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.
Jiang Q, Wei Y, Huang Y, Jiang H, Guo Y, Lan G, Liao J.The Debao pony (Equus caballus) is the most important local variety of domestic horses, and is strictly protected by the Chinese government. Their average adult withers height is 94.42±3.76 cm for males and 98.35±4.55 cm for females, respectively. In the present study, the complete sequence of the Debao pony mitochondrial genome was determined (GenBank Accession No. EU939445), and was found to be similar to other equine mitochondrial genomes. However, there were 85 nucleotide substitutions in the 13 protein-coding genes; the percentage of substitution was 0.8±0.1. Polymorphisms of mtDNA con...
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...
Austbø L, Røed KH, Dolvik NI, Skretting G.The aim of this study was to investigate genes for differential expression in cartilage of foals predisposed to osteochondrosis (OC). Tissue was sampled from the cranial part of the distal intermediate ridge of the tibia in the tarso-crural joint. Foals were considered predisposed to OC when parents had OC at the distal intermediate ridge of the tibia. RNA was isolated and subjected to arbitrarily primed PCR (RAP-PCR) followed by fingerprinting to screen for differentially expressed genes. By verification of results from the RAP-PCR fingerprint screening using real-time RT-PCR, we identified t...
Rourke KM, Coe S, Kohn CW, Rosol TJ, Mendoza FJ, Toribio RE.Epithelial calcium transport occurs by paracellular and transcellular mechanisms. Transcellular transport in intestinal and renal epithelia involves several transport proteins, including transient receptor potential vanilloid member 5 (TRPV5), member 6 (TRPV6), calbindin D9k (CB9), calbindin D28k (CB28), sodium calcium exchanger 1 (NCX1), plasma membrane calcium ATPase 1 (PMCA1), and the vitamin D receptor (VDR). We are interested in the horse because of its unique calcium physiology (high blood calcium, high intestinal calcium absorption, high renal excretion of calcium, low vitamin D concent...
Serteyn D, Piquemal D, Vanderheyden L, Lejeune JP, Verwilghen D, Sandersen C.Osteochondrosis (OC) is a developmental disease that affects growing horses and that severely affects their ability to perform. The genetic basis of its pathogenesis is poorly understood. The aim of the study was to analyze the transcript profile of leukocytes from horses affected with OC. Two transcriptome libraries were constructed from leukocytes of OC-affected and non-OC-affected horses using digital gene expression analysis (DGE) and real-time PCR. Statistical analysis allowed selection of 1,008 tags upregulated in the non-OC-affected group and 1,545 tags upregulated in the OC-affected gr...
Tallmadge RL, Campbell JA, Miller DC, Antczak DF.The genomic sequences of 15 horse major histocompatibility complex (MHC) class I genes and a collection of MHC class I homozygous horses of five different haplotypes were used to investigate the genomic structure and polymorphism of the equine MHC. A combination of conserved and locus-specific primers was used to amplify horse MHC class I genes with classical and nonclassical characteristics. Multiple clones from each haplotype identified three to five classical sequences per homozygous animal and two to three nonclassical sequences. Phylogenetic analysis was applied to these sequences, and gr...
Huby-Chilton F, Murphy J, Chilton NB, Gajadhar AA, Blais BW.Single-strand conformation polymorphism (SSCP) analysis of amplicons produced from a mitochondrial DNA region between the tRNA(Lys) and ATPase8 genes was applied for the detection of animal product within livestock feeds. Identification of prohibited animal (cattle, elk, sheep, deer, and goat) and nonprohibited animal (pig and horse) products from North America was possible based on the differential display of the single-stranded DNA fragments for the different animal species on SSCP gels. This method allowed specific detection and identification of mixed genomic DNA from different animal spec...
Levionnois OL, Mevissen M, Thormann W, Spadavecchia C.The objective of this study was to assess a pharmacokinetic algorithm to predict ketamine plasma concentration and drive a target-controlled infusion (TCI) in ponies. Firstly, the algorithm was used to simulate the course of ketamine enantiomers plasma concentrations after the administration of an intravenous bolus in six ponies based on individual pharmacokinetic parameters obtained from a previous experiment. Using the same pharmacokinetic parameters, a TCI of S-ketamine was then performed over 120 min to maintain a concentration of 1 microg/mL in plasma. The actual plasma concentrations of ...
McGivney BA, Eivers SS, MacHugh DE, MacLeod JN, O'Gorman GM, Park SD, Katz LM, Hill EW.Selection for exercise-adapted phenotypes in the Thoroughbred racehorse has provided a valuable model system to understand molecular responses to exercise in skeletal muscle. Exercise stimulates immediate early molecular responses as well as delayed responses during recovery, resulting in a return to homeostasis and enabling long term adaptation. Global mRNA expression during the immediate-response period has not previously been reported in skeletal muscle following exercise in any species. Also, global gene expression changes in equine skeletal muscle following exercise have not been reported...
Severa L, Máchal L, Svábová L, Mamica O.This study quantified and evaluated the variability of sperm head shape for 10 different stallions. Sperm head shape characteristics including sperm head length to width ratio, position of the center of gravity, curvature, and degree of roundness were assessed and analysed from images using elliptic Fourier descriptors and inverse Fourier transformation. The first four principal components accounted for 88.46-92.33% of the total variance and provided a good summary of the overall data. In the case of the ejaculate with defective sperm heads the components accounted for 97.35-98.21% of variatio...
BMC research notesDecember 16, 2009
Volume 2 255 doi: 10.1186/1756-0500-2-255
Rendo F, Iriondo M, Manzano C, Estonba A.The Cantabrian Coast horse breeds of the Iberian Peninsula have mainly black or bay colored coats, but alleles responsible for a chestnut coat color run in these breeds and occasionally, chestnut horses are born. Chestnut coat color is caused by two recessive alleles, e and e(a), of the melanocortin-1 receptor gene, whereas the presence of the dominant, wild-type E allele produces black or bay coat horses. Because black or bay colored coats are considered as the purebred phenotype for most of the breeds from this region, it is important to have a fast and reliable method to detect alleles caus...
BMC research notesDecember 11, 2009
Volume 2 246 doi: 10.1186/1756-0500-2-246
Smits K, Goossens K, Van Soom A, Govaere J, Hoogewijs M, Vanhaesebrouck E, Galli C, Colleoni S, Vandesompele J, Peelman L.Application of reverse transcription quantitative real-time polymerase chain reaction is very well suited to reveal differences in gene expression between in vivo and in vitro produced embryos. Ultimately, this may lead to optimized equine assisted reproductive techniques. However, for a correct interpretation of the real-time PCR results, all data must be normalized, which is most reliably achieved by calculating the geometric mean of the most stable reference genes. In this study a set of reliable reference genes was identified for equine in vivo and fresh and frozen-thawed in vitro embryos....
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...
The Journal of heredityNovember 25, 2009
Volume 101, Issue 2 246-250 doi: 10.1093/jhered/esp091
Mittmann EH, Lampe V, Mömke S, Zeitz A, Distl O.The availability of a high-quality draft sequence of the horse makes known the physical location of microsatellites. The aim of the present study was to establish a highly polymorphic minimal screening set of microsatellite markers for horses (MSSH) annotated on the horse genome assembly EquCab2.0. We have used the previously reported linkage and radiation hybrid maps and have extended these marker sets by filling in gaps as noted from annotation on the horse sequence. This MSSH covers all autosomes and the X chromosome with 322 evenly spaced microsatellites whose positions were determined on ...
Oliveira Filho JP, Badial PR, Cunha PHJ, Cruz TF, Araújo JP, Divers TJ, Winand NJ, Borges AS.Equine serum or plasma iron concentration drops quickly during inflammation. Accumulation of iron inside macrophages and reduction of the intestinal absorption of this element cause hypoferremia during systemic inflammatory processes. These mechanisms are mediated by hepcidin, a 25 amino acids peptide synthesized mainly in the liver in response to iron stores and inflammation. Hepcidin is an important peptide for systemic iron homeostasis and also has antibacterial and antifungal activities. Hepcidin up-regulation is particularly useful during acute inflammation, especially before adaptive imm...
Burocziova M, Riha J.Genetic relationships and population structure of 8 horse breeds in the Czech and Slovak Republics were investigated using classification methods for breed discrimination. To demonstrate genetic differences among these breeds, we used genetic information - genotype data of microsatellite markers and classification algorithms - to perform a probabilistic prediction of an individual's breed. In total, 932 unrelated animals were genotyped for 17 microsatellite markers recommended by the ISAG for parentage testing (AHT4, AHT5, ASB2, HMS3, HMS6, HMS7, HTG4, HTG10, VHL20, HTG6, HMS2, HTG7, ASB17, AS...
Padua MB, Kowalski AA, Cañas MY, Hansen PJ.Uterine serpins (USs), designated as SERPINA14, are expressed in the endometrium in response to progesterone. All species identified as having USs exhibit epitheliochorial placentation and are in the Ruminantia and Suidae orders of the Laurasiatheria superorder. The objective was to identify US genes in species within and outside Laurasiatheria and evaluate whether evolution of the US gene was associated with development of the epitheliochorial placenta. Through queries of nucleotide and genomic databases, known US genes were identified (caprine, bovine, porcine, water buffalo), and new US cod...
Bright LA, Burgess SC, Chowdhary B, Swiderski CE, McCarthy FM.The horse genome is sequenced, allowing equine researchers to use high-throughput functional genomics platforms such as microarrays; next-generation sequencing for gene expression and proteomics. However, for researchers to derive value from these functional genomics datasets, they must be able to model this data in biologically relevant ways; to do so requires that the equine genome be more fully annotated. There are two interrelated types of genomic annotation: structural and functional. Structural annotation is delineating and demarcating the genomic elements (such as genes, promoters, and ...
Graham NS, Clutterbuck AL, James N, Lea RG, Mobasheri A, Broadley MR, May ST.Affymetrix GeneChip arrays are a powerful tool for transcriptome profiling and have been applied to a wide range of species. A genomic DNA (gDNA)-based probe selection method has been developed which broadens the range of species to which GeneChips may be successfully applied. This study demonstrated that gDNA-based probe selection on the Affymetrix U133+2 GeneChip array can be used to study the equine transcriptome which, to date, has received only limited attention. More than 29,000 transcripts can be detected in equine brain and liver and in primary cultures of equine articular chondrocytes...
Lake SL, Matthews JB, Kaplan RM, Hodgkinson JE.Genetic resistance against benzimidazole (BZ) anthelmintics is widespread in cyathostomins, the commonest group of intestinal parasitic nematodes of horses. Studies of BZ-resistant nematodes of sheep, particularly Haemonchus contortus, have indicated that an anthelmintic resistance-conferring T/A polymorphism, encoding an F (phenylalanine) to Y (tyrosine) substitution, in beta-tubulin isotype 1 is present at two loci, codons 167 and 200 (F167Y, F200Y). Recent studies using complementary (c) DNA derived from BZ-susceptible and -resistant cyathostomins identified statistical differences in the f...
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...
Chen JW, Uboh CE, Soma LR, Li X, Guan F, You Y, Liu Y.Proper identification of racehorses competing in an official race and maintenance of defensible chain of custody are important in doping control regulations. The purpose of this study was to develop a reliable multiplex PCR method for providing genetic evidence for matching donors to test samples by using short tandem repeat (STR) loci. Amplification of 21 STR loci from blood, urine or hair root was achieved in a single tube and STR length polymorphism was analyzed using fluorescent labeled capillary electrophoresis. This novel approach showed an allele confidence interval of 0.19-0.43 bp and ...
