Topic:Cluster Analysis
Cluster analysis is a statistical method used to group objects, such as horses, into clusters based on similarities in their characteristics or behaviors. In equine research, cluster analysis can help identify patterns and relationships within large datasets, such as genetic information, performance metrics, or health parameters. This technique is valuable for categorizing horses into distinct groups for further analysis, such as distinguishing between different breeds, identifying common traits in performance horses, or assessing health risks. This page aggregates peer-reviewed research studies and scholarly articles that explore the application, methodologies, and findings of cluster analysis in various aspects of equine science.
Mapping of equine mesenchymal stromal cell surface proteomes for identification of specific markers using proteomics and gene expression analysis: an in vitro cross-sectional study. Stem cells have great potential for tissue regeneration, but before stem cell populations can be used in the clinic, it is crucial that the stem cells have been definitely characterized by a set of specific markers. Although there have been attempts to identify a set of immunophenotypic markers to characterize equine mesenchymal stromal cells (MSCs), immunophenotyping of equine MSCs is still challenging due to the limited availability of suitable antibodies of high quality and consistent performance across different laboratories. The aim of this study was to evaluate a strategy for mapping the...
Epidemiological situation of vesicular stomatitis virus infection in cattle in the state of Paraíba, semiarid region of Brazil. The aim of this survey was to estimate the apparent herd-level and animal-level prevalences, as well as to identify risk factors and spatial clustering of vesicular stomatitis virus (VSV) positive herds in the state of Paraíba, semiarid of Brazil. The state was divided into three sampling strata: Sertão, Borborema and Zona da Mata/Agreste. For each sampling stratum, herd-level and animal-level prevalences were estimated by a two-stage sampling survey. First, a pre-established number of herds (primary sampling units) were randomly selected; second, within each herd, a pre-established number o...
Prevalence of antibodies against Toxoplasma gondii and Neospora spp. in equids of Western Pará, Brazil. The present study aimed to determine the prevalence of antibodies against Toxoplasma gondii and Neospora spp. in equids raised for distinct purposes in the western state of Pará, Brazil, and to identify potential risk factors associated with parasite infection. A cross-sectional study was conducted with cluster sampling in 101 farms from 18 municipalities (farm horses). In visited municipalities, samples from sport and cart horses were included. Serum was obtained for detecting antibodies against T. gondii and Neospora spp. using indirect fluorescent antibody test, with a cut-off point of 1:6...
Characterization of the fecal microbiota of healthy horses. OBJECTIVE To characterize the fecal microbiota of horses and to investigate alterations in that microbiota on the basis of sample collection site (rectum vs stall floor), sample location within the fecal ball (center vs surface), and duration of environmental exposure (collection time). ANIMALS 6 healthy adult mixed-breed mares. PROCEDURES From each horse, feces were collected from the rectum and placed on a straw-bedded stall floor. A fecal ball was selected for analysis immediately after removal from the rectum and at 0 (immediately), 2, 6, 12, and 24 hours after placement on the stall floor...
Use of principle component analysis to quantitatively score the equine metabolic syndrome phenotype in an Arabian horse population. Equine metabolic syndrome (EMS), like human metabolic syndrome, comprises a collection of clinical signs related to obesity, insulin dysregulation and susceptibility to secondary inflammatory disease. Although the secondary conditions resulting from EMS can be life-threatening, diagnosis is not straightforward and often complicated by the presence of other concurrent conditions like pituitary pars intermedia dysfunction (PPID). In order to better characterize EMS, we sought to describe the variation within, and correlations between, typical physical and endocrine parameters for EMS. Utilizing ...
Analysis of Genetic Diversity and Structure of Guanzhong Horse Using Microsatellite Markers. To determine the genetic diversity and validate the pedigree record of Chinese Guanzhong horse, 67 individuals were genotyped with eight microsatellite markers. In our study, the mean observed and expected heterozygosities were 0.51 and 0.66, respectively. The mean observed number of alleles for the Guanzhong horse was 3.88. Nonetheless, the total value of F multiloci clearly indicates that about 0.5% of overall genetic variation is due to line founder differences, while differences among individuals are responsible for the remaining 99.5%. In addition, the polymorphic information content (PIC...
