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.
Genome-wide search reveals the uniqueness of DNA regions associated with coat color and innate immunity in Hokkaido Native Horse. Hokkaido Native Horse (HKD) is a horse breed native to Hokkaido in Japan known for the traits such as coat color with no white spots and adaptability to the local cold climate. To examine whether those traits of HKD are conferred at the DNA level, we attempted to identify fixed DNA regions in HKD individuals, that is, the selection signatures of HKD. A comparison of genome-wide single nucleotide polymorphism genotypes in 58 HKD individuals by principal component analysis, and cluster analysis between breeds, including HKD, and within the HKD individuals indicated the genetic independence of HK...
Pilot study of locomotor asymmetry in horses walking in circles with and without a rider. Horses commonly show asymmetries that manifest as left (L)-right (R) differences in vertical excursion of axial body segments. Moving on a circle confounds inherent individual asymmetries. Our goals were to evaluate individual and group asymmetry patterns and compare objective data with subjective impressions of side preference/laterality in horses walking on L and R circles. Unassigned: Fifteen horses walked on L and R circles unridden and ridden on long and short reins. Optical motion capture (150 Hz) tracked skin-fixed markers. Variables were trunk horizontal angle; neck-to-trunk angle; ver...
Decoding the transcriptomic expression and genomic methylation patterns in the tendon proper and its peritenon region in the aging horse. Equine tendinopathies are challenging because of the poor healing capacity of tendons commonly resulting in high re-injury rates. Within the tendon, different regions - tendon proper (TP) and peritenon (PERI) - contribute to the tendon matrix in differing capacities during injury and aging. Aged tendons have decreased repair potential; the underlying transcriptional and epigenetic changes that occur in the TP and PERI regions are not well understood. The objective of this study was to assess TP and PERI regional differences in adolescent, midlife, and geriatric horses using RNA sequencing and ...
Comparative Analysis of Protein Digestion Characteristics in Human, Cow, Goat, Sheep, Mare, and Camel Milk under Simulated Infant Condition. An infant in vitro digestion model was utilized to investigate protein digestion characteristics in human and diverse mammalian milk (i.e., cow, goat, sheep, mare, and camel milk) using electrophoresis and chromatography. Digestive differences among milks were mainly manifested in the infant gastric phase, as evidenced by varying degrees of protein digestion. Notably, proteins (i.e., lactoferrin, serum albumin, and immunoglobulin G-heavy chain) remained partially intact in human milk, whereas these proteins in animal milk were exclusively degraded after gastrointestinal digestion. The peptide ...
Multi-Omic Temporal Landscape of Plasma and Synovial Fluid-Derived Extracellular Vesicles Using an Experimental Model of Equine Osteoarthritis. Extracellular vesicles (EVs) contribute to osteoarthritis pathogenesis through their release into joint tissues and synovial fluid. Synovial fluid-derived EVs have the potential to be direct biomarkers in the causal pathway of disease but also enable understanding of their role in disease progression. Utilizing a temporal model of osteoarthritis, we defined the changes in matched synovial fluid and plasma-derived EV small non-coding RNA and protein cargo using sequencing and mass spectrometry. Data exploration included time series clustering, factor analysis and gene enrichment interrogation. ...
Core genome multilocus sequence typing analysis of Finnish Taylorella equigenitalis isolates. In Finland, Taylorella equigenitalis, the causative agent of contagious equine metritis (CEM), was first detected in 1992. The aim of this study was to genotype Finnish T. equigenitalis isolates to investigate the epidemiology of the infection in the Finnish horse population. A total of 34 T. equigenitalis isolates from 24 horses obtained during 1992-2021 were subjected to whole genome sequencing (WGS) and subsequent local ad hoc core genome multi-locus sequence typing (cgMLST) targeting 1259 loci. Classical MLST profiles were extracted from the whole-genome sequence data. Three novel MLST ty...
Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach. The Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism (SNP) and whole-genome sequencing data from 116 WB (94 UK WB and 22 European WB) and 36 CP (33 UK CP and 3 US CP), we studied the genomic diversity, inbreeding and population structure of th...
Fecal Microbiota and Diet Composition of Buryatian Horses Grazing Warm- and Cold-Season Grass Pastures. The Buryatian horse is an ancient breed and, as an indigenous breed, they have unique adaptive abilities to use scarce pastures, graze in winter, and survive in harsh conditions with minimal human care. In this study, fecal microbiota of Buryatian horses grazing in the warm and cold seasons were investigated using NGS technology on the Illumina MiSeq platform. We hypothesized that the composition of microbial communities in the feces of horses maintained on pasture would change in the different seasons, depending on the grass availability and different plant diets. We conducted microhistologic...
Genomic Analysis of Clostridioides difficile Recovered from Horses in Western Australia. Clostridioides difficile poses an ongoing threat as a cause of gastrointestinal disease in humans and animals. Traditionally considered a human healthcare-related disease, increases in community-associated C. difficile infection (CDI) and growing evidence of inter-species transmission suggest a wider perspective is required for CDI control. In horses, C. difficile is a major cause of diarrhoea and life-threatening colitis. This study aimed to better understand the epidemiology of CDI in Australian horses and provide insights into the relationships between horse, human and environmental strains...
Genetic Diversity and Maternal Phylogenetic Relationships among Populations and Strains of Arabian Show Horses. Genetic diversity and phylogenetic relationships within the Arabian show horse populations are of particular interest to breeders worldwide. Using the complete mitochondrial DNA D-loop sequence (916 pb), this study aimed (i) to understand the genetic relationship between three populations, the Desert-Bred (DB), a subset of the Kingdom of Saudi Arabia (KSA), United Arab Emirates (UAE) and Bahrain (BAH), the Straight Egyptian (EG) and the Polish bloodline (PL), and (ii) to assess the accuracy of the traditional strain classification system based on maternal lines, as stated by the Bedouin cultur...
The Interfascicular Matrix of Energy Storing Tendons Houses Heterogenous Cell Populations Disproportionately Affected by Aging. Energy storing tendons such as the human Achilles and equine superficial digital flexor tendon (SDFT) are prone to injury, with incidence increasing with aging, peaking in the 5 decade of life in the human Achilles tendon. The interfascicular matrix (IFM), which binds tendon fascicles, plays a key role in energy storing tendon mechanics, and aging alterations to the IFM negatively impact tendon function. While the mechanical role of the IFM in tendon function is well-established, the biological role of IFM-resident cell populations remains to be elucidated. Therefore, the aim of this study was...
Dynamics of extracellular vesicle-coupled microRNAs in equine follicular fluid associated with follicle selection and ovulation. Innumerable similarities in reproductive cyclicity and hormonal alterations highlight the considerable utility of the mare to study aspects of follicular dynamics and reproductive function in view of the largely constricted, human research subjects. The bi-directional communication between the growing oocyte and the surrounding somatic cells embodies the hallmark of mammalian follicular development, partially mediated by extracellular vesicles (EVs) encapsulated with microRNAs (miRNAs) and present in the follicular fluid (FF). Here, we aimed to decipher the dynamics of the miRNAs in EVs from e...
Vaccination against Borna Disease: Overview, Vaccine Virus Characterization and Investigation of Live and Inactivated Vaccines. (1) Background: Vaccination of horses and sheep against Borna disease (BD) was common in endemic areas of Germany in the 20th century but was abandoned in the early 1990s. The recent occurrence of fatal cases of human encephalitis due to Borna disease virus 1 (BoDV-1) has rekindled the interest in vaccination. (2) Methods: The full genomes of the BD live vaccine viruses "Dessau" and "Giessen" were sequenced and analyzed for the first time. All vaccination experiments followed a proof-of-concept approach. Dose-titration infection experiments were performed in rabbits, based on both cell culture...
Clustering and Correlations amongst NEFA, Selected Adipokines and Morphological Traits-New Insights into Equine Metabolic Syndrome. Obesity is a common feature in horses suffering from metabolic syndrome. While adipokines involvement as biomarkers is better established in human pathology, little data are available on horses. This study aimed to investigate the possible association and relationship between selected metabolic parameters and morphological traits in equine metabolic syndrome. Adiposity was evaluated using body condition score (BCS) and cresty neck score (CNS). Plasma levels of total cholesterol, insulin, NEFA, and adipokines (omentin and chemerin) were determined using enzyme-linked immunosorbent assays. Spear...
Characterization of preantral follicle clustering and neighborhood patterns in the equine ovary. Understanding the transition from quiescent primordial follicles to activated primary follicles is vital for characterizing ovarian folliculogenesis and improving assisted reproductive techniques. To date, no study has investigated preantral follicle crowding in the ovaries of livestock or characterized these crowds according to follicular morphology and ovarian location (portions and regions) in any species. Therefore, the present study aimed to assess the crowding (clustering and neighborhood) patterns of preantral follicles in the equine ovary according to mare age, follicular morphology an...