Tompkins D, Hudgens E, Horohov D, Baldwin CL.This report describes the initial cloning and characterization of the equine interleukin-17 (IL-17) expressed gene sequence from mRNA obtained from equine intestinal tissue and interleukin-23 (IL-23) expressed gene sequence from mRNA obtained from equine peripheral blood mononuclear cells. Equine IL-17 has 462 nucleotides in the translated region, determined by homology with known human and mouse sequences, and shares 84% and 75% identity, respectively. For the deduced amino acid sequences, the identity with human and mouse is 76% and 70%. Equine IL-23 has 579 nucleotides in the translated reg...
Lampe V, Dierks C, Komm K, Distl O.In this study we present a newly detected QTL associated with osteochondrosis in Hanoverian warmblood horses on equine chromosome 18 (ECA18). We developed a highly polymorphic and evenly distributed marker set on ECA18 employing the horse genome assembly EquCab2. The marker set included 11 newly developed microsatellites. Average polymorphism information content was 62.1% at an average spacing of 3 Mb. For genotyping of this marker set comprising a total of 27 highly polymorphic microsatellites, we used the same 14 paternal half-sib families as in the previous whole genome scan. The chromosome...
Barrey E, Mucher E, Jeansoule N, Larcher T, Guigand L, Herszberg B, Chaffaux S, Guérin G, Mata X, Benech P, Canale M, Alibert O, Maltere P, Gidrol X.Several cases of myopathies have been observed in the horse Norman Cob breed. Muscle histology examinations revealed that some families suffer from a polysaccharide storage myopathy (PSSM). It is assumed that a gene expression signature related to PSSM should be observed at the transcriptional level because the glycogen storage disease could also be linked to other dysfunctions in gene regulation. Thus, the functional genomic approach could be conducted in order to provide new knowledge about the metabolic disorders related to PSSM. We propose exploring the PSSM muscle fiber metabolic disorder...
Lin M, Zhang C, Gibson K, Rikihisa Y.Neorickettsia risticii is an obligate intracellular bacterium of the trematodes and mammals. Horses develop Potomac horse fever (PHF) when they ingest aquatic insects containing encysted N. risticii-infected trematodes. The complete genome sequence of N. risticii Illinois consists of a single circular chromosome of 879 977 bp and encodes 38 RNA species and 898 proteins. Although N. risticii has limited ability to synthesize amino acids and lacks many metabolic pathways, it is capable of making major vitamins, cofactors and nucleotides. Comparison with its closely related human pathogen N. senn...
Matéos A, Miclo L, Mollé D, Dary A, Girardet JM, Gaillard JL.alpha(S1)-Casein was isolated from Haflinger mare's milk by hydrophobic interaction chromatography and displayed great micro-heterogeneity by 2-dimensional electrophoresis, probably because of a variable degree of phosphorylation and alternative splicing events. The aim of the present work was to investigate the complexity of the mare's alpha(S1)-casein. The different isoforms present in milk were submitted to a double treatment of dephosphorylation, first by using alkaline phosphatase and then acid phosphatase to achieve complete dephosphorylation. The apoforms were then analyzed by electrosp...
Espino-Solis GP, Calderon-Amador J, Calderon-Aranda ES, Licea AF, Donis-Maturano L, Flores-Romo L, Possani LD.A three-dimensional model of the alphaX I-domain of the horse integrin CD11c from dendritic cells provided information for selecting two segments of the primary structure for peptide synthesis. Peptide 1 contains 20 amino acids and peptide 2 has 17 amino acid residues. The first spans from position Thr229 to Arg248 of an alpha-helix segment of the structure, whereas peptide 2 goes from Asp158 to Phe174 and corresponds to an exposed segment of the loop considered to be the metal ion-dependent adhesion site. Murine polyclonal antisera against both peptides were generated and assayed in periphera...
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...
Green MK, Johnston MV, Larsen BS.To elucidate the role of high mass accuracy in mass spectrometric peptide mapping and database searching, selected proteins were subjected to tryptic digestion and the resulting mixtures were analyzed by electrospray ionization on a 7 Tesla Fourier transform mass spectrometer with a mass accuracy of 1 ppm. Two extreme cases were examined in detail: equine apomyoglobin, which digested easily and gave very few spurious masses, and bovine alpha-lactalbumin, which under the conditions used, gave many spurious masses. The effectiveness of accurate mass measurements in minimizing false protein match...
Marsico TV, Valente RS, Annes K, Oliveira AM, Silva MV, Sudano MJ.A wide-ranging review study regarding the molecular characterization of the first cell lineages of the developmental embryo is lacking, especially for the primary events during earliest differentiation which leads to the determination of cellular fate. Here, a systematic review and meta-analysis were conducted according to PRISMA guidelines. MEDLINE-PubMed was searched based on an established search strategy through April 2021. Thirty-six studies fulfilling the inclusion criteria were subjected to qualitative and quantitative analysis. Among the studies, 50 % (18/36) used mice as an animal mod...
Semik-Gurgul E, Gurgul A, Szmatoła T.Recent publications confirmed that long non-coding RNAs (lncRNAs) perform an essential function in gene-specific transcription regulation. Nevertheless, despite its important role, lncRNA has not yet been described in equine sarcoids, the skin neoplasia of horses. Therefore, the aim of this study is to deepen the knowledge about lncRNA expression in the pathogenesis of equine sarcoids and provide new insight into the regulatory function of lncRNA in the bovine papillomavirus-dependent neoplasia of horse dermal tissues. RNA sequencing (RNA-seq) data from 12 equine sarcoid samples and the corres...
Kakoi H, Kijima-Suda I, Gawahara H, Kinoshita K, Tozaki T, Hirota K, Yoshizawa M.To construct a system for identifying individual horses from urine samples that are submitted for postracing doping tests, we developed a genotyping assay based on 26-plex single-nucleotide polymorphisms (SNPs). DNA was isolated from urine using a commercially available DNA/RNA extraction kit, and SNP genotyping was achieved with a SNaPshot(™) technique. DNA profiles including 26 SNPs were acquired from urine samples and blood/hair samples. Within the studied Thoroughbred population, the 26-plex assay showed a probability of identity of 5.80 × 10(-11). Compared to the conventional short tan...
McCoy AM, Arrington J, Yau PM.The protein content of amnion is thought to be the primary contributor to its efficacy as a biological dressing for wounds. Protein elution into antibiotic processing media has been reported, but the effect of antiseptic-based processing methods is unknown. Amniotic membranes were collected from eight healthy mares. Samples were collected after removal of gross debris. Tissues were subsequently divided and processed with either 0.05% chlorhexidine or 2% iodine/0.25% acetic acid. After protein extraction and trypsin digestion, the proteins were labeled with 8-plex iTRAQ tags, combined, and anal...
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...
Hanzawa K, Lear TL, Piumi F, Bailey E.Consensus DNA sequences from human, mouse and/or rat were used to design oligonucleotide primers for equine homologues of exons 16, 17 and 20-23 of potassium chloride co-transporter (SLC12A4) and exons 10, 11 and 3, 4, respectively, for two amino acid transporters (SLC7A10 and SLC7A9). DNA sequences of the PCR products showed high sequence identity to these regions. Equine BAC clones were obtained for SLC12A4 and SLC7A10 and mapped to equine chromosomes ECA3p13 and ECA10p15, respectively, by fluorescence in situ hybridization (FISH). Several single nucleotide polymorphisms (SNP) were found. Su...
Reyes AM, Jahr H, van Schie HT, Weinans H, Zadpoor AA.The elastic strain limit (ESL) of tendons is the point where maximum elastic modulus is reached, after which micro-damage starts. Study of damage progression in tendons under repetitive (fatigue) loading requires a priori knowledge about ESL. In this study, we propose three different approaches for predicting ESL. First, one single value is assumed to represent the ESL of all tendon specimens. Second, different extrapolation curves are used for extrapolating the initial part of the stress-strain curve. Third, a method based on comparing the shape of the initial part of the stress-strain curve ...
