Digital dermatitis (DD) is a superficial infectious dermatitis of the digital skin of cattle and sheep that can be very painful, causing severe lameness in affected animals. Bovine digital dermatitis (BDD) in dairy cattle has now been reported in most countries they are farmed, and DD in sheep, known as contagious ovine digital dermatitis (CODD) is rapidly emerging as a severe infectious foot disease since first reports from the UK in 1997. Spirochaetes, of the genus Treponema have frequently been found in large numbers in BDD lesions and are now considered the primary causative bacteria of BDD. Three treponeme phylogroups are consistently isolated from dairy cattle BDD in the UK and the USA, which are known as Treponema medium- like, Treponema phagedenis- like spirochaetes and Treponema pedis. Over the past 40 years research has focused on dairy cattle BDD and overlooked whether the disease exists in beef cattle herds in the UK, and whether the same aetiological agents are causal. There is also limited information on the causative bacteriological agents of CODD. Furthermore, no definