Topic:Bioinformatics
Bioinformatics in horses involves the application of computational tools and techniques to analyze and interpret biological data related to equine species. This interdisciplinary field integrates biology, computer science, and information technology to study genetic, genomic, and proteomic information in horses. Bioinformatics can be used to investigate genetic variations, understand disease mechanisms, and assist in the development of targeted therapies and breeding programs. Key areas of focus include genome sequencing, gene expression analysis, and the identification of genetic markers associated with specific traits or conditions. This page compiles peer-reviewed research studies and scholarly articles that explore the application and impact of bioinformatics on equine genetics, health, and breeding.
Alternative solution of virtual biomodeling based on CT-scans. In this paper, an alternative method is presented to convert computed tomography (CT)-scans into 3D biomodels. The CT-data of an equine spine was converted into TIF format to work with it in a 2D CAD program. Then the bony structure has been marked manually with closed splines and saved as IGS files for the next procedure with 3D CAD software to create virtual biomodels of every single bone. Therefore, the different layers of the CT-scans were positioned in correct distance and then a closed surface was created to cover all spline-curves. Finally, the cover was filled up with material to creat...
A genome scan for positive selection in thoroughbred horses. Thoroughbred horses have been selected for exceptional racing performance resulting in system-wide structural and functional adaptations contributing to elite athletic phenotypes. Because selection has been recent and intense in a closed population that stems from a small number of founder animals Thoroughbreds represent a unique population within which to identify genomic contributions to exercise-related traits. Employing a population genetics-based hitchhiking mapping approach we performed a genome scan using 394 autosomal and X chromosome microsatellite loci and identified positively selec...
In silico detection and characteristics of novel microRNA genes in the Equus caballus genome using an integrated ab initio and comparative genomic approach. The importance of microRNAs at the post-transcriptional regulation level has recently been recognized in both animals and plants. We used the simple but effective sequential method of first Blasting known animal miRNAs against the horse genome and then using the located candidates to search for novel miRNAs by RNA folding method in the vicinity (+ -500 bp) of the candidates. Here, a total of 407 novel horse miRNA genes including 354 mature miRNAs were identified, of these, 75 miRNAs were grouped into 32 families based on seed sequence identity. MiRNA genes tend to be present as clusters in som...
Equine thrombospondin II and secreted protein acidic and cysteine-rich in a model of normal and pathological wound repair. Wound healing in horses is complicated, particularly when wounds are on the limb. The objectives of this study were to clone equine thrombospondin II (THBS2) and secreted protein acidic and cysteine-rich (SPARC) cDNAs and to compare the spatiotemporal expression of mRNAs and proteins during repair of body and limb wounds. These molecules were targeted in view of their potential biological contribution to angiogenesis, which is exacerbated during the repair of limb wounds in horses. Cloning was achieved by screening size-selected cDNA libraries previously derived from 7-day-old wounds. Expressi...
Determination of internal control for gene expression studies in equine tissues and cell culture using quantitative RT-PCR. Quantitative reverse transcription polymerase chain reaction (RT-PCR) has become a basic, reliable and sensitive modern technique, in both biological research and clinical diagnosis, for investigation of gene expression and validation of cDNA microarray analysis. Accurate mRNA quantification using quantitative RT-PCR commonly requires data normalization through stable housekeeping genes (HKGs). Selection of HKGs for data normalization is critical for accurate mRNA quantification. Our objective was to evaluate a set of candidate HKGs as internal controls for gene expression studies using quanti...
Structural model of the Rev regulatory protein from equine infectious anemia virus. Rev is an essential regulatory protein in the equine infectious anemia virus (EIAV) and other lentiviruses, including HIV-1. It binds incompletely spliced viral mRNAs and shuttles them from the nucleus to the cytoplasm, a critical prerequisite for the production of viral structural proteins and genomic RNA. Despite its important role in production of infectious virus, the development of antiviral therapies directed against Rev has been hampered by the lack of an experimentally-determined structure of the full length protein. We have used a combined computational and biochemical approach to gen...