Guan F, You Y, Fay S, Li X, Robinson MA.To address the limitations of current targeted analytical methods that can only detect known doping agents, a novel methodology that permits untargeted drug detection (UDD) has been developed to help in the fight against doping in sports. Fifty-seven drugs were spiked into blank equine plasma and were treated as unknowns since their exact masses and chromatographic retention times were not utilized for detection. The spiked drugs were extracted from the plasma samples and were analyzed using liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS). The acquired LC-HRMS raw ...
Cox L, Vanderwall DK, Parkinson KC, Sweat A, Isom SC.There is compelling evidence that oocytes from mares >18 years of age have a high incidence of inherent defects that result in early embryonic loss. In women, an age-related decrease in oocyte quality is associated with an increased incidence of aneuploidy and it has recently been determined that the gene expression profile of human oocytes is altered with advancing age. We hypothesised that similar age-related aberrations in gene expression occur in equine oocytes. Therefore, the aim of the present study was to compare gene expression profiles of individual oocytes and cumulus cells from y...
Graham NS, Clutterbuck AL, James N, Lea RG, Mobasheri A, Broadley MR, May ST.Affymetrix GeneChip arrays are a powerful tool for transcriptome profiling and have been applied to a wide range of species. A genomic DNA (gDNA)-based probe selection method has been developed which broadens the range of species to which GeneChips may be successfully applied. This study demonstrated that gDNA-based probe selection on the Affymetrix U133+2 GeneChip array can be used to study the equine transcriptome which, to date, has received only limited attention. More than 29,000 transcripts can be detected in equine brain and liver and in primary cultures of equine articular chondrocytes...
Ząbek T, Semik-Gurgul E, Szmatoła T, Gurgul A, Fornal A, Bugno-Poniewierska M.Horses are one of the longest-living species of farm animals. Advanced age is often associated with a decrease in body condition, dysfunction of immune system, and late-onset disorders. Due to this, the search for new solutions in the prevention and treatment of pathological conditions of the advanced age of horses is desirable. That is why the identification of aging-related changes in the horse genome is interesting in this respect. In the recent years, the research on aging includes studies of age-related epigenetic effects observed on the DNA methylation level. We applied reduced represent...
Riveroll AL, Skyba-Lewin S, Lynn KD, Mubyeyi G, Abd-El-Aziz A, Kibenge FST, Kibenge MJT, Cohen AM, Esparza-Gonsalez B, McD￮ L, Montelpare WJ.Adipose-derived stem cells (ADSCs) are used in tissue regeneration therapies. The objective of this study is to identify stable reference genes (RGs) for use in gene expression studies in a characterized equine adipose-derived mesenchymal stem cell (EADMSC) differentiation model. ADSCs were differentiated into adipocytes (ADs) or osteoblasts (OBs), and the proteomes from these cells were analyzed by liquid chromatography tandem mass spectrometry. Proteins that were stably expressed in all three cells types were identified, and the mRNA expression stabilities for their corresponding genes were ...
Knych HK, Harrison LM, Steinmetz SJ, Chouicha N, Kass PH.Clenbuterol, a beta2-adrenergic receptor agonist, is used therapeutically to treat respiratory conditions in the horse. However, by virtue of its mechanism of action it has been suggested that clenbuterol may also have repartitioning affects in horses and as such the potential to affect performance. Clenbuterol decreases the percent fat and increases fat-free mass following high dose administration in combination with intense exercise in horses. In the current study, microarray analysis and real-time PCR were used to study the temporal effects of low and high dose chronic clenbuterol administr...
Salau J, Hildebrandt F, Czycholl I, Krieter J.Sensors delivering information on the position of farm animals have been widely used in precision livestock farming. Global Positioning System (GPS) sensors are already known from applications in military, private and commercial environments, and their application in animal science is increasing. However, as trade-offs between sensor cost, battery life and sensor weight have to be made, GPS based studies scheduling long data collection periods and including a high number of animals, have to deal with problems like high hardware costs and data disruption during recharging of sensors. Furthermor...
