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.
Pawlina-Tyszko K, Semik-Gurgul E, Ząbek T, Witkowski M.Horses are of great importance in recreation, livestock production, as working animals in poorly developed countries, and for equine-assisted therapy. Equine sarcoids belong to the most commonly diagnosed tumors in this species. They may cause discomfort, pain, and can lead to the permanent impairment of motor function. The molecular bases of their formation are still under investigation. Our previous studies revealed altered microRNA (miRNA) expression and DNA methylation levels in sarcoid tumors. Abnormal patterns of methylation may be responsible for changes in gene expression levels, inclu...
Murase H, El-Sheikh Ali H, Ruby RE, Scoggin KE, Ball BA.Equine premature placental separation (PPS) is poorly understood and represents an important risk factor for fetal/neonatal hypoxia. Objective: To examine transcriptomic changes in the chorioallantois (CA) from mares with clinical PPS compared with the CA from normal foaling mares. Differential gene expression was determined and gene ontology as well as molecular pathways related to PPS were characterised. Methods: Retrospective case: control study. Methods: CA were collected from Thoroughbred mares with a clinical history of PPS (n = 33) and from control Thoroughbred mares (n = 4) with no...
Fedorka CE, El-Sheikh Ali H, Scoggin KE, Loux SC, Ball BA, Troedsson MHT.Ascending placentitis is the leading cause of abortion in the horse. The pleiotropic cytokine tumor necrosis factor (TNF) is an upstream regulator of this disease, but little is understood regarding its function in pregnancy maintenance or placental infection. To assess this, RNA sequencing was performed on chorioallantois and endometrium of healthy pregnant mares at various gestational lengths (n = 4/gestational age), in addition to postpartum chorioallantois, and diestrus endometrium to assess expression of TNF, TNFR-1, and TNFR-2. Additionally, ascending placentitis was induced via trans-...
Gurgul A, Szmatoła T, Ocłoń E, Jasielczuk I, Semik-Gurgul E, Finno CJ, Petersen JL, Bellone R, Hales EN, Ząbek T, Arent Z, Kotula-Balak M....In recent years, a vast amount of sequencing data has been generated and large improvements have been made to reference genome sequences. Despite these advances, significant portions of reads still do not map to reference genomes and these reads have been considered as junk or artificial sequences. Recent studies have shown that these reads can be useful, e.g., for refining reference genomes or detecting contaminating microorganisms present in the analyzed biological samples. A special case of this is RNA sequencing (RNA-Seq) reads that come from tissue transcriptomes. Unmapped reads from RNA-...
Marzahl C, Hill J, Stayt J, Bienzle D, Welker L, Wilm F, Voigt J, Aubreville M, Maier A, Klopfleisch R, Breininger K, Bertram CA.Pulmonary hemorrhage (P-Hem) occurs among multiple species and can have various causes. Cytology of bronchoalveolar lavage fluid (BALF) using a 5-tier scoring system of alveolar macrophages based on their hemosiderin content is considered the most sensitive diagnostic method. We introduce a novel, fully annotated multi-species P-Hem dataset, which consists of 74 cytology whole slide images (WSIs) with equine, feline and human samples. To create this high-quality and high-quantity dataset, we developed an annotation pipeline combining human expertise with deep learning and data visualisation te...
Brangsch H, Saqib M, Sial AUR, Melzer F, Linde J, Elschner MC.Burkholderia (B.) mallei is a host-adapted equine pathogen that causes glanders, a re-emerging zoonotic disease, which is endemic in Pakistan and other developing countries and seriously impacts the global equine movement. Due to globalization, the geographical restriction of diseases vanishes and the lack of awareness of and experience with eradicated diseases in industrialized countries also promotes the re-introduction of infections in these regions. Owing to the high equine population, the Pakistani province Punjab is a potential hotspot where several glanders outbreaks have been seen over...
Carlos-Pinedo S, Wang Z.Long-term sustainable biogas production requires different raw material alternatives, especially when reducing the most desirable organic substrate, food waste, which has been set as a goal in the 2030 Agenda. In Sweden, horse manure (HM) is generated in large quantities, and due to its physical and chemical characteristics, it has the potential to be used as a raw material to produce biogas through anaerobic digestion (AD). In order to investigate the challenges that HM digestion can impose in terms of methane yield and/or digestate quality, the modified ORganic WAste REsearch (ORWARE) AD mod...
