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.
Evaluation of key miRNAs during early pregnancy in Kazakh horse using RNA sequencing. miRNA has an important role in cell differentiation, biological development, and physiology. Milk production is an important quantitative trait in livestock and miRNA plays a role in the amount of milk produced. Methods: The role of regulatory miRNAs involved in equine milk production is not fully understood. We constructed two miRNA libraries for Kazakh horse milk production from higher-producing (H group) and lower-producing (L group) individuals, and used RNA-Seq technology to identify the differentially expressed miRNAs between the two milk phenotypes of Kazakh horses. Results: A total of ...
The pelvic flexure separates distinct microbial communities in the equine hindgut. As hindgut fermenters, horses are especially dependent on the microbiota residing in their cecum and large intestines. Interactions between these microbial populations and the horse are critical for maintaining gut homeostasis, which supports proper digestion. The current project was motivated to determine if any features of the fecal microbiota are informative of the microbial communities from the cecum, ventral colon, or dorsal colon. Digesta from the cecum, ventral colon, dorsal colon and feces were collected from 6 yearling miniature horses. Microbial DNA was isolated and the microbiota fr...
Genomic comparisons of Persian Kurdish, Persian Arabian and American Thoroughbred horse populations. The present research aimed to characterize the Persian Kurdish horse population relative to the Persian Arabian and American Thoroughbred populations using genome-wide SNP data. Fifty-eight Kurdish, 38 Persian Arabian and 83 Thoroughbred horses were genotyped across 670,796 markers. After quality control and pruning to eliminate linkage disequilibrium between loci which resulted in 13,554 SNPs in 52 Kurdish, 24 Persian Arabian and 58 Thoroughbred horses, the Kurdish horses were generally distinguished from the Persian Arabian samples by Principal Component Analyses, cluster analyses and calcul...
Comparative Analysis of Serum Mineral and Biochemical Parameter Profiles Between Late Pregnant and Early Lactating Jennies. The purpose of this study was to investigate the profile change of serum trace and major elements, and biochemical and hematological parameters in jennies during late pregnancy and early lactation. Twenty-five healthy Chinese Liaoxi jennies were used in late pregnancy and early lactation. Results showed that the levels of Fe, total protein (TP), and aspartate aminotransferase (AST) were highly variable interindividual among the jennies. Early lactating jennies showed significantly lower serum levels of K, Se, AST, total cholesterol (TC), and triglyceride than late pregnant jennies (P < .05)...
Differential gene expression analysis reveals pathways important in early post-traumatic osteoarthritis in an equine model. Post-traumatic osteoarthritis (PTOA) is a common and significant problem in equine athletes. It is a disease of the entire joint, with the synovium thought to be a key player in disease onset and progression due to its role in inflammation. The development of effective tools for early diagnosis and treatment of PTOA remains an elusive goal. Altered gene expression represents the earliest discernable disease-related change, and can provide valuable information about disease pathogenesis and identify potential therapeutic targets. However, there is limited work examining global gene expression c...
Gene Expression Profile in Similar Tissues Using Transcriptome Sequencing Data of Whole-Body Horse Skeletal Muscle. Horses have been studied for exercise function rather than food production, unlike most livestock. Therefore, the role and characteristics of tissue landscapes are critically understudied, except for certain muscles used in exercise-related studies. In the present study, we compared RNA-Seq data from 18 Jeju horse skeletal muscles to identify differentially expressed genes (DEGs) between tissues that have similar functions and to characterize these differences. We identified DEGs between different muscles using pairwise differential expression (DE) analyses of tissue transcriptome expression d...
Genetic characterization of West Nile Virus strains during neuroinvasives infection outbreak in Tunisia, 2018. West Nile Virus (WNV) is an arbovirus transmitted by mosquito bite involving birds as reservoirs, humans and equines as accidental hosts. Eight distinct lineages (WNV-1 to WNV-8) have been identified: WNV-1 and WNV-2 infect humans and animals, and WNV-3 to WNV-8 have been identified only in vectors. WNV has been implicated in neuroinvasives infections, especially meningitis and encephalitis. Tunisia experienced three epidemics in 1997, 2003 and 2012. Serological studies on humans, equines and birds as well as the detection of the virus in the vector favour a fairly frequent circulation in the ...