Nucleotide structure and expression of equine pigment epithelium-derived factor during repair of experimentally induced wounds in horses. To clone full-length equine pigment epithelium-derived factor (PEDF) complementary DNA (cDNA) and to evaluate its temporal expression during repair of wounds in horses. Methods: 4 clinically normal 2-to 3-year-old Standardbred mares. Methods: Full-length equine PEDF cDNA was cloned by screening size-selected cDNA libraries derived from biopsy specimens obtained from the wound edge 7 days after experimental creation of a 6.25-cm(2) full-thickness wound in the skin of the lateral thoracic wall. Expression was evaluated in normal skin and in biopsy specimens obtained weekly from experimentally in...
[Applications of SSCP and HMA for polymorphic analysis of horse MHC-I alleles]. In this article, we report the analysis of genetic polymorphisms of horse MHC-I molecules by SSCP and HMA, which are methods based on the technique of polyacrylamide gel electrophoresis (PAGE). Our results showed that SSCP was not a suitable method for the analysis of genetic polymorphisms of horse MHC-I molecules due to the failure in generating satisfied separation of DNA fragments, even if experimental conditions were optimized. However, the HMA method produced clearly separated DNA fragments of horse MHC-I molecules, after the experimental conditions, such as the running temperature and th...
Novel interferon delta genes in mammals: cloning of one gene from the sheep, two genes expressed by the horse conceptus and discovery of related sequences in several taxa by genomic database screening. Interferons (IFNs) are cytokines of vertebrates with many biological effects including antiviral, immunoregulatory and antiproliferative activities. Among them, mammalian type I IFNs represents a large family of related proteins, mainly virus-inducible, divided in 10 distinct subfamilies named alpha, beta, omega, delta, epsilon, alphaomega, nu, tau, kappa and zeta (or Limitin). Some type I IFN subfamilies are physiologically expressed by the conceptus during early pregnancy in ungulates. This is the case in ruminants with IFN-tau (which triggers the maintenance of the maternal corpus luteum du...
Different mechanisms of spinal fusion using equine bone protein extract, rhBMP-2 and autograft during the process of anterior lumbar interbody fusion. To elucidate the molecular mechanisms of spinal fusion with different graft materials during an anterior lumbar interbody fusion, we examined the gene-expression profiles after implantation of equine bone protein extract, rhBMP-2 and autograft using microarray technology and data analysis, including hierarchical clustering, self-organizing maps (SOM), KEGG pathway and Biological process GO analyses in a porcine model. The results suggest that equine bone protein extract exhibited a more similar expression pattern with autograft than that of rhBMP-2. rhBMP-2 recruits progenitor cells, prolifera...
MRI-based inverse finite element approach for the mechanical assessment of patellar articular cartilage from static compression test. The mechanical property of articular cartilage determines to a great extent the functionality of diarthrodial joints. Consequently, the early detection of mechanical and, thus, functional changes of cartilage is crucial for preventive measures to maintain the mobility and the quality of life of individuals. An alternative to conventional mechanical testing is the inverse finite element approach, enabling non-destructive testing of the tissue. We evaluated a method for the assessment of the equilibrium material properties of the patellar cartilage based on magnetic resonance imaging during pate...
Expression microarrays in equine sciences. Microarrays have become an important research tool for life science researchers. Expression microarrays are capable of profiling the gene expression pattern of tens of thousands of genes in a single experiment. It appears to be the platform of choice for parallel gene expression profiling. Various equine-specific gene expression microarrays have been generated and used. However, homologous microarrays are not yet commercially available for the horse. An alternative is the use of heterologous microarrays, mainly microarrays specific for mice or humans. Although the use of microarrays in equine ...
Development of an ELA-DRA gene typing method based on pyrosequencing technology. 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...
Complementary DNA cloning, functional expression and characterization of a novel cytochrome P450, CYP2D50, from equine liver. 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...
Elucidation of the MD-2/TLR4 interface required for signaling by lipid IVa. LPS signals through a membrane bound-complex of the lipid binding protein MD-2 and the receptor TLR4. In this study we identify discrete regions in both MD-2 and TLR4 that are required for signaling by lipid IVa, an LPS derivative that is an agonist in horse but an antagonist in humans. We show that changes in the electrostatic surface potential of both MD-2 and TLR4 are required in order that lipid IVa can induce signaling. In MD-2, replacing horse residues 57-66 and 82-89 with the equivalent human residues confers a level of constitutive activity on horse MD-2, suggesting that conformational...