Retrospective analysis of insulin responses to standard dosed oral glucose tests (OGTs) via naso-gastric tubing towards definition of an objective cut-off value. Insulin dysregulation (ID) with basal or postprandial hyperinsulinemia is one of the key findings in horses and ponies suffering from the equine metabolic syndrome (EMS). Assessment of ID can easily be performed in clinical settings by the use of oral glucose challenge tests. Oral glucose test (OGT) performed with 1 g/kg bodyweight (BW) glucose administered via naso-gastric tube allows the exact administration of a defined glucose dosage in a short time. However, reliable cut-off values have not been available so far. Therefore, the aim of the study was to describe variations in insulin respo...
Population Networks Associated with Runs of Homozygosity Reveal New Insights into the Breeding History of the Haflinger Horse. Within the scope of current genetic diversity analyses, population structure and homozygosity measures are independently analyzed and interpreted. To enhance analytical power, we combined the visualization of recently described high-resolution population networks with runs of homozygosity (ROH). In this study, we demonstrate that this approach enabled us to reveal important aspects of the breeding history of the Haflinger horse. We collected high-density genotype information of 531 horses originating from 7 populations which were involved in the formation of the Haflinger, namely 32 Italian Ha...
Regulatory pathway analysis of coat color genes in Mongolian horses. Studies on the molecular genetics of horse skin pigmentation have typically focused on very few genes and proteins. In this study, we used Illumina sequencing to determine the global gene expression profiles in horses with white-colored coats and those with black-colored coats, with the goal of identifying novel genes that could regulate horse coat color. Results: Genes encoding ribosomal-associated proteins were highly expressed in horse skin. We found a total of 231 unigenes that were differentially expressed between horses with white coats and horses with black coats; 119 were down-regulate...
Hydrochemical and multivariate analysis of groundwater quality in the northwest of Sinai, Egypt. The northwestern coast of Sinai is home to many economic activities and development programs, thus evaluation of the potentiality and vulnerability of water resources is important. The present work has been conducted on the groundwater resources of this area for describing the major features of groundwater quality and the principal factors that control salinity evolution. The major ionic content of 39 groundwater samples collected from the Quaternary aquifer shows high coefficients of variation reflecting asymmetry of aquifer recharge. The groundwater samples have been classified into four clu...
Genetic diversity of Syrian Arabian horses. Although Arabian horses have been bred in strains for centuries and pedigrees have been recorded in studbooks, to date, little is known about the genetic diversity within and between these strains. In this study, we tested if the three main strains of Syrian Arabian horses descend from three founders as suggested by the studbook. We examined 48 horses representing Saglawi (n = 18), Kahlawi (n = 16) and Hamdani (n = 14) strains using the Equine SNP70K BeadChip. For comparison, an additional 24 Arabian horses from the USA and three Przewalski's horses as an out group were added. Observed h...
Application of Genomic Estimation Methods of Inbreeding and Population Structure in an Arabian Horse Herd. Horse breeders rely heavily on pedigrees for identification of ancestry in breeding stock. Inaccurate pedigrees may erroneously assign individuals to false lineages or breed memberships resulting in wrong estimates of inbreeding and coancestry. Moreover, discrepancies in pedigree records can lead breeders seeking to limit inbreeding into making misguided breeding decisions. Genome-wide SNPs provide a quantitative tool to aid in the resolution of lineage assignments and the calculation of genomic measures of relatedness. The aim of this project was to pilot a comparison between pedigree and gen...
LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells. Lipopolysaccharide (endotoxin, LPS) is a strong inducer of the innate immune response. It is widespread in our environment, e.g. in house dust and contributes to asthma. Compared to humans, horses are even more sensitive to LPS. However, data on LPS effects on the equine transcriptome are very limited. Using RNA-seq we analysed LPS-induced differences in the gene expression in equine peripheral blood mononuclear cells at the gene and gene-network level in two half-sib families and one group of unrelated horses. 24 h-LPS challenge of equine immune cells resulted in substantial changes in the t...
Genetic diversity of the Yonaguni horse based on polymorphisms in microsatellites and mitochondrial DNA. Thirty-two microsatellites and a mitochondrial DNA haplotypes of endangered Yonaguni horses were analyzed to establish a pedigree registration system and to understand their genetic diversity for planning effective conservation. Blood samples were collected from 78 of the 130 horses in existence, and DNA was extracted and genotyped. There were two major findings. One is that it is possible to use microsatellites for Yonaguni horse pedigree registration in the future because the power of exclusion of parentage testing is reliable at 0.999998. The second is the clarification of the current genet...