Dube F, Hinas A, Roy S, Martin F, Åbrink M, Svärd S, Tydén E.The nematode Parascaris univalens is one of the most prevalent parasitic pathogens infecting horses but anthelmintic resistance undermines treatment approaches. The molecular mechanisms underlying drug activity and resistance remain poorly understood in this parasite since experimental in vitro models are lacking. The aim of this study was to evaluate the use of Caenorhabditis elegans as a model for P. univalens drug metabolism/resistance studies by a comparative gene expression approach after in vitro exposure to the anthelmintic drug ivermectin (IVM). Methods: Twelve adult P. univalens worms...
Plummer CE, Polk T, Sharma J, Bae SS, Barr O, Jones A, Kitchen H, Wilhelmy M, Devin K, Clay Smith W, Kolaczkowski BD, Larkin J.Equine recurrent uveitis (ERU) is a painful and debilitating autoimmune disease and represents the only spontaneous model of human recurrent uveitis (RU). Despite the efficacy of existing treatments, RU remains a leading cause of visual handicap in horses and humans. Cytokines, which utilize Janus kinase 2 (Jak2) for signaling, drive the inflammatory processes in ERU that promote blindness. Notably, suppressor of cytokine signaling 1 (SOCS1), which naturally limits the activation of Jak2 through binding interactions, is often deficient in autoimmune disease patients. Significantly, we previous...
Suchan T, Chauvey L, Poullet M, Tonasso-Calvière L, Schiavinato S, Clavel P, Clavel B, Lepetz S, Seguin-Orlando A, Orlando L.Ancient DNA preservation in subfossil specimens provides a unique opportunity to retrieve genetic information from the past. As ancient DNA extracts are generally dominated by molecules originating from environmental microbes, capture techniques are often used to economically retrieve orthologous sequence data at the population scale. Post-mortem DNA damage, especially the deamination of cytosine residues into uracils, also considerably inflates sequence error rates unless ancient DNA extracts are treated with the USER enzymatic mix prior to library construction. While both approaches have rec...
Deng L, Yang Y, Li Z, Li J, Zhu Y, Meng Q, Liu J, Wang X.Despite mare's milk being highly nutritious and beneficial to human health, the effects of different dietary regimens on the lipid profile of mare's milk remain to be completely understood. Herein we employed targeted multiple reaction monitoring-based lipidomics with ultra-high performance liquid chromatography-quadrupole time-of-flight-mass spectrometry to compare the milk lipid profiles of mares fed: pasture grass (P), corn stover and concentrate (H), or cornsilage and concentrate (S). Overall, 461 lipids belonging to 17 subclasses were identified; 261 significantly different lipids were id...
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-...
Deng L, Li Z, Tang C, Han Y, Zhang L, Liao Q.Equine pregnancy is currently diagnosed by rectal palpation, ultrasonographic examination, or by measuring changes in hormones in the blood. In the present study, we identified proteins that are differentially expressed in the sera of early pregnant and non-pregnant mares in order to develop a novel method for diagnosing equine pregnancy. Serum samples were obtained from 18 adult mares, pregnancy at day 32 after ovulation (n = 9) and in diestrus (n = 9). Proteomic analysis of the samples was conducted using liquid chromatography-electrospray ionization-tandem mass spectrometry. We iden...
Özben M, von Samson-Himmelstjerna G, Freiin von Streit MKB, Wilkes EJA, Hughes KJ, Krücken J.Benzimidazoles resistance is widespread in strongyle parasitic nematodes and associated with polym orphisms in the codons 167, 198 and 200 of isotype 1 β-tubulin (tbb-1). In ascarids, benzimidazole (BZ) resistance has rarely been reported and in none of these cases were any of these polymorphisms detected. Here, available genome and transcriptome data from WormBase ParaSite were used to compare the complete β-tubulin reservoirs of , and . Adult spp. specimens collected in Australia from horses after BZ treatment (susceptible, n = 13) or surviving BZ treatment and collected after ivermectin...
ELKhamary AN, Keenihan EK, Schnabel LV, Redding WR, Schumacher J.While MRI is the modality of choice for the diagnosis of longitudinal tears (LTs) of the deep digital flexor tendon (DDFT) of horses, differentiating between various grades of tears based on imaging characteristics is challenging due to overlapping imaging features. In this retrospective, exploratory, diagnostic accuracy study, a machine learning (ML) scheme was applied to link quantitative features and qualitative descriptors to leverage MRI characteristics of different grades of tearing of the DDFT of horses. A qualitative MRI characteristic scheme, combining tendon morphologic features, alt...
Santibáñez R, Lara F, Barros TM, Mardones E, Cuadra F, Thomson P.The ocular microbiome in horses is poorly described compared to other species, and most of the information available in the literature is based on traditional techniques, which has limited the depth of the knowledge on the subject. The objective of this study was to characterize and predict the metabolic pathways of the ocular microbiome of a group of healthy horses. Conjunctival swabs were obtained from both eyes of 14 horses, and DNA extraction was performed from the swabs, followed by next generation sequencing and bioinformatics analyses employing DADA2 and PICRUSt2. A total of 17 phyla we...
Wang M, Liu Y, Bi X, Ma H, Zeng G, Guo J, Guo M, Ling Y, Zhao C.In the present study, genome-wide CNVs were detected in a total of 301 samples from 10 Chinese indigenous horse breeds using the Illumina Equine SNP70 Bead Array, and the candidate genes related to adaptability to high temperature and humidity in Jinjiang horses were identified and validated. We determined a total of 577 CNVs ranging in size from 1.06 Kb to 2023.07 Kb on the 31 pairs of autosomes. By aggregating the overlapping CNVs for each breed, a total of 495 CNVRs were detected in the 10 Chinese horse breeds. As many as 211 breed-specific CNVRs were determined, of which 64 were found in t...
Gilroy R, Leng J, Ravi A, Adriaenssens EM, Oren A, Baker D, La Ragione RM, Proudman C, Pallen MJ.The horse plays crucial roles across the globe, including in horseracing, as a working and companion animal and as a food animal. The horse hindgut microbiome makes a key contribution in turning a high fibre diet into body mass and horsepower. However, despite its importance, the horse hindgut microbiome remains largely undefined. Here, we applied culture-independent shotgun metagenomics to thoroughbred equine faecal samples to deliver novel insights into this complex microbial community. We performed metagenomic sequencing on five equine faecal samples to construct 123 high- or medium-quality...
Qi PF, Gao XY, Ji JK, Zhang Y, Yang SH, Cheng KH, Cui N, Zhu ML, Hu T, Dong X, Yan B, Wang CF, Yang HJ, Shi WF, Zhang W.Equine coronavirus (ECoV) was first identified in the USA and has been previously described in several countries. In order to test the presence of ECoV in China, we collected 51 small intestinal samples from donkey foals with diarrhoea from a donkey farm in Shandong Province, China between August 2020 and April 2021. Two samples tested positive for ECoV and full-length genome sequences were successfully obtained using next-generation sequencing, one of which was further confirmed by Sanger sequencing. The two strains shared 100% sequence identity at the scale of whole genome. Bioinformatics an...
Gavriliuc S, Reza S, Jeong C, Getachew F, McLoughlin PD, Poissant J.The development of high-throughput sequencing has prompted a transition in wildlife genetics from using microsatellites toward sets of single nucleotide polymorphisms (SNPs). However, genotyping large numbers of targeted SNPs using non-invasive samples remains challenging due to relatively large DNA input requirements. Recently, target enrichment has emerged as a promising approach requiring little template DNA. We assessed the efficacy of Tecan Genomics' Allegro Targeted Genotyping (ATG) for generating genome-wide SNP data in feral horses using DNA isolated from fecal swabs. Total and host-sp...
Chapuis RJJ, Becker AAMJ, Dowling PM, Weese JS.Antimicrobial-associated diarrhoea is a common adverse effect of antimicrobial treatment in horses and has been reported following the administration of oral doxycycline. The administration of antimicrobials has also been associated with changes in the equine intestinal microbiota diversity yet has not been explored under doxycycline treatment. Objective: To describe the dynamics of the faecal microbial diversity following a 5-day oral administration of doxycycline in healthy horses with Streptococcus zooepidemicus infected tissue chambers. Methods: Experimental prospective cohort study in a s...
Li Y, Liu C, Liu Q, Liu W.Ligilactobacillus equi is common in the horse intestine, alleviates the infection of Salmonella, and regulates intestinal flora. Despite this, there have been no genomic studies on this species. Here, we provide the genomic basis for adaptation to the intestinal habitat of this species. We sequenced the genome of L. equi IMAU81196, compared this with published genome information from three strains in NCBI, and analyzed genome characteristics, phylogenetic relationships, and functional genes. The mean genome size of L. equi strains was 2.08 ± 0.09 Mbp, and the mean GC content was 39.17% ± 0.1...
Van Steenkiste G, Delhaas T, Hermans B, Vera L, Decloedt A, van Loon G.In human cardiology, the anatomical origin of atrial premature depolarizations (APDs) is derived from P wave characteristics on a 12-lead electrocardiogram (ECG) and from vectorcardiography (VCG). The objective of this study is to differentiate between anatomical locations of APDs and to differentiate APDs from sinus rhythm (SR) based upon VCG characteristics in seven horses without cardiovascular disease. A 12-lead ECG was recorded under general anaesthesia while endomyocardial atrial pacing was performed (800−1000 ms cycle length) at the left atrial free wall and septum, right atrial free ...
Fitzgerald CCJ, Hedman R, Uduwela DR, Paszerbovics B, Carroll AJ, Neeman T, Cawley A, Brooker L, McLeod MD.The study of urinary phase II sulfate metabolites is central to understanding the role and fate of endogenous and exogenous compounds in biological systems. This study describes a new workflow for the untargeted metabolic profiling of sulfated metabolites in a urine matrix. Analysis was performed using ultra-high-performance liquid chromatography-high resolution tandem mass spectrometry (UHPLC-HRMS/MS) with data dependent acquisition (DDA) coupled to an automated script-based data processing pipeline and differential metabolite level analysis. Sulfates were identified through -means clustering...
Loux S, Robles M, Chavatte-Palmer P, de Mestre A.Development and the subsequent function of the fetal membranes of the equine placenta require both complex and precise regulation of gene expression. Advancements in recent years in bioinformatic techniques have allowed more extensive analyses into gene expression than ever before. This review starts by combining publically available transcriptomic data sets obtained from a range of embryonic, placental and maternal tissues, with previous knowledge of equine placental development and physiology, to gain insights into key gene families relevant to placentation in the horse. Covering the whole o...
Focková V, Styková E, Simonová MP, Maďar M, Kačírová J, Lauková A.Bacteriocin-producing bacteria with probiotic character are known as nutritional supplements mainly for livestock. Among those beneficial bacteria we also found enterococci. Because the species strains Enterococcus mundtii also can produce bacteriocins, this study was focused on fecal strains E. mundtii from horses and their bioactivity with a view to their possible future use in breeding. Rectal removal from 47 horses (40 mares and 7 stallions), the Norik breed from Muráň were sampled in eastern Slovakia during November 2019 year. Horses age ranged from five months up to 23 years. Using MAL...
Maniego J, Pesko B, Hincks P, Taylor P, Stewart G, Proudman C, Scarth J, Ryder E.The misuse of gene therapy by the introduction of transgenes via plasmid or viral vectors as a doping agent is an increasing concern in human and animal sports, not only in consideration to fair competition but also in potential detrimental effects to welfare. Doping events can be detected by polymerase chain reaction (PCR) amplification of a transgene-specific region of DNA. Quantitative real-time PCR (qPCR) is particularly suited to confirmatory investigations where precise limits of detection can be calculated. To fully validate a qPCR experiment, it is highly desirable to confirm the ident...
Klein C.Maintenance of pregnancy is dependent on the exchange of signals between the conceptus and the endometrium. The objective of this study was to use next-generation sequencing to determine transcriptome blueprints of the conceptus and endometrium 16 days after ovulation in the horse. There were 7760 and 10 182 genes expressed in the conceptus and endometrium, respectively, of which 7029 were present in both. Genes related to developmental processes were enriched among conceptus-specific transcripts, whereas many endometrium-specific genes had known roles in cell communication, cell adhesion and ...
Beisel CE, Edwards JF, Dunn LL, Rice NR.Transcription of pathogenic equine infectious anemia virus (EIAV) in an acutely infected horse was examined by using the polymerase chain reaction and nucleotide sequencing. Four spliced transcripts were identified in liver tissue, in contrast to the multiplicity of alternatively spliced messages reported for in vitro-propagated human immunodeficiency virus, simian immunodeficiency virus, and, to a lesser extent, EIAV. Nucleotide sequence analysis demonstrated that three of these mRNAs encode known viral proteins: the envelope precursor, the product of the S2 open reading frame, and the regula...
Finno CJ, Bordbari MH, Valberg SJ, Lee D, Herron J, Hines K, Monsour T, Scott E, Bannasch DL, Mickelson J, Xu L.Specific spontaneous heritable neurodegenerative diseases have been associated with lower serum and cerebrospinal fluid α-tocopherol (α-TOH) concentrations. Equine neuroaxonal dystrophy (eNAD) has similar histologic lesions to human ataxia with vitamin E deficiency caused by mutations in the α-TOH transfer protein gene (TTPA). Mutations in TTPA are not present with eNAD and the molecular basis remains unknown. Given the neuropathologic phenotypic similarity of the conditions, we assessed the molecular basis of eNAD by global transcriptome sequencing of the cervical spinal cord. Differential...
Chintapalli SV, Bhardwaj G, Patel R, Shah N, Patterson RL, van Rossum DB, Anishkin A, Adams SH.The mechanism(s) by which fatty acids are sequestered and transported in muscle have not been fully elucidated. A potential key player in this process is the protein myoglobin (Mb). Indeed, there is a catalogue of empirical evidence supporting direct interaction of globins with fatty acid metabolites; however, the binding pocket and regulation of the interaction remains to be established. In this study, we employed a computational strategy to elucidate the structural determinants of fatty acids (palmitic & oleic acid) binding to Mb. Sequence analysis and docking simulations with a horse (E...
Gim JA, Hong CP, Kim DS, Moon JW, Choi Y, Eo J, Kwon YJ, Lee JR, Jung YD, Bae JH, Choi BH, Ko J, Song S, Ahn K, Ha HS, Yang YM, Lee HK, Park KD....Athletic performance is an important criteria used for the selection of superior horses. However, little is known about exercise-related epigenetic processes in the horse. DNA methylation is a key mechanism for regulating gene expression in response to environmental changes. We carried out comparative genomic analysis of genome-wide DNA methylation profiles in the blood samples of two different thoroughbred horses before and after exercise by methylated-DNA immunoprecipitation sequencing (MeDIP-Seq). Differentially methylated regions (DMRs) in the pre-and post-exercise blood samples of superio...
Birn-Jeffery AV, Higham TE.Animals must continually respond dynamically as they move through complex environments, and slopes are a common terrain on which legged animals must move. Despite this, non-level locomotion remains poorly understood. In this study, we first review the literature on locomotor mechanics, metabolic cost, and kinematic strategies on slopes. Using existing literature we then performed scaling analyses of kinematic variables, including speed, duty factor, and stride-length across a range of body sizes from ants to horses. The studies that examined locomotion on inclines vastly outnumbered those focu...
Legarra A, Croiseau P, Sanchez MP, Teyssèdre S, Sallé G, Allais S, Fritz S, Moreno CR, Ricard A, Elsen JM.With dense genotyping, many choices exist for methods to detect quantitative trait loci (QTL) in livestock populations. However, no across-species study has been conducted on the performance of different methods using real data. We compared three methods that correct for relatedness either implicitly or explicitly: linkage and linkage disequilibrium haplotype-based analysis (LDLA), efficient mixed-model association (EMMA) analysis, and Bayesian whole-genome regression (BayesC). We analyzed one chromosome in each of five datasets (dairy cattle, beef cattle, sheep, horses, and pigs) using real g...
Smits K, De Coninck DI, Van Nieuwerburgh F, Govaere J, Van Poucke M, Peelman L, Deforce D, Van Soom A.Although the equine oviduct clearly affects early embryo development and the selective transport of equine embryos through the oviduct indicates a reciprocal interaction, the influence of the embryo on gene expression in the oviduct remains to be determined in the horse. The aim of this study was to examine this by means of RNA sequencing. Four days after ovulation, epithelial cells ipsilateral and contralateral to the ovulation side from five cyclic and five pregnant mares were collected from the oviduct. RNA was extracted, samples were sequenced, and data analysis was performed to determine ...
Li B, He X, Zhao Y, Bai D, Du M, Song L, Liu Z, Yin Z, Manglai D.Horse testis development and spermatogenesis are complex physiological processes. To study these processes, three immature and three mature testes were collected from the Mongolian horse, and six libraries were established using high-throughput RNA sequencing technology (RNA-Seq) to screen for genes related to testis development and spermatogenesis. A total of 16,237 upregulated genes and 8,641 downregulated genes were detected in the testis of the Mongolian horse. These genes play important roles in different developmental stages of spermatogenesis and testicular development. Five genes with ...
Hestand MS, Kalbfleisch TS, Coleman SJ, Zeng Z, Liu J, Orlando L, MacLeod JN.Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced mRNA from a pool of forty-three different tissues. From these, we derived the structures of 68,594 transcripts. In addition, we identified 301,829 positions with SNPs or small indels within these transcripts relative to EquCab2. Interestingly, 780 variants extend the open reading frame of the transcri...
Sarin JK, Te Moller NCR, Mancini IAD, Brommer H, Visser J, Malda J, van Weeren PR, Afara IO, Töyräs J.Arthroscopic assessment of articular tissues is highly subjective and poorly reproducible. To ensure optimal patient care, quantitative techniques (e.g., near infrared spectroscopy (NIRS)) could substantially enhance arthroscopic diagnosis of initial signs of post-traumatic osteoarthritis (PTOA). Here, we demonstrate, for the first time, the potential of arthroscopic NIRS to simultaneously monitor progressive degeneration of cartilage and subchondral bone in vivo in Shetland ponies undergoing different experimental cartilage repair procedures. Osteochondral tissues adjacent to the repair sites...
Pacholewska A, Jagannathan V, Drögemüller M, Klukowska-Rötzler J, Lanz S, Hamza E, Dermitzakis ET, Marti E, Leeb T, Gerber V.Recurrent airway obstruction (RAO) is a common and potentially debilitating lower airway disease in horses, which shares many similarities with human asthma. In susceptible horses RAO exacerbation is caused by environmental allergens and irritants present in hay dust. The objective of this study was the identification of genes and pathways involved in the pathology of RAO by global transcriptome analyses in stimulated peripheral blood mononuclear cells (PBMCs). We performed RNA-seq on PBMCs derived from 40 RAO affected and 45 control horses belonging to three cohorts of Warmblood horses: two h...
Janova E, Matiasovic J, Vahala J, Vodicka R, Van Dyk E, Horin P.The major histocompatibility complex genes coding for antigen binding and presenting molecules are the most polymorphic genes in the vertebrate genome. We studied the DRA and DQA gene polymorphism of the family Equidae. In addition to 11 previously reported DRA and 24 DQA alleles, six new DRA sequences and 13 new DQA alleles were identified in the genus Equus. Phylogenetic analysis of both DRA and DQA sequences provided evidence for trans-species polymorphism in the family Equidae. The phylogenetic trees differed from species relationships defined by standard taxonomy of Equidae and from trees...
Ellis SA, Martin AJ, Holmes EC, Morrison WI.Nineteen horse MHC class I specificities have been serologically identified previously at a single locus (ELA-A), and two other specificities appear to be coded at other loci. Biochemical studies indicate that there are at least two expressed loci. In order to establish the number of transcribed horse MHC class I genes, we made a cDNA library from a heterozygous animal (ELA-A3/A7), and screened for positive clones using a bovine class I probe. More than 200 class I clones were isolated in this way, and so far seven unique full length sequences have been identified. All of the sequences are pre...
Bryan K, McGivney BA, Farries G, McGettigan PA, McGivney CL, Gough KF, MacHugh DE, Katz LM, Hill EW.A single bout of exercise induces changes in gene expression in skeletal muscle. Regular exercise results in an adaptive response involving changes in muscle architecture and biochemistry, and is an effective way to manage and prevent common human diseases such as obesity, cardiovascular disorders and type II diabetes. However, the biomolecular mechanisms underlying such responses still need to be fully elucidated. Here we performed a transcriptome-wide analysis of skeletal muscle tissue in a large cohort of untrained Thoroughbred horses (n = 51) before and after a bout of high-intensity exe...
Nagao S, Osuka H, Yamada T, Uni T, Shomura Y, Imai K, Higuchi Y, Hirota S.Myoglobin (Mb) stores dioxygen in muscles, and is a fundamental model protein widely used in molecular design. The presence of dimeric Mb has been known for more than forty years, but its structural and oxygen binding properties remain unknown. From an X-ray crystallographic analysis at 1.05 Å resolution, we found that dimeric metMb exhibits a domain-swapped structure with two extended α-helices. Each new long α-helix is formed by the E and F helices and the EF-loop of the original monomer, and as a result the proximal and distal histidines of the heme originate from different protomers. Th...
Geddes LA, Tacker WA, Rosborough JP, Moore AG, Cabler PS.Electrical ventricular defibrillation of heavy subjects (over 100 kg body weight) is uncommon for the human or any animal species. This paper reports trans-chest ventricular defibrillation of subjects ranging in weight from 2.3 to 340 kg using conventional defibrillation current (heavily damped sine wave) of 0.3-30 ms duration. It was found that a body weight-to-electrical-shock strength relationship exists and can be expressed in terms of either electrical energy or peak current. For the duration of current pulse used clinically (3-10 ms), the relationship between energy requirement and body ...
Alzan HF, Knowles DP, Suarez CE.Apicomplexa tick-borne hemoparasites, including Babesia bovis, Babesia microti, and Theileria equi are responsible for bovine and human babesiosis and equine theileriosis, respectively. These parasites of vast medical, epidemiological, and economic impact have complex life cycles in their vertebrate and tick hosts. Large gaps in knowledge concerning the mechanisms used by these parasites for gene regulation remain. Regulatory genes coding for DNA binding proteins such as members of the Api-AP2, HMG, and Myb families are known to play crucial roles as transcription factors. Although the reperto...
Ghosh M, Sharma N, Singh AK, Gera M, Pulicherla KK, Jeong DK.For more than a quarter of a century, sequencing technologies from Sanger's method to next-generation high-throughput techniques have provided fascinating opportunities in the life sciences. The continuing upward trajectory of sequencing technologies will improve livestock research and expedite the development of various new genomic and technological studies with farm animals. The use of high-throughput technologies in livestock research has increased interest in metagenomics, epigenetics, genome-wide association studies, and identification of single nucleotide polymorphisms and copy number va...
Zhang J.Prion diseases (e.g. Creutzfeldt-Jakob disease (CJD), variant CJD (vCJD), Gerstmann-Straussler-Scheinker syndrome (GSS), Fatal Familial Insomnia (FFI) and Kuru in humans, scrapie in sheep, bovine spongiform encephalopathy (BSE or 'mad-cow' disease) and chronic wasting disease (CWD) in cattles) are invariably fatal and highly infectious neurodegenerative diseases affecting humans and animals. However, by now there have not been some effective therapeutic approaches or medications to treat all these prion diseases. Rabbits, dogs, and horses are the only mammalian species reported to be resistant...
Vandewege MW, Platt RN, Ray DA, Hoffmann FG.PIWI proteins and PIWI-interacting RNAs (piRNAs) are part of a cellular pathway that has evolved to protect genomes against the proliferation of transposable elements (TEs). PIWIs and piRNAs assemble into complexes that are involved in epigenetic and post-transcriptional repression of TEs. Most of our understanding of the mechanisms of piRNA-mediated TE silencing comes from fruit fly and mouse models. However, even in these well-studied animals it is unclear how piRNA responses relate to variable TE expression and whether the strength of the piRNA response affects TE content over time. Here, w...
Gilroy R, Leng J, Ravi A, Adriaenssens EM, Oren A, Baker D, La Ragione RM, Proudman C, Pallen MJ.The horse plays crucial roles across the globe, including in horseracing, as a working and companion animal and as a food animal. The horse hindgut microbiome makes a key contribution in turning a high fibre diet into body mass and horsepower. However, despite its importance, the horse hindgut microbiome remains largely undefined. Here, we applied culture-independent shotgun metagenomics to thoroughbred equine faecal samples to deliver novel insights into this complex microbial community. We performed metagenomic sequencing on five equine faecal samples to construct 123 high- or medium-quality...
Ebert DW, Roberts C, Farrar SK, Johnston WM, Litsky AS, Bertone AL.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...
Stock KF, Reents R.Technical advances and development in the market for genomic tools have facilitated access to whole-genome data across species. Building-up on the acquired knowledge of the genome sequences, large-scale genotyping has been optimized for broad use, so genotype information can be routinely used to predict genetic merit. Genomic selection (GS) refers to the use of aggregates of estimated marker effects as predictors which allow improved individual differentiation at young age. Realizable benefits of GS are influenced by several factors and vary in quantity and quality between species. General cha...
Mitchell KJ, Schwarzwald CC.Heart rate variability (HRV) analysis has been performed on ECG-derived data sets for more than 170 years but is currently undergoing a rapid evolution, thanks to the expansion of the human and veterinary medical technology sector. Traditional HRV analysis was initially performed to identify changes in vago-sympathetic balance, while the most recent focus has expanded to include the use of complex computer algorithms, neural networks and machine learning technology to identify cardiac arrhythmias, particularly atrial fibrillation (AF). Some of these techniques have recently been translated for...
Mienaltowski MJ, Huang L, Frisbie DD, McIlwraith CW, Stromberg AJ, Bathke AC, Macleod JN.Full-thickness articular cartilage lesions that reach to the subchondral bone yet are restricted to the chondral compartment usually fill with a fibrocartilage-like repair tissue which is structurally and biomechanically compromised relative to normal articular cartilage. The objective of this study was to evaluate transcriptional differences between chondrocytes of normal articular cartilage and repair tissue cells four months post-microfracture. Methods: Bilateral one-cm2 full-thickness defects were made in the articular surface of both distal femurs of four adult horses followed by subchond...
Shin EK, Rijkers T, Pastink A, Meek K.We reported previously that the genetic SCID disease observed in Arabian foals is explained by a defect in V(D)J recombination that profoundly affects both coding and signal end joining. As in C.B-17 SCID mice, the molecular defect in SCID foals is in the catalytic subunit of the DNA-dependent protein kinase (DNA-PKCS); however, in SCID mice, signal end resolution remains relatively intact. Moreover, recent reports indicate that mice that completely lack DNA-PKCS also generate signal joints at levels that are indistinguishable from those observed in C.B-17 SCID mice, eliminating the possibilit...
Holyoak GR, Premathilake HU, Lyman CC, Sones JL, Gunn A, Wieneke X, DeSilva U.The goal of this study was to understand the composition and existence of the resident uterine microbiome in healthy mares and to establish the presence of a core microbiome for the healthy equine uterus. We analyzed the microbiomes of 35 healthy mares that are long-time residents of three farms in Oklahoma, Louisiana, and Australia as well as that of 19 mares purchased from scattered owners in the Southern Mid-Western states of the United States. Over 6 million paired-end reads of the V4 region of the 16S rRNA gene were obtained resulting in 19,542 unique Amplicon Sequence Variants (ASVs). AS...
Brault LS, Cooper CA, Famula TR, Murray JD, Penedo MC.Equine Cerebellar Abiotrophy (CA) is a neurological disease found in Arabian horses. CA is characterized by post-natal degeneration of the Purkinje cells of the cerebellum. Signs of CA include ataxia, head tremors, and a lack of balance equilibrium. We have discovered a linkage of the CA phenotype to a microsatellite marker on ECA2 and identified a region of conserved homozygosity spanning approximately 142 kb. Complete sequencing of the four genes in this region identified one SNP found only in Arabian horses, located in exon 4 of TOE1 and approximately 1200 base pairs upstream of MUTYH, adja...
Giaretta E, Munerato M, Yeste M, Galeati G, Spinaci M, Tamanini C, Mari G, Bucci D.Setting an open-access computer assisted sperm analysis (CASA) may benefit the evaluation of motility in mammalian sperm, especially when economic constraints do not allow the use of a commercial system. There have been successful attempts to develop such a device in Zebra fish sperm and the system has been used in very few studies on mammalian spermatozoa. Against this background, the present study aimed at developing an open-access CASA system for mammalian sperm using the horse as a model and based upon the Image J software previously established for Zebra fish sperm. Along with determining...