A novel application of quantile regression for identification of biomarkers exemplified by equine cartilage microarray data. Identification of biomarkers among thousands of genes arrayed for disease classification has been the subject of considerable research in recent years. These studies have focused on disease classification, comparing experimental groups of effected to normal patients. Related experiments can be done to identify tissue-restricted biomarkers, genes with a high level of expression in one tissue compared to other tissue types in the body. Results: In this study, cartilage was compared with ten other body tissues using a two color array experimental design. Thirty-seven probe sets were identified as...
Developments in stallion semen evaluation. The conventional approach to evaluation of stallion semen dates back several decades, and includes evaluation of spermatozoal concentration, semen volume, spermatozoon morphological characteristics, and spermatozoal motility patterns initially and following in-vitro storage. While an analysis performed in this manner does have predictive value, incorporation of some more newly developed techniques may improve the predictive value of the examination. This communication addresses some newer tests that can be applied today for evaluation of semen, as well some tests that may be available in the c...
Exercise induced stress in horses: selection of the most stable reference genes for quantitative RT-PCR normalization. Adequate stress response is a critical factor during athlete horses' training and is central to our capacity to obtain better performances while safeguarding animal welfare. In order to investigate the molecular mechanisms underlying this process, several studies have been conducted that take advantage of microarray and quantitative real-time PCR (qRT-PCR) technologies to analyse the expression of candidate genes involved in the cellular stress response. Appropriate application of qRT-PCR, however, requires the use of reference genes whose level of expression is not affected by the test, by ge...
A BAC contig map over the proximal approximately 3.3 Mb region of horse chromosome 21. A total of 207 BAC clones containing 155 loci were isolated and arranged into a map of linearly ordered overlapping clones over the proximal part of horse chromosome 21 (ECA21), which corresponds to the proximal half of the short arm of human chromosome 19 (HSA19p) and part of HSA5. The clones form two contigs - each corresponding to the respective human chromosomes - that are estimated to be separated by a gap of approximately 200 kb. Of the 155 markers present in the two contigs, 141 (33 genes and 108 STS) were generated and mapped in this study. The BACs provide a 4-5x coverage of the regio...
Characterization of clinically-attenuated Burkholderia mallei by whole genome sequencing: candidate strain for exclusion from Select Agent lists. Burkholderia mallei is an understudied biothreat agent responsible for glanders which can be lethal in humans and animals. Research with this pathogen has been hampered in part by constraints of Select Agent regulations for safety reasons. Whole genomic sequencing (WGS) is an apt approach to characterize newly discovered or poorly understood microbial pathogens. Results: We performed WGS on a strain of B. mallei, SAVP1, previously pathogenic, that was experimentally infected in 6 equids (4 ponies, 1 mule, 1 donkey), natural hosts, for purposes of producing antibodies. Multiple high inocula wer...
Potential applications of equine genomics in dissecting diseases and fertility. Following the recent development of high-resolution gene maps and generation of several basic tools and resources to use them in analyzing traits that are economically important to horse owners, genome analysis in horses is witnessing a shift towards developing an ability to analyze complex traits. The likelihood of this happening in the very near future is great, mainly because of the recent availability of the whole genome sequence in the horse. The latter has triggered the development of novel tools like SNP-chip and expression arrays that will permit rapid genome-wide analysis. While these...
Glycogen synthase (GYS1) mutation causes a novel skeletal muscle glycogenosis. Polysaccharide storage myopathy (PSSM) is a novel glycogenosis in horses characterized by abnormal glycogen accumulation in skeletal muscle and muscle damage with exertion. It is unlike glycogen storage diseases resulting from known defects in glycogenolysis, glycolysis, and glycogen synthesis that have been described in humans and domestic animals. A genome-wide association identified GYS1, encoding skeletal muscle glycogen synthase (GS), as a candidate gene for PSSM. DNA sequence analysis revealed a mutation resulting in an arginine-to-histidine substitution in a highly conserved region of G...
Stereological characteristics of the equine accessory nerve. Stereological techniques have been increasingly employed for assessment and characterization of neuromuscular diseases in humans and animals. As an adjunct to histopathology, morphometrical algorithms provide quantitative evidence of the peripheral nerve composition, thereby shedding light on its fibre characteristics and basic electrophysiological properties. In the horse, stereological investigations already have focussed on the recurrent laryngeal, deep peroneal and lateral palmar nerves (LPN). Of these, only the latter is suitable for taking biopsies in clinical settings, however, it does ...