Di Bernardo G, Del Gaudio S, Galderisi U, Cipollaro M.Ancient DNA extracted from 2000 year-old equine bones was examined in order to amplify mitochondrial and nuclear DNA fragments. A specific equine satellite-type sequence representing 3.7%-11% of the entire equine genome, proved to be a suitable target to address the question of the presence of aDNA in ancient bones. The PCR strategy designed to investigate this specific target also allowed us to calculate the molecular weight of amplifiable DNA fragments. Sequencing of a 370 bp DNA fragment of mitochondrial control region allowed the comparison of ancient DNA sequences with those of modern hor...
Varona L, Legarra A.(1) Background: Ranking traits are used commonly for breeding purposes in several equine populations; however, implementation is complex, because the position of a horse in a competition event is discontinuous and is influenced by the performance of its competitors. One approach to overcoming these limitations is to assume an underlying Gaussian liability that represents a horse's performance and dictates the observed classification in a competition event. That approach can be implemented using Montecarlo Markov Chain (McMC) techniques with a procedure known as the Thurstonian model. (2) Metho...
Vimercati S, Elli S, Jagannathan V, Pandey AV, Peduto N, Leeb T, Mevissen M.Cytochrome P450 enzymes (CYPs) of the equine CYP3A subfamily are predominantly involved in drug metabolism. In this study, genetic variants of the equine CYP3A94, CYP3A95, and CYP3A97 were identified and characterized using in silico modeling and in vitro enzyme kinetics. The genomes of 81 horses were sequenced to obtain the genetic variants. Structural CYP modifications of the most frequent variants were analyzed in silico using the 3D-structures predicted by homology modeling. Enzyme kinetic analyses were performed using testosterone as substrate. Twenty genetic variants were found including...
Pintado CO, Friend M, Llanes D.This paper describes two anti-glycoprotein IIb/IIIa or CD41/61 murine monoclonal antibodies (Co.35E4 and Co.2oA1). The cellular distribution and apparent molecular weight of the antigen detected by these antibodies is consistent with their reaction with ruminant and equine glycoprotein IIb/IIIa. Biochemical analysis of the equine molecule using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) revealed bands of 24, 100 and 110 kDa under reducing conditions and 115 and 80 kDa under nonreducing conditions. Biochemical analysis of ruminant antigen revealed that the 24 kDa band...
Murungi EK, Kariithi HM.The apicomplexan parasite Sarcocystis neurona causes equine protozoal myeloencephalitis (EPM), a degenerative neurological disease of horses. Due to its host range expansion, S. neurona is an emerging threat that requires close monitoring. In apicomplexans, protein kinases (PKs) have been implicated in a myriad of critical functions, such as host cell invasion, cell cycle progression and host immune response evasion. Here, we used various bioinformatics methods to define the kinome of S. neurona and phylogenetic relatedness of its PKs to other apicomplexans. We identified 97 putative PKs clust...
Cui Z, Shi J, Li Y.The spent wheat straw from horse stall bedding has lower cellulose and hemicellulose contents, but higher volatile fatty acid content than raw wheat straw. Biogas production from solid-state anaerobic digestion (SS-AD) of spent wheat straw and raw wheat straw was compared in this study. The SS-AD tests were conducted at 22% total solids (TS) content using inoculum from a liquid AD system at three feedstock-to-inoculum (F/I) ratios of 2.0, 4.0, and 6.0. Daily methane yields of spent wheat straw peaked 8 and 3 days earlier than those of raw wheat straw at F/I ratios of 2.0 and 4.0, respectively....
Rathelot J, Canioni P, Bosc-Bierne I, Sarda L, Kamoun A, Kaptein R, Cozzone PJ.Porcine and equine colipases have been submitted to mild tryptic digestion. Proteolysis occurs at the Arg5-Gly6 bond with the loss of the N-terminal pentapeptide. Studies of native and trypsin-treated colipases by circular dichroism and laser chemically induced dynamic nuclear polarization indicate that proteolysis induces conformational changes in the region of the tyrosine cluster. Experiments in the presence of phospholipid provide further evidence showing that these residues are in or close to the region of the protein interacting with aggregated lipids. Kinetic studies of the reaction of ...