Pre-Activated Granulocytes from an Autoimmune Uveitis Model Show Divergent Pathway Activation Profiles upon IL8 Stimulation In Vitro. In the pathophysiology of autoimmune-mediated uveitis, granulocytes have emerged as possible disease mediators and were shown to be pre-activated in equine recurrent uveitis (ERU), a spontaneous disease model. We therefore used granulocytes from ERU horses to identify early molecular mechanisms involved in this dysregulated innate immune response. Primary granulocytes from healthy and ERU horses were stimulated with IL8, and cellular response was analyzed with differential proteomics, which revealed significant differences in protein abundance of 170 proteins in ERU. Subsequent ingenuity pathw...
Population structure and genomic footprints of selection in five major Iranian horse breeds. The genetic structure and characteristics of Iranian native breeds are yet to be comprehensibly investigated and studied. Therefore, we employed genomic information of 364 Iranian native horses representing the Asil (n = 109), Caspian (n = 40), Dareshuri (n = 44), Kurdish (n = 95), and Turkoman (n = 76) breeds to reveal the genetic structure and characteristics. For these and 19 other horse breeds, principal component analysis, Bayesian model-based, Neighbor-Net, and bootstrap-based TreeMix approaches were applied to investigate and compare their genetic structure. Additionally, thre...
Variations in the fecal microbiota and their functions of Thoroughbred, Mongolian, and Hybrid horses. The horse gut is colonized by a rich and complex microbial community that has important roles in horse physiology, metabolism, nutrition, and immune functions. Fewer across-breed variations in horse gut microbial diversity have been illustrated. In this article, the gut microbiota of Thoroughbred, Mongolian, and Hybrid horses [first filial generation (F1) of Mongolian (maternal) and Thoroughbred (paternal)] were studied by second-generation high-throughput sequencing technology. Differences in gut microbiota composition and function between breeds were determined using diversity and functional...
Relationship between anatomical characteristics and personality traits in Lipizzan horses. We tested 35 Lipizzan horses older than 5 years, ridden and healthy in three behavioural tests (handling, fear-reaction, and target training test). Physiological (heart rate and heart rate variability) and anatomical measurements (120 head and body distances and angles) were collected to validate parameters that reliably inform on handling/cooperation, fear/exploration and trainability in horses. Utilizing a standard clustering methodology on the behavioural data, we identified four general types of responses and categorised an individual as intermediate, low fearful, horses with low cooperati...
Mitochondrial Whole D-Loop Variability in Polish Draft Horses of Sztumski Subtype. The Polish draft horse (PDH) breed is a result of crossing local mares with imported cold-blooded stallions, such as Belgians, Ardennes, Fjords, and others. A part of the broodmare stock investigated in this study was also imported from various countries, such as Denmark. In this study, we investigate the genetic composition of the PDH by analyzing the whole mitochondrial d-loop variability and comparing it to previously demonstrated whole d-loop sequences of other cold-blooded breeds: Ardennais, Belgian, Breton, Clydesdale, Noriker, Norwegian Fjord, Percheron, and Suffolk. Our results show hi...
Does Feeding Management Make a Difference to Behavioural Activities and Welfare of Horses Reared for Meat Production? Horses reared for meat production are generally fed a diet rich in starch with the aim of maximizing production performances. This study evaluated the effects of two feeding management systems on horse welfare by analysing the relative time spent engaged in different behavioural activities. Nineteen Bardigiano horses aged 14.3 ± 0.7 months were randomly assigned to one of two group pens: one group was fed high amounts of starch-rich concentrates (HCG; = 10), the other was fed a fibre-based diet (HFG; = 9). Behavioural activities performed by each horse were video-recorded over a 96-h period...
Transcriptomic analysis of the chorioallantois in equine premature placental separation. Equine premature placental separation (PPS) is poorly understood and represents an important risk factor for fetal/neonatal hypoxia. Objective: To examine transcriptomic changes in the chorioallantois (CA) from mares with clinical PPS compared with the CA from normal foaling mares. Differential gene expression was determined and gene ontology as well as molecular pathways related to PPS were characterised. Methods: Retrospective case: control study. Methods: CA were collected from Thoroughbred mares with a clinical history of PPS (n = 33) and from control Thoroughbred mares (n = 4) with no...
The Impact of Noise Anxiety on Behavior and Welfare of Horses from UK and US Owner’s Perspective. Noise anxiety is an over-reaction to loud noises commonly detected among pets and can greatly impact on their welfare and on their management. When exposed to noisy events, horses can show intense escape attempts, which may cause severe accidents for the horse and the rider/handler. The aim of the present study was to investigate, through a web survey, UK and US owners' perception of noise anxiety severity in their horses, their management strategies and perceived efficacy. The questionnaire was shared via social networking and advertised as "What is your horse afraid of?". Over a total of 183...