Horse welfare at slaughter: A novel approach to analyse bruised carcasses based on severity, damage patterns and their association with pre-slaughter risk factors. The study presents a novel veterinary forensic approach to analyse the bruising of horse carcasses, based on the nature of the bruises and how they are grouped in certain anatomical areas. Data on pre-slaughter logistics was obtained for 113 journeys with horses that travelled from Mexico and the USA to a Mexican abattoir. We found that carcass bruising was a highly prevalent problem (79% of carcasses had bruising) and was especially problematic in journeys lasting longer than 12 h, independently of the animal's country of origin, sex, age, lairage time or vehicle type. Multivariable logistic...
Functional contexts of adipose and gluteal muscle tissue gene co-expression networks in the domestic horse. A gene's response to an environment is tightly bound to the underlying genetic variation present in an individual's genome and varies greatly depending on the tissue it is being expressed in. Gene co-expression networks provide a mechanism to understand and interpret the collective transcriptional responses of genes. Here, we use the Camoco co-expression network framework to characterize the transcriptional landscape of adipose and gluteal muscle tissue in 83 domestic horses (Equus caballus) representing 5 different breeds. In each tissue, gene expression profiles, capturing transcriptional re...
Welfare of horses from Mexico and the United States of America transported for slaughter in Mexico: Fitness profiles for transport and pre-slaughter logistics. Every year thousands of horses from Mexico and the United States of America (USA) are transported to slaughter in Mexico, but little is known about their welfare or pre-slaughter logistics. In this study, we recorded the origin, sex, age and condition of horses (121 journeys, 2648 animals) upon arrival to an abattoir in northern Mexico, including transport details. Horse welfare was measured indirectly via individual scores for body condition, coat quality, lameness, ocular and nasal discharge, as well as reactivity to a chute restraint test, all performed shortly after unloading. The average ...
Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites. STRUCTURE remains the most applied software aimed at recovering the true, but unknown, population structure from microsatellite or other genetic markers. About 30% of structure-based studies could not be reproduced (, 21, 2012, 4925). Here we use a large set of data from 2,323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellites, to evaluate how program settings impact the estimation of the optimal number of population clusters that best describe the observed data. Domestic horses are suited as a test case as there is extensive background knowledge on the his...
Iron Biomineral Growth from the Initial Nucleation Seed in L-Ferritin. X-ray structures of homopolymeric human L-ferritin and horse spleen ferritin were solved by freezing protein crystals at different time intervals after exposure to a ferric salt and revealed the growth of an octa-nuclear iron cluster on the inner surface of the protein cage with a key role played by some glutamate residues. An atomic resolution view of how the cluster formation develops starting from a (μ -oxo)tris[(μ -glutamato-κO:κO')](glutamato-κO)(diaquo)triiron(III) seed is provided. The results support the idea that iron biomineralization in ferritin is a process initiating at the l...
Borna disease outbreak with high mortality in an alpaca herd in a previously unreported endemic area in Germany. Borna disease virus 1 (BoDV-1) is the causative agent of Borna disease, an often fatal neurologic condition of domestic mammals, including New World camelids, in endemic areas in Central Europe. Recently, BoDV-1 gained further attention by the confirmation of fatal zoonotic infections in humans. Although Borna disease and BoDV-1 have been described already over the past decades, comprehensive reports of Borna disease outbreaks in domestic animals employing state-of-the-art diagnostic methods are missing. Here, we report a series of BoDV-1 infections in a herd of 27 alpacas (Vicugna pacos) in t...
Effect of work on body language of ranch horses in Brazil. The horses' responses to exercise are commonly monitored using physiological variables, nonetheless physical and mental states can also be expressed through body language. The aims of this study were: (i) to identify how facial expressions and other behavioural variables change in ranch horses after a routine workday, and (ii) to investigate if these changes can be used as indicators of physical tiredness by relating them to known variables of physical fitness and workload. Fourteen crossbred ranch horses were assessed pre- and post-workday on two farms, recording the body language, physiologi...
Practice of Noseband Use and Intentions Towards Behavioural Change in Dutch Equestrians. Understanding equestrians' noseband tightening practices and intentions is necessary to target welfare improvement strategies. Firstly, we measured tightness in dressage and show jumping horses in The Netherlands, shortly after implementation of the two-finger rule by the Royal Dutch Equestrian Federation. Noseband tightness decreased with age, was less tight in dressage horses than in show jumpers, and was dependent on the interaction between competition level and discipline. Fifty-nine percent of the riders tightened nosebands to such an extent that they adhered to the new regulation. Second...
Characterization of the placental transcriptome through mid to late gestation in the mare. The placenta is a dynamic organ which undergoes extensive remodeling throughout pregnancy to support, protect and nourish the developing fetus. Despite the importance of the placenta, very little is known about its gene expression beyond very early pregnancy and post-partum. Therefore, we utilized RNA-sequencing to characterize the transcriptome from the fetal (chorioallantois) and maternal (endometrium) components of the placenta from mares throughout gestation (4, 6, 10, 11 m). Within the endometrium, 47% of genes changed throughout pregnancy, while in the chorioallantois, 29% of genes under...
Refinement of Global Domestic Horse Biogeography Using Historic Landrace Chinese Mongolian Populations. The Mongolian horse is one of the oldest extant horse populations and although domesticated, most animals are free-ranging and experience minimal human intervention. As an ancient population originating in one of the key domestication centers, the Mongolian horse may play a key role in understanding the origins and recent evolutionary history of horses. Here we describe an analysis of high-density genome-wide single-nucleotide polymorphism (SNP) data in 40 globally dispersed horse populations (n = 895). In particular, we have focused on new results from Chinese Mongolian horses (n = 100) that ...
First Complete Coding Sequence of a Venezuelan Equine Encephalitis Virus Strain Isolated from an Equine Encephalitis Case in Costa Rica. The first complete coding sequence of the Venezuelan equine encephalitis virus IE, isolated from a Costa Rican mare with severe encephalitis, was confirmed by histological and viral whole-genome analyses. The isolated virus grouped in the Pacific cluster.
Training practices, speed and distances undertaken by Thoroughbred racehorses in Victoria, Australia. Musculoskeletal injuries (MSI) in racehorses are commonly due to bone fatigue, a function of the number of cycles (strides) and the magnitude of load applied to the limb. These parameters can be estimated using speed and distance, with greater than 6000 m/month at a gallop (>14 m/s), in combination with canter distances greater than 44,000 m/month, reported to increase fracture risk. Despite their importance, there are limited data on the distances and speeds horses are exposed to during training. Objective: Estimate training volume at different speeds undertaken by Australian Thoroughbr...
Determinants of Undesirable Behaviors in American Quarter Horses Housed in Box Stalls. The objective of this study was to investigate the management practices that affect undesirable behaviors in American Quarter Horses (AQH) confined to box stalls. A total of 105 adult AQH, comprising 29 females, 22 intact males, and 54 castrated males, housed in box stalls for at least 30 days, were included in the study. Behavioral activities were recorded through visual inspection at 5-min intervals over a 24-h period by two observers who took turns in shifts of 4 hours. Parameters related to animal characteristics, stall conditions, handling, training, nutrients supplied, and feeding beha...
Genetic diversity and relationships among native Japanese horse breeds, the Japanese Thoroughbred and horses outside of Japan using genome-wide SNP data. Eight horse breeds-Hokkaido, Kiso, Misaki, Noma, Taishu, Tokara, Miyako and Yonaguni-are native to Japan. Although Japanese native breeds are believed to have originated from ancient Mongolian horses imported from the Korean Peninsula, the phylogenetic relationships among these breeds are not well elucidated. In the present study, we compared genetic diversity among 32 international horse breeds previously evaluated by the Equine Genetic Diversity Consortium, the eight Japanese native breeds and Japanese Thoroughbreds using genome-wide SNP genotype data. The proportion of polymorphic loci and ...
Unraveling the effects of the gut microbiota composition and function on horse endurance physiology. An integrated analysis of gut microbiota, blood biochemical and metabolome in 52 endurance horses was performed. Clustering by gut microbiota revealed the existence of two communities mainly driven by diet as host properties showed little effect. Community 1 presented lower richness and diversity, but higher dominance and rarity of species, including some pathobionts. Moreover, its microbiota composition was tightly linked to host blood metabolites related to lipid metabolism and glycolysis at basal time. Despite the lower fiber intake, community type 1 appeared more specialized to produce ace...
A cross-sectional study of horse owners’ awareness and perceived risk of exotic diseases in the United Kingdom. The international nature of the equine industry provides opportunities for the spread of infectious diseases between countries. While incursions of exotic diseases into the United Kingdom (UK) equine population have been rare, the potential socioeconomic and welfare impacts are a significant concern. However, little is known about leisure horse owners' ability or willingness to prepare for an exotic disease incursion. The objectives of this study were to describe UK leisure horse owners' awareness and perceptions of exotic diseases, and to identify clusters of horse owners characterised by the...
Multiple adrenocortical steroid response to administration of exogenous adrenocorticotropic hormone to hospitalized foals. The hypothalamic-pituitary-adrenal axis regulates the response to sepsis-associated stress. Relative adrenal insufficiency or adrenocorticotropic hormone (ACTH):cortisol imbalance, defined as a poor cortisol response to administration of ACTH, is common and associated with death in hospitalized foals. However, information on other adrenal steroid response to ACTH stimulation in sick foals is minimal. Objective: To investigate the response of multiple adrenocortical steroids to administration of ACTH in foals. Methods: Hospitalized (n = 34) and healthy (n = 13) foals. Methods: In this prospecti...
Spatiotemporal Analysis of Glanders in Brazil. In Brazil, glanders remains a serious problem, with the obligatory sacrifice of disease-positive animals without compensation. Each year, glanders cases are reported in several regions of the country, causing severe economic losses and trade restrictions. The present study describes and discusses the occurrence of glanders foci in Brazil during a 12-year period from 2005 to 2016. The highest frequency of reported affected holdings during the study period was in the northeast region. Moreover, during this period, the disease incidence in Brazil showed an overall increasing tendency. The number ...
Identification of piRNAs and piRNA clusters in the testes of the Mongolian horse. P-element induced wimpy testis-interacting RNAs (piRNAs) are essential for testicular development and spermatogenesis in mammals. Comparative analyses of the molecular mechanisms of spermatogenesis among different organisms are therefore dependent on accurate characterizations of piRNAs. At present, little is known of piRNAs in non-model organisms. Here, we characterize piRNAs in the Mongolian horse, a hardy breed that reproduces under extreme circumstances. A thorough understanding of spermatogenesis and reproduction in this breed may provide insights for the improvement of fecundity and repr...
Effect of oral supplementation of probiotic strains of Lactobacillus rhamnosus and Enterococcus faecium on the composition of the faecal microbiota of foals. Effects of probiotics on the intestinal microbiota of foals are yet insufficiently studied. The aim of this study was to investigate whether supplementation of Lactobacillus rhamnosus (DSM 7133) and Enterococcus faecium (DSM 7134) influences the bacterial composition of the faecal microbiota of foals. A total of 34 newborn foals were randomly assigned to the placebo group (PG, n = 16) and the treatment group (TG, n = 18). From day 1 to day 14 of life, foals orally received 3 ml of either a probiotic preparation (1.05 × 10 CFU E. faecium and 4.50 × 10 CFU L. rhamnosus) or placebo (...
Association between nutritional values of hays fed to horses and sensory properties as perceived by human sight, touch and smell. Although hay is the foundation of most equine diets, horse owners rarely ask for biochemical analysis and the routine practice is to choose hay based on its 'perceived' nutritional value. The present study aimed at exploring the relationship between sensory properties as perceived by sight, touch and smell, and the nutritional value of hay measured by biochemical analysis using a 'free sorting task' method. Fifty-four non-expert participants were asked individually to: (1) observe 21 hays samples, (2) group together hays that they perceived as similar for each of the three modalities (hay appe...
Eye Surface Temperature as a Potential Indicator of Physical Fitness in Ranch Horses. This study aimed to investigate the use of maximum eye surface temperature (EST), recorded by infrared thermography, as an indicator of physical fitness in ranch horses. Data collection was carried out with 16 horses by recording six physical fitness biomarkers (EST, respiratory rate, creatine kinase activity [CK], and concentrations of total serum protein, plasmatic cortisol, and lactate) before and after a regular working day. We also recorded heart rate during the exercise, exercise duration, average velocity, distance traveled, and air temperature and humidity. The variation between the sa...
Structure and gene cluster of the O antigen of Escherichia coli F17, a candidate for a new O-serogroup. Escherichia coli F17 isolated from horse feces was studied in respect to the O antigen (O polysaccharide) structure and genetics. The lipopolysaccharide was isolated by phenol-water extraction of bacterial cells and cleaved by mild acid hydrolysis to yield the O polysaccharide, which was studied by sugar analysis and selective solvolysis with CFCOH along with one- and two-dimensional H and C NMR spectroscopy. The O polysaccharide was found to have a branched pentasaccharide repeat (O-unit) containing one residue each of d-galactose, d-mannose, l-rhamnose, d-glucuronic acid, and N-acetyl-d-gluc...