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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.
Rapid method for the simultaneous determination of six ionophores in feed by liquid chromatography/mass spectrometry. A simple and highly sensitive LC/MS method was developed for the simultaneous determination of six ionophores--lasalocid, monensin, laidlomycin, maduramycin, salinomycin, and narasin--in feed. The procedure involved extraction of 1 g of feed with 4 mL of methanol-water (9 + 1, v/v) by shaking on a platform shaker for 45 min. After centrifugation, the extracts were diluted with methanol-water (75 + 25, v/v) and analyzed without any cleanup. The analysis was performed on a Betasil C18 column (150 x 4.6 mm id, 5 pm particle size) connected to an LC/MS system operated in the atmospheric pressure c...
Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq. Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes derived from transcriptomes. Results: We present a large-scale analysis of whole transcriptome data. We sequenced the whole mRNA from the blood and muscle tissues of six thoroughbred horses before and after exercise. By comparing current genome annotations, we identified 32,361 unigene cluster...
Finite element analysis of stress in the equine proximal phalanx. To improve understanding of the internal structure of the proximal phalanx (P1), response of the bone to load and possible relation to the pathogenesis of fractures in P1. Objective: To model the P1 and replicate the loads experienced by the bone in stance, walk, trot and gallop using finite element analysis. Methods: The geometry of the P1 was captured using micro-computed tomography (μCT) and was reconstructed in 3 dimensions. Values for material properties and forces experienced at stance, walk, trot and gallop were taken from the literature and were applied to the reconstructed model. Usi...
Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice. Locomotion in mammals relies on a central pattern-generating circuitry of spinal interneurons established during development that coordinates limb movement. These networks produce left-right alternation of limbs as well as coordinated activation of flexor and extensor muscles. Here we show that a premature stop codon in the DMRT3 gene has a major effect on the pattern of locomotion in horses. The mutation is permissive for the ability to perform alternate gaits and has a favourable effect on harness racing performance. Examination of wild-type and Dmrt3-null mice demonstrates that Dmrt3 is exp...
Feasibility of infrared spectroscopy with pattern recognition techniques to identify a subpopulation of mares at risk of producing foals diagnosed with failure of transfer of passive immunity. To assess the feasibility of a serum-based test using infrared spectroscopy to identify a subpopulation of mares at risk of producing foals susceptible to failure of passive transfer of immunity (FPT) because of mare-associated factors. Methods: Serum was collected from post-parturient mares (n = 126) and their foals at 24-72 h of age. A radial immunodiffusion IgG test was used to determine each foal's serum IgG concentration. Infrared absorbance spectra of dam sera were collected in the wave number range of 400-4000 cm(-1). Following data preprocessing, pattern recognition techniques were use...
Structural and oxygen binding properties of dimeric horse myoglobin. 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...
Transcriptome analyses of bovine, porcine and equine endometrium during the pre-implantation phase. Different reproductive strategies evolved in various mammalian groups to achieve recognition, establishment and maintenance of pregnancy. The complexity of these processes is reflected by a high incidence of embryonic loss during this critical period in many mammalian species. Besides studies in mice and humans a number of transcriptome studies of endometrial tissue samples and also of early embryos have been performed during the pre-implantation phase in cattle, swine and horse to identify genes associated with embryo-maternal interaction. Results of these studies are reviewed and compared be...
Characterisation of retroviruses in the horse genome and their transcriptional activity via transcriptome sequencing. The recently released draft horse genome is incompletely characterised in terms of its repetitive element profile. This paper presents characterisation of the endogenous retrovirus (ERVs) of the horse genome based on a data-mining strategy using murine leukaemia virus proteins as queries. 978 ERV gene sequences were identified. Sequences were identified from the gamma, epsilon and betaretrovirus genera. At least one full length gammaretroviral locus was identified, though the gammaretroviral sequences are very degenerate. Using these data the RNA expression of these ERVs were derived from RNA ...
A computer-assisted microscopic analysis of bone tissue developed inside a polyactive polymer implanted into an equine articular surface. One of the most promising applications for the restoration of small or moderately sized focal articular lesions is mosaicplasty (MP). Although recurrent hemarthrosis is a rare complication after MP, recently, various strategies have been designed to find an effective filling material to prevent postoperative bleeding from the donor site. The porous biodegradable polymer Polyactive (PA; a polyethylene glycol terephthalate - polybutylene terephthalate copolymer) represents a promising solution in this respect. A histological evaluation of the longterm PA-filled donor sites obtained from 10 exper...
Genetic Diversity of mtDNA D-loop and Maternal Origin of Three Chinese Native Horse Breeds. In order to protect the genetic resource of native horse breeds, the genetic diversity of mitochondrial DNA (mtDNA) D-loop of three native horse breeds in western China were investigated. Forty-three 600 bp mtDNA D-loop sequences were analyzed by PCR and sequencing techniques, 33 unique haplotypes with 70 polymorphic sites were detected in these horses, which account for 11.67% of 600 bp sequence analyzed, showing the abundant genetic diversity of the three native horse breeds in western China. The Neighbour-Joining (NJ) phylogenetic tree based on 247 bp of 43 D-loop sequences demonstrated the...