Sporadic worldwide “clusters” of feed driven Zilpaterol identifications in racing horses: a review and analysis. Zilpaterol is a β2-adrenergic agonist medication approved in certain countries as a cattle feed additive to improve carcass quality. Trace amounts of Zilpaterol can transfer to horse feed, yielding equine urinary "identifications" of Zilpaterol. These "identifications" occur because Zilpaterol is highly bioavailable in horses, resistant to biotransformation and excreted as unchanged Zilpaterol in urine, where it has a 5 day or so terminal half-life.In horses, urinary steady-state concentrations are reached 25 days (5 half-lives) after exposure to contaminated feed. Zilpaterol readily presen...
Network analysis of Standardbred horse movements between racetracks in Canada and the United States in 2019: Implications for disease spread and control. Horse movements are one of the most important factors for the spread of equine diseases, and past epidemics indicate that contact networks play an important role. Network analysis was used to describe the spatial and temporal characteristics of horse movements between Standardbred racetracks in Canada and the United States during 2019, and to characterize the network to provide a better understanding of the potential racetrack-to-racetrack spread of infectious disease within the network. Networks were constructed and analyzed as an overall network (the entire study period) and monthly networks...
Genetic diversity and population structure of Mongolian regional horses with 14 microsatellite markers. This study aimed to identify the genetic diversity and population structure of Mongolian horse populations according to the province of residence (Khentii, KTP; Uvs, USP; Omnogovi and Dundgovi, GOP; Khovsgol, KGP) using 14 microsatellite (MS) markers. Methods: A total of 269 whole blood samples were obtained from the four populations (KTP, USP, GOP, KGP) geographically distinct provinces. Multiplex polymerase chain reaction (PCR) was conducted using 14 MS markers (AHT4, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, and VHL20), as recommended by the International So...
Outbreak of neuropathogenic equid herpesvirus 1 causing abortions in Yili horses of Zhaosu, North Xinjiang, China. EHV-1 is one of the most serious viral pathogens that frequently cause abortion in horses around the world. However, so far, relatively little information is available on EHV-1 infections as they occur in China. In January 2021, during an abortion storm which occurred in Yili horses at the Chinese State Studs of Zhaosu (North Xinjiang, China), 43 out of 800 pregnant mares aborted. Results: PCR detection revealed the presence of EHV-1 in all samples as the possible cause of all abortions, although EHV-4, EHV-2 and EHV-5 were also found to circulate in the aborted fetuses. Furthermore, the parti...
Profiling Urinary Sulfate Metabolites With Mass Spectrometry. The study of urinary phase II sulfate metabolites is central to understanding the role and fate of endogenous and exogenous compounds in biological systems. This study describes a new workflow for the untargeted metabolic profiling of sulfated metabolites in a urine matrix. Analysis was performed using ultra-high-performance liquid chromatography-high resolution tandem mass spectrometry (UHPLC-HRMS/MS) with data dependent acquisition (DDA) coupled to an automated script-based data processing pipeline and differential metabolite level analysis. Sulfates were identified through -means clustering...
Impact of Seminal Plasma Antioxidants on Donkey Sperm Cryotolerance. This study investigated whether the activities of the antioxidant components of donkey seminal plasma (SP)-both enzymatic (superoxide dismutase (SOD), catalase-like (CAT), glutathione peroxidase-like (GPX), and paraoxonase type 1 (PON1)) and non-enzymatic (measured in terms of total thiol, copper-reducing antioxidant capacity (CUPRAC), ferric-reducing ability of plasma (FRAP), and Trolox equivalent antioxidant capacity (TEAC))-and oxidative stress index (OSI) are related to sperm cryotolerance. For this purpose, 15 ejaculates from jackasses (one per individual) were collected and split into tw...
Genetic Variability Trend of Lusitano Horse Breed Reared in Italy. The Lusitano Horse (LH) originates from Portugal, but is reared worldwide. Since 1994, the University of Milan has routinely tested the LHs bred in Italy for parentage control. This study aims to assess the genetic variability of the LH reared in Italy using 16 microsatellites markers. Moreover, the genetic variability changes over the years in the total population (n.384) and in unrelated horses (n.47) were evaluated. Horses were grouped according to their date of birth (1975-1990, 1991-2000, 2001-2010, 2010-2019). Standard genetic diversity parameters, including observed (Ho) and expected (H...