Profiling of exercise-induced transcripts in the peripheral blood cells of Thoroughbred horses. Transcriptome analyses based on DNA microarray technology have been used to investigate gene expression profiles in horses. In this study, we aimed to identify exercise-induced changes in the expression profiles of genes in the peripheral blood of Thoroughbred horses using DNA microarray technology (15,429 genes on 43,603 probes). Blood samples from the jugular vein were collected from six horses before and 1 min, 4 hr, and 24 hr after all-out running on a treadmill. After the normalization of microarray data, a total of 26,830 probes were clustered into four groups and 11 subgroups showing si...
Vertical transmission of hepatitis C virus-like non-primate hepacivirus in horses. Non-primate hepacivirus (NPHV), a recently discovered hepatotropic virus infecting horses, is phylogenetically the closest known homologue of hepatitis C virus (HCV). The main route for acquiring HCV infection in childhood is vertical transmission. However, nothing is known about the natural mode of transmission for NPHV. To investigate the possibility of vertically transmitted NPHV infection in horses, 20 Thoroughbred broodmares and their foals were monitored during foaling season 2015 until 6 months post-partum. Prepartal serum was taken from the mares, and during foaling umbilical cord bloo...
Comparison of a modified phenol/chloroform and commercial-kit methods for extracting DNA from horse fecal material. There are many choices for methods of extracting bacterial DNA for Next Generation Sequencing (NGS) from fecal samples. Here, we compare our modifications of a phenol/chloroform extraction method plus an inhibitor removal solution (C3) (ph/Chl+C3) to the PowerFecal® DNA Isolation Kit (MoBio-K). DNA quality and quantity coupled to NGS results were used to assess differences in relative abundance, Shannon diversity index, unique species, and principle coordinate analysis (PCoA) between biological replicates. Six replicate samples, taken from a single ball of horse feces manually collected from ...
Classification of Horse Gaits Using FCM-Based Neuro-Fuzzy Classifier from the Transformed Data Information of Inertial Sensor. In this study, we classify four horse gaits (walk, sitting trot, rising trot, canter) of three breeds of horse (Jeju, Warmblood, and Thoroughbred) using a neuro-fuzzy classifier (NFC) of the Takagi-Sugeno-Kang (TSK) type from data information transformed by a wavelet packet (WP). The design of the NFC is accomplished by using a fuzzy c-means (FCM) clustering algorithm that can solve the problem of dimensionality increase due to the flexible scatter partitioning. For this purpose, we use the rider's hip motion from the sensor information collected by inertial sensors as feature data for the cla...
The prevalence, abundance and distribution of cyathostomins (small stongyles) in horses from Western Romania. Forty seven working horses from Romania were post-mortem examined for small strongyles (Cyathostominae) infections. All horses were found infected. The overall cyathostomins intensity ranged from 390 to 13,010 and horses were infected by 8-24 species. The intensity was higher in ventral colon (1531) and dorsal colon (824), the lowest in the caecum (524). Twenty four species were identified. Cyathostomum catinatum, Cylicocyclus insigne, and C. Nassatus had 100% of prevalence. Over 50% of horses were infected by Coronocyclus coronatus, Cylicostephanus calicatus, C. goldi, and C. longibursatus. O...
The Equine Embryo Influences Immune-Related Gene Expression in the Oviduct. 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 ...
The complete mitochondrial genome of Hequ horse. The complete mitochondrial genome of Hequ horse was determined in this study. The mitogenome is 16 656 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a D-loop region. The overall base composition of the H-strand is 32.20% for A, 28.55% for C, 13.38% for G and 25.86% for T. Tree constructed using MEGA 6 with Maximum-likelihood (ML) methods demonstrated that Hequ horse was clustered in subfamily Equidae.
Equine grass sickness in Scotland: A case-control study of environmental geochemical risk factors. We hypothesised that the apparent geographical distribution of equine grass sickness (EGS) is partly attributable to suboptimal levels of soil macro- and trace elements in fields where EGS occurs. If proven, altering levels of particular elements could be used to reduce the risk of EGS. Objective: To determine whether the geographical distribution of EGS cases in eastern Scotland is associated with the presence or absence of particular environmental chemical elements. Methods: Retrospective time-matched case-control study. Methods: This study used data for 455 geo-referenced EGS cases and 910 ...
