyping success can be improved through the use of mini-STRs, by which primers are placed adjacent to the repeat motifs to reduce amplicon size. Here, we present a genetic profiling system comprising 13 autosomal and one X-linked dinucleotide-repeat markers and the SRY gene based on the internationally accepted equine parentage panel. The markers are divided into two panels with all alleles falling at or below 182 bp. The application of this method significantly increases the ability to profile difficult samples and to p...
Vidal MA, Lopez MJ.Equine adipose tissue-derived mesenchymal stem cells (ASCs) have only recently been investigated for their adipogenic, chondrogenic, and osteogenic differentiation potential. This chapter will briefly outline the molecular mechanisms leading to adipogenesis and the methods of equine adipose tissue harvest, ASC isolation, and adipogenic differentiation. The reader is also directed to other reported methods of adipogenesis for ASCs and mesenchymal stem cells (MSCs) from other tissues.
Broad TE, Forrest JW, Lewis PE, Pearce PD, Phua SH, Pugh PA, Stewart-Scott IA.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.
Farley DC, Bannister R, Leroux-Carlucci MA, Evans NE, Miskin JE, Mitrophanous KA.The release of lentiviral vectors for clinical use requires the testing of vector material, production cells, and, if applicable, ex vivo-transduced cells for the presence of replication-competent lentivirus (RCL). Vectors derived from the nonprimate lentivirus equine infectious anemia virus (EIAV) have been directly administered to patients in several clinical trials, with no toxicity observed to date. Because EIAV does not replicate in human cells, and because putative RCLs derived from vector components within human vector production cells would most likely be human cell-tropic, we previous...
Stewart F, Thomson JA, Leigh SE, Warwick JM.Several cDNA clones corresponding to mRNA for the alpha-subunit of the horse (Equus caballus) pituitary and placental (chorionic) gonadotrophic hormones have been isolated and sequenced. Polyadenylated mRNA was purified from horse pituitary glands (the source of FSH and LH) and horse placental tissues (the source of chorionic gonadotrophin; CG). The mRNA preparations were characterized by in-vitro translation and Northern hybridization techniques using human and ovine gonadotrophin cDNA clones as probes. Complementary DNA libraries were created from the pituitary and placental mRNAs and a huma...
Druzhkova AS, Makunin AI, Vorobieva NV, Vasiliev SK, Ovodov ND, Shunkov MV, Trifonov VA, Graphodatsky AS. is an extinct subgenus of first characterized and delineated in 2010. The almost complete mitochondrial genome is available only for a single specimen of - a 40,000 years old from Proskuryakova cave (Khakassia, Russia). Our studies of ancient horses from Denisova cave (Altai, Russia) revealed mitochondrial DNA of this species in a 32,000 years old sample. Using alignments to multiple mitochondrial genomes of non-caballine equids, we recovered 100% complete mitochondrial genome of for the first time. Phylogenetic analysis demonstrates close relationship between this individual and the one ...
Te Moller NCR, Pitkänen M, Sarin JK, Väänänen S, Liukkonen J, Afara IO, Puhakka PH, Brommer H, Niemelä T, Tulamo RM, Argüelles Capilla D....Arthroscopic optical coherence tomography (OCT) is a promising tool for the detailed evaluation of articular cartilage injuries. However, OCT-based articular cartilage scoring still relies on the operator's visual estimation. Objective: To test the hypothesis that semi-automated International Cartilage Repair Society (ICRS) scoring of chondral lesions seen in OCT images could enhance intra- and interobserver agreement of scoring and its accuracy. Methods: Validation study using equine cadaver tissue. Methods: Osteochondral samples (n = 99) were prepared from 18 equine metacarpophalangeal joint...
Data in briefJune 20, 2020
Volume 31 105887 doi: 10.1016/j.dib.2020.105887
Martín-Cano FE, Gaitskell-Phillips G, Ortiz-Rodríguez JM, Silva A, Gil C, Ortega-Ferrusola C, Peña FJ.This paper provides the dataset of proteins of stallion ejaculates before and after cryopreservation. The data report the analysis and identification of stallion sperm proteins obtained from the same ejaculates and split in two subsamples. The first aliquot consisted on fresh spermatozoa and the second aliquot was frozen and thawed spermatozoa. Samples were analyzed using a UHPLC/MS/MS system consisting of an Agilent 1290 infinity series UHPLC coupled to an Agilent 6550 Q-TOF mass spectrometer (Agilent Technologies, Santa Clara, CA, USA). We provide a data set of 2226 different proteins, with ...