Journée SL, Journée HL, Reed SM, Berends HI, de Bruijn CM, Delesalle CJG.Adhesive surface electrodes are worthwhile to explore in detail as alternative to subcutaneous needle electrodes to assess myogenic evoked potentials (MEP) in human and horses. Extramuscular characteristics of both electrode types and different brands are compared in simultaneous recordings by also considering electrode impedances and background noise under not mechanically secured (not taped) and taped conditions. Methods: In five ataxic and one non-ataxic horses, transcranial electrical MEPs, myographic activity, and noise were simultaneously recorded from subcutaneous needle (three brands) ...
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...
Pretorius A, Faber FE, van Kleef M.Development of African horsesickness (AHS) subunit vaccines will have to include a rational approach that uses knowledge of how the virus interacts with the host immune system. The global in vivo immune response induced by attenuated AHSV serotype 4 in horses was characterised using transcriptome sequencing. PBMC were collected with 24h intervals for four days after inoculation and four days after a second boost, 21 days later. Transcriptome data were normalised to the day 0 naïve transcriptome and up- or down-regulated immune genes identified using the CLC workbench. Peak expression was obse...
Dunstan RH, Macdonald MM, Thorn B, Wood D, Roberts TK.Horses in heavy training in preparation for racing and competition have increased metabolic demands to support the more intensive levels of exercise and recovery. However, little is known at the metabolic level about amino acid turnover and the specific alterations of demand caused by high intensity exercise. During exercise, certain amino acids are required in greater quantities due to disproportionate losses via excretory systems and usage in biosynthetic pathways. This investigation has built a theoretical computer model in an attempt to bring together the published rates of protein intake ...
Liu L, Yu W, Cai K, Ma S, Wang Y, Ma Y, Zhao H. () is a zoonotic opportunistic pathogen that can cause life-threatening infections. The rapid evolution of multidrug-resistant and the fact that there is no currently licensed effective vaccine against warrant the need for vaccine development. Reverse vaccinology (RV), which involves screening a pathogen's entire genome and proteome using various web-based prediction tools, is considered one of the most effective approaches for identifying vaccine candidates. Here, we performed a pangenome analysis to determine the core proteins of . We then used the RV approach to examine the subcellular l...
DiMaio Knych HK, Stanley SD.Members of the CYP2D family constitute only about 2-4% of total hepatic CYP450s, however, they are responsible for the metabolism of 20-25% of commonly prescribed therapeutic compounds. CYP2D enzymes have been identified in a number of different species. However, vast differences in the metabolic activity of these enzymes have been well documented. In the horse, the presence of a member of the CYP2D family has been suggested from studies with equine liver microsomes, however its presence has not been definitively proven. In this study a cDNA encoding a novel CYP2D enzyme (CYP2D50) was cloned f...
Schröper F, Baumann A, Offenhäusser A, Mayer D.During the last decade protein electrochemistry at miniaturized electrodes has become important not only for functional studies of the charge transfer properties of redox proteins but also for fostering the development of sensitive biosensor and bioelectronic devices. One of the major challenges in this field is the directed coupling between electronic and biologically active components. A prerequisite for a fast and reversible electron transfer between electrode and protein is that the protein can be bound to the electrode in a favourable orientation. We examined electrostatic and bioaffinity...
Yu J, Wang Z, Wang F, Yang G, Cheng J, Ji C, Li M, Liu B, Wang Y, Dang R.Testicular development and spermatogenesis are tightly regulated by the number of genes and noncoding genes, and mRNAs and lncRNAs play vital roles in regulating posttranscriptional gene expression. However, mRNAs and lncRNAs have not been systematically identified in the testes of donkeys. In this study, mRNA and lncRNA expression profiles in the testes of DeZhou donkeys between 2 months and 2 years of age were comprehensively analysed by RNA sequencing. We identified 56,605 lncRNAs and 61,857 mRNAs by gene expression analysis, and 21,845 lncRNAs (p < .05) and 14,109 mRNAs (p < .0...