Immune gene expression profiling of PBMC isolated from horses vaccinated with attenuated African horsesickness virus serotype 4. 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...
Could it be colic? Horse-owner decision making and practices in response to equine colic. Little is known about lay understanding and decision making in response to colic. Horse-owners/carers are key to identifying colic and initiating veterinary intervention. Understanding how owners think and act in relation to colic could assist veterinary surgeons in tailoring information about colic with the aim of improving colic outcomes. Methods: A mixed methods approach was employed including qualitative in-depth interviews and a cross-sectional questionnaire. Qualitative data were analysed using Grounded theory to conceptualise processes involved in horse-owner management of colic. Follow...
Impact of race training on volumetric bone mineral density and its spatial distribution in the distal epiphysis of the third metatarsal bone of 2-year-old horses. The aim of the study was to use spatial and multiple correspondence analysis (MCA) to describe and compare the regional proportion and spatial pattern of volumetric bone mineral density (BMDv) values within loaded regions of the plantar metatarsal epiphysis of young horses in race training. A single 2 mm transverse peripheral quantitative computed tomography 'slice', 10 mm proximal from the distal limit of the sagittal ridge of the distal metatarsal epiphysis was obtained from 14 2-year-old Thoroughbred fillies (7 exercised and 7 controls). Six regions of interest were generated and examin...
Evaluation of a mouse model for the West Nile virus group for the purpose of determining viral pathotypes. West Nile virus (WNV; family Flaviviridae; genus Flavivirus) group members are an important cause of viral meningoencephalitis in some areas of the world. They exhibit marked variation in pathogenicity, with some viral lineages (such as those from North America) causing high prevalence of severe neurological disease, whilst others (such as Australian Kunjin virus) rarely cause disease. The aim of this study was to characterize WNV disease in a mouse model and to elucidate the pathogenetic features that distinguish disease variation. Tenfold dilutions of five WNV strains (New York 1999, MRM16 a...
RNA-seq transcriptome profiling of equine inner cell mass and trophectoderm. Formation of the inner cell mass (ICM) and trophectoderm (TE) marks the first differentiation event in mammalian development. These two cell types have completely divergent fates for the remainder of the developmental process. The molecular mechanisms that regulate ICM and TE formation are poorly characterized in horses. The objective of this study was to establish the transcriptome profiles of ICM and TE cells from horse blastocysts using RNA sequencing (RNA-seq). A total of 12 270 genes were found to be expressed in either lineage. Global analysis of the transcriptome profiles by unsupervi...
Untangling the complex inter-relationships between horse managers’ perceptions of effectiveness of biosecurity practices using Bayesian graphical modelling. On-farm biosecurity practices have been promoted in many animal industries to protect animal populations from infections. Current approaches based on regression modelling techniques for assessing biosecurity perceptions and practices are limited for analysis of the interrelationships between multivariate data. A suitable approach, which does not require background knowledge of relationships, is provided by Bayesian network modelling. Here we apply such an approach to explore the complex interrelationships between the variables representing horse managers' perceptions of effectiveness of on-far...
Macrolide- and rifampin-resistant Rhodococcus equi on a horse breeding farm, Kentucky, USA. Macrolide and rifampin resistance developed on a horse breeding farm after widespread use was instituted for treatment of subclinical pulmonary lesions in foals. Resistance occurred in 6 (24%) of 25 pretreatment and 8 (62%) of 13 (62%) posttreatment isolates from affected foals. Drug-resistant isolates formed 2 distinct genotypic clusters.
Exploration of global gene expression changes during the estrous cycle in equine endometrium. The equine endometrium exhibits characteristic morphological and functional changes during the estrous cycle controlled by the interplay of progesterone and estradiol. A microarray analysis of endometrial tissue samples derived from five time points of the estrous cycle (Day [D] 0, D3, D8, D12, and D16) was performed to study the dynamics of equine endometrial gene expression. Statistical analysis revealed 4996 genes differentially expressed during the estrous cycle. Clustering of similar expression profiles was performed to find groups of coregulated genes. This revealed eight major profiles:...