Pedigrees as a source of information in mtDNA studies of dogs and horses. The goal of this study was to demonstrate the usefulness of pedigree data in studies of mitochondrial DNA diversity in dogs and horses. Pedigree information allows for precisely choosing animals with distinct haplotypes for analysis, makes it possible to find rare haplotypes present exclusively in single individuals and helps to evaluate haplotype frequencies at the present and in the past. Estimating founder contributions to gene pools enables evaluating the parts of gene pools observed with the help of mtDNA analysis. An important aspect is also the financial benefits: using pedigree data, r...
The xCELLigence system for real-time and label-free analysis of neuronal and dermal cell response to equine herpesvirus type 1 infection. Real-time cell electronic sensing (RT-CES) based on impedance measurements is an emerging technology for analyzing the status of cells in vitro. It allows label-free, real time monitoring of the biological status of cells. The present study was designed to assess dynamic data on the cell processes during equine herpesvirus type 1 (EHV-1) infection of ED (equine dermal) cells and primary murine neuronal cell culture. We have demonstrated that the xCELLigence system with dynamic monitoring can be used as a rapid diagnostic tool both to analyze cellular behavior and to investigate the effect of v...
Culture and characterisation of equine peripheral blood mesenchymal stromal cells. Although the use of mesenchymal stromal cells (MSCs) for the treatment of orthopaedic injuries in horses has been reported, no official guidelines exist that classify a particular cell as an equine MSC. Given the limited characterisation of peripheral blood (PB)-derived equine MSCs in particular, this study aimed to provide more detailed information in relation to this cell type. Mesenchymal stromal cells were isolated from equine PB samples and colony forming unit (CFU) assays as well as population doubling times (PDTs) (from P(0) to P(10)) were performed. Two types of colonies, 'fingerprint'...
Evaluation of recombinant proteins of Burkholderia mallei for serodiagnosis of glanders. Glanders is a contagious disease caused by the Gram-negative bacillus Burkholderia mallei. The number of equine glanders outbreaks has increased steadily during the last decade. The disease must be reported to the Office International des Epizooties, Paris, France. Glanders serodiagnosis is hampered by the considerable number of false positives and negatives of the internationally prescribed tests. The major problem leading to the low sensitivity and specificity of the complement fixation test (CFT) and enzyme-linked immunosorbent assay (ELISA) has been linked to the test antigens currently us...
Accuracy and precision of equine gait event detection during walking with limb and trunk mounted inertial sensors. The increased variations of temporal gait events when pathology is present are good candidate features for objective diagnostic tests. We hypothesised that the gait events hoof-on/off and stance can be detected accurately and precisely using features from trunk and distal limb-mounted Inertial Measurement Units (IMUs). Four IMUs were mounted on the distal limb and five IMUs were attached to the skin over the dorsal spinous processes at the withers, fourth lumbar vertebrae and sacrum as well as left and right tuber coxae. IMU data were synchronised to a force plate array and a motion capture sy...
The equine intestinal microbiome. The equine intestinal tract contains a complex microbial population (microbiota) that plays an important role in health and disease. Despite the undeniable importance of a 'normal' microbiota, understanding of the composition and function of this population is currently limited. As methods to characterize the microbiota and its genetic makeup (the microbiome) have evolved, the composition and complexity of this population are starting to be revealed. As is befitting a hindgut fermenter, members of the Firmicutes phylum appear to predominate, yet there are significant populations of numerous ot...
CACG: a database for comparative analysis of conjoined genes. A conjoined gene is defined as one formed at the time of transcription by combining at least part of one exon from each of two or more distinct genes that lie on the same chromosome, in the same or opposite orientation, which translate independently into different proteins. We comparatively studied the extent of conjoined genes in thirteen genomes by analyzing the public databases of expressed sequence tags and mRNA sequences using a set of computational tools designed to identify conjoined genes on the same DNA strand or opposite DNA strands of the same genomic locus. The CACG database, avail...
Improving the performance of true single molecule sequencing for ancient DNA. Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and extinct species. Recently, third generation Helicos sequencing platforms, which perform true Single-Molecule DNA Sequencing (tSMS), have shown great potential for sequencing DNA molecules from Pleistocene fossils. Here, we aim at improving even further the performance of tSMS for ancient DNA by testing two novel tSMS template preparation methods for Pleistocene bone fossils, namely oligonucl...
Comparison of the efficacy of alpha-lactalbumin from equine, bovine, and human milk in the growth of intestinal IEC-6 cells. Native alpha-lactalbumins (α-LA) from equine, bovine, and human milk were not cytotoxic. However, after treatment with trifluoroethanol (TFE), all three α-LAs exhibited cytotoxicity. Toxic potencies were distinctly different among them. Equine α-LA was the most robust, bovine α-LA was moderate, and human α-LA was weak. There were no significant structural changes as between the native and the TFE-treated α-LAs.
IL-22 is expressed by the invasive trophoblast of the equine (Equus caballus) chorionic girdle. The invasive trophoblast cells of the equine placenta migrate into the endometrium to form endometrial cups, dense accumulations of trophoblast cells that produce equine chorionic gonadotropin between days 40 and 120 of normal pregnancy. The mechanisms by which the trophoblast cells invade the endometrium while evading maternal immune destruction are poorly defined. A gene expression microarray analysis performed on placental tissues obtained at day 34 of gestation revealed a >900-fold upregulation of mRNA encoding the cytokine IL-22 in chorionic girdle relative to noninvasive chorion. Quan...
Genetic diversity and admixture among Canadian, Mountain and Moorland and Nordic pony populations. As part of the requirements of the Convention on Biological Diversity, Canada has been investigating the genetic diversity of its native equine and pony populations. Along with examining four indigenous Canadian equine populations (Canadian horse, Lac La Croix pony, Newfoundland pony and Sable Island population), another 10 Mountain and Moorland, three Nordic, four horse and two feral equine populations (thought to have influenced some pony breeds) were also investigated. In total, 821 individuals were genotyped at 38 microsatellite loci. Results of the analysis of molecular variance indicated...
Innovative approach to investigating the microstructure of calcified tissues using specular reflectance Fourier transform-infrared microspectroscopy and discriminant analysis. Although bone fracture has become a serious global health issue, current clinical assessments of fracture risk based on bone mineral density are unable to accurately predict whether an individual is likely to suffer a fracture. There is increasing recognition that the chemical structure and composition, or microstructure, of mineralized tissues has an important role to play in determining the fracture resistance of bone. The objective of this preliminary study was to evaluate the use of specular reflectance Fourier transform infrared (SR FT-IR) microspectroscopy in conjunction with discriminan...
A simplified PCR-based method for detection of gray coat color allele in horse. Coat color of gray horses is associated with a 4.6-kb duplication, which can be determined using PCR amplification of about 5-kb DNA fragment. In practice, this means that amplification might fail frequently. Therefore, a novel genetic screening method based on amplification of the 246 bp DNA fragment has been developed.
Accuracy and precision of computer-assisted analysis of bone density via conventional and digital radiography in relation to dual-energy x-ray absorptiometry. To evaluate the precision and accuracy of assessing bone mineral density (BMD) by use of mean gray value (MGV) on digitalized and digital images of conventional and digital radiographs, respectively, of ex vivo bovine and equine bone specimens in relation to the gold-standard technique of dual-energy x-ray absorptiometry (DEXA). Methods: Left and right metatarsal bones from 11 beef cattle and right femurs from 2 horses. Methods: Bovine specimens were imaged by use of conventional radiography, whereas equine specimens were imaged by use of computed radiography (digital radiography). Each specim...
Identification of copy number variants in horses. Copy number variants (CNVs) represent a substantial source of genetic variation in mammals. However, the occurrence of CNVs in horses and their subsequent impact on phenotypic variation is unknown. We performed a study to identify CNVs in 16 horses representing 15 distinct breeds (Equus caballus) and an individual gray donkey (Equus asinus) using a whole-exome tiling array and the array comparative genomic hybridization methodology. We identified 2368 CNVs ranging in size from 197 bp to 3.5 Mb. Merging identical CNVs from each animal yielded 775 CNV regions (CNVRs), involving 1707 protein- and...
Direct electrochemistry of novel affinity-tag immobilized recombinant horse heart cytochrome c. 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...
Characterization of cytochrome b diversity in Chinese domestic horses. Previous mitochondrial DNA (mtDNA) D-loop and microsatellite studies have shown that Chinese horses have multiple maternal origins and high genetic diversity. To better characterize maternal genetic origins and diversity of Chinese domestic horses, we conducted a comprehensive analysis of 407 complete 1140 bp sequences of the horse mitochondrially encoded cytochrome b (CYTB) gene, including 323 horses from 13 Chinese indigenous breeds and 84 reference sequences from GenBank. A total of 114 haplotypes were identified, of which 73 appeared among the 13 Chinese horse breeds. The high mitochondria...
Mathematical modelling of tissue formation in chondrocyte filter cultures. In the field of cartilage tissue engineering, filter cultures are a frequently used three-dimensional differentiation model. However, understanding of the governing processes of in vitro growth and development of tissue in these models is limited. Therefore, this study aimed to further characterise these processes by means of an approach combining both experimental and applied mathematical methods. A mathematical model was constructed, consisting of partial differential equations predicting the distribution of cells and glycosaminoglycans (GAGs), as well as the overall thickness of the tissue....