Menzeleev RF, Smirnova GP, Chekareva NV, Zvonkova EN, Krasnopol'skiĭ IuM, Shvets VI.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.
Klingberg J, Cawley A, Shimmon R, Fu S.The constant evolution of the illicit drug market makes the identification of unknown compounds problematic. Obtaining certified reference materials for a broad array of new analogues can be difficult and cost prohibitive. Machine learning provides a promising avenue to putatively identify a compound before confirmation against a standard. In this study, machine learning approaches were used to develop class prediction and retention time prediction models. The developed class prediction model used a naïve Bayes architecture to classify opioids as belonging to either the fentanyl analogues, AH...
Park Y, Pariza MW.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.
Sheikh A.The Arabian horse breed is well known for its purity and played a key role in the genetic improvement of other horses worldwide. The mitochondrial genome plays a vital role in maternal inheritance and it's helpful to evaluate its genetic diversity and conservation. It has higher mutation rates than nuclear DNA in vertebrates and therefore reveals phylogenetic relationships and haplotypes. In this study, the mitochondrial genome mutations in two Saudi horse strains, Kehilan and Hamdani demonstrated various changes in the gene and amino acid levels and included two other Saudi horses (Hadban and...
Du Cheyne C, Chen Y, De Craene J, Thas O, De Spiegelaere W.Accurate tools to measure RNA integrity are essential to obtain reliable gene expression data. The reverse transcription quantitative PCR (RT-qPCR) based 3':5' assay permits a direct determination of messenger RNA (mRNA) integrity. However, the use of standard curves and the possible effect of PCR inhibitors make this method cumbersome and prone to variation, especially in small samples. Here we developed a triplex digital PCR (dPCR) 3':5' assay for assessing RNA integrity in equine samples as rapid and simple alternative to RT-qPCR. This dPCR assay not only provides a straight forward analysi...
Maniego J, Giles O, Hincks P, Stewart G, Proudman C, Ryder E.We present here the use of targeted, long-read sequencing of the myostatin (MSTN) gene as a model to detect potential gene editing events in Thoroughbred horses. MSTN is a negative regulator of muscle development, making the gene a prime candidate target for gene doping. By sequencing the complete gene in one PCR product, we can catalogue all mutations without the need to produce short-fragment libraries. A panel of reference material fragments with defined mutations was constructed and successfully sequenced by both Oxford Nanopore and Illumina-based methods, showing that gene doping editing ...
Ascacio-Martínez JA, Barrera-Saldaña HA.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.
Díaz S, Echeverría MG, It V, Posik DM, Rogberg-Muñoz A, Pena NL, Peral-García P, Vega-Pla JL, Giovambattista G.The polymorphism of equine lymphocyte antigen (ELA) class II DRA gene had been detected by polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP) and reference strand-mediated conformation analysis. These methodologies allowed to identify 11 ELA-DRA exon 2 sequences, three of which are widely distributed among domestic horse breeds. Herein, we describe the development of a pyrosequencing-based method applicable to ELA-DRA typing, by screening samples from eight different horse breeds previously typed by PCR-SSCP. This sequence-based method would be useful in high-throug...
Giudicelli J, Boudouard M, Delqué P, Vannier C, Sudaka P.Neutral alpha-D-glucosidase (alpha-D-glucoside glucohydrolase, EC 3.2.1.20) from horse kidney brush-border membranes was solubilized using Emulphogene BC 720 and purified by an affinity chromatography technique. The enzyme preparation (390-fold purified), which was free of other known microvillus hydrolases, exhibited one precipitate line in crossed immunoelectrophoresis and migrated as a single band on sodium dodecyl sulfate polyacrylamide gel electrophoresis. Several criteria (charge-shift crossed immunoelectrophoresis and hydrophobic chromatography) revealed the purified detergent form of t...
Kriegshäuser G, Wutz G, Lea S, Stuart D, Skern T, Kuechler E.Mouse monoclonal antibodies (mAbs) were employed to select neutralization escape mutants of equine rhinitis A virus (ERAV). Amino acid changes in the ERAV mutants resulting in resistance to neutralization were identified in capsid protein VP1 at Lys-114, Pro-240 and Thr-241. Although the changes were located in different parts of the polypeptide chain, these mutants exhibited cross-resistance against all four mAbs employed, indicating that these residues contribute to a single immunogenic site. To explain this result, we constructed a model of the three-dimensional structure of the ERAV capsid...
Shorten PR, Legacki EL, Chavatte-Palmer P, Conley AJ.Hormone secretion by the maternal ovaries, trophoblast/placenta and fetus occurs sequentially, creating distinct steroid metabolomic 'signatures' in systemic blood of pregnant mares that vary with gestational stage. Algorithms were developed to predict the gestational day (GD) from the maternal steroid metabolome (nine steroids; pregnenolone (P5), progesterone (P4), 5α-dihydroprogesterone (DHP), 17α-hydroxyprogesterone, allopregnanolone, 20α-hydroxy-DHP, 3β,20α-dihydroxy-DHP, DHEA and androstenedione) determined by liquid chromatography-tandem mass spectrometry (LC-MS/MS) of eight thoroug...
Hisey EA, Martins BC, Donnelly CG, Cassano JM, Katzman SA, Murphy CJ, Thomasy SM, Leonard BC.This study aimed to define the antimicrobial peptide (AMP) expression pattern of the equine ocular surface and amniotic membrane using a targeted qPCR approach and 3'Tag-sequencing. It will serve as a reference for future studies of ocular surface innate immunity and amniotic membrane therapies. Methods: A targeted qPCR approach was used to investigate the presence of orthologs for three of the most highly expressed beta-defensins (DEFB1, DEFB4B, and DEFB103A) of the human ocular surface and amniotic membrane in equine corneal epithelium, conjunctiva, and amniotic membrane. 3'Tag-sequencing wa...
Yokomori T, Ohnuma A, Tozaki T, Segawa T, Itou T.Considering the personality traits of racehorses (e.g., flightiness, anxiety, and affability) is considered essential to improve training efficiency and decrease accident frequency, especially when retraining for a second career that may involve contact with inexperienced personnel after retiring from racing. Studies on human personality-related genes are frequently conducted; however, such studies are rare in horses because a consistent methodology for personality evaluation is lacking. Using the recently published whole genome variant database of 101 Thoroughbred horses, we compared horse ge...
Caetano AR, Lyons LA, Laughlin TF, O'Brien SJ, Murray JD, Bowling AT.Comparative anchor tagged sequences (CATS) from human Chromosome 5 (HSA5) were used as PCR primers to produce molecular markers for synteny mapping in the horse. Primer sets for 21 genes yielded eight horse-specific markers, which were mapped with the UC Davis horse-mouse somatic cell hybrid panel into two synteny groups: UCD14 and UCD21. These data, in conjunction with earlier human chromosome painting studies of the horse karyotype and synteny mapping of horse microsatellite markers physically mapped by FISH, confirm the assignment of UCD21 to ECA21 and suggest that UCD14 is located on ECA14...
Stock KF, Distl O, Hoeschele I.Requirements for successful implementation of multivariate animal threshold models including phenotypic and genotypic information are not known yet. Here simulated horse data were used to investigate the properties of multivariate estimators of genetic parameters for categorical, continuous and molecular genetic data in the context of important radiological health traits using mixed linear-threshold animal models via Gibbs sampling. The simulated pedigree comprised 7 generations and 40000 animals per generation. Additive genetic values, residuals and fixed effects for one continuous trait and ...
Machmoum M, Badaoui B, Petit D, Germot A, El Alaoui MA, Boujenane I, Piro M.Genetic diversity and phylogenetic relationships within the Arabian show horse populations are of particular interest to breeders worldwide. Using the complete mitochondrial DNA D-loop sequence (916 pb), this study aimed (i) to understand the genetic relationship between three populations, the Desert-Bred (DB), a subset of the Kingdom of Saudi Arabia (KSA), United Arab Emirates (UAE) and Bahrain (BAH), the Straight Egyptian (EG) and the Polish bloodline (PL), and (ii) to assess the accuracy of the traditional strain classification system based on maternal lines, as stated by the Bedouin cultur...