Determination of IGF-I in horse plasma by LC electrospray ionisation mass spectrometry. The insulin-like-growth factor (IGF-I) peptide is considered to be the main indirect marker for growth hormone administration (GH) in a horse. Further to a previous investigation on measurement of IGF-I in plasma samples by mass spectrometry, this study focuses on quantitative and qualitative analysis of intact IGF-I in horse plasma. First, protein-transposing software has been developed for IGF-I to facilitate its quantification by HPLC-electrospray-ion-trap mass spectrometry. Second, product-ion scan experiments on IGF-I have been conducted on standard samples, non-fortified equine plasma sa...
Equine CTNNB1 and PECAM1 nucleotide structure and expression analyses in an experimental model of normal and pathological wound repair. Wound healing in horses is fraught with complications. Specifically, wounds on horse limbs often develop exuberant granulation tissue which behaves clinically like a benign tumor and resembles the human keloid in that the evolving scar is trapped in the proliferative phase of repair, leading to fibrosis. Clues gained from the study of over-scarring in horses should eventually lead to new insights into how to prevent unwanted scar formation in humans. cDNA fragments corresponding to CTNNB1 (coding for beta-catenin) and PECAM1, genes potentially contributing to the proliferative phase of repair,...
Molecular cloning and characterization of the alphaX subunit from CD11c/CD18 horse integrin. This work reports the cloning and sequence determination of the horse alpha subunit of the integrin CD11c/CD18, a marker of dendritic cells. A cDNA clone of 4582 base pairs was obtained. It encodes a protein segment of 1086 amino acid residues of the extracellular domain with 10 potential sites of glycosylation, a transmembrane domain of 32 residues and a C-terminal cytoplasmic tail of 24 residues. A phylogenetic analysis of this integrin shows close similarity (83%) with that of Canis familiaris.
Molecular characterization and chromosomal assignment of equine cartilage derived retinoic acid sensitive protein (CD-RAP)/melanoma inhibitory activity (MIA). Cartilage-derived retinoic acid sensitive protein (CD-RAP) also known as melanoma inhibitory activity (MIA) has already been established as a marker for chondrocyte differentiation and a number of cancerous conditions in humans. Studies have also shown that CD-RAP/MIA is a potential marker of joint disease. The objective of this study was to characterize the equine CD-RAP/MIA gene and thus make it available as a marker in cartilage research and clinical studies. Gene analysis revealed that the equine gene (GenBank accession no. EF679787) consists of four exons and three introns, and the homolo...
A hidden Markov model-based stride segmentation technique applied to equine inertial sensor trunk movement data. Inertial sensors are now sufficiently small and lightweight to be used for the collection of large datasets of both humans and animals. However, processing of these large datasets requires a certain degree of automation to achieve realistic workloads. Hidden Markov models (HMMs) are widely used stochastic pattern recognition tools and enable classification of non-stationary data. Here we apply HMMs to identify and segment into strides, data collected from a trunk-mounted six degrees of freedom inertial sensor in galloping Thoroughbred racehorses. A data set comprising mixed gait sequences from...
Estimation of genetic parameters and prediction of breeding values for multivariate threshold and continuous data in a simulated horse population using Gibbs sampling and residual maximum likelihood. Simulated horse data were used to compare multivariate estimation of genetic parameters and prediction of breeding values (BV) for categorical, continuous and molecular genetic data using linear animal models via residual maximum likelihood (REML) and best linear unbiased prediction (BLUP) and mixed linear-threshold animal models via Gibbs sampling (GS). Simulation included additive genetic values, residuals and fixed effects for one continuous trait, liabilities of four binary traits, and quantitative trait locus (QTL) effects and genetic markers with different recombination rates and polymor...
Characterization of the equine glycogen debranching enzyme gene (AGL): Genomic and cDNA structure, localization, polymorphism and expression. Glycogen debranching enzyme (AGL) is a multifunctional enzyme acting in the glycogen degradation pathway. In humans, the AGL activity deficiency causes a type III glycogen storage disease (Cori-Forbes disease). One particularity of AGL gene expression lies in the multiple alternative splicing in its 5' region. The AGL gene was localized on ECA5q14-q15. The sequence of the equine cDNA was determined to be 7.5 kb in length with an open reading frame of 4602 bp. The gene is 69 kb long and contains 35 exons. The equine AGL gene has an ubiquitous expression and presents five tissue-dependent cDNA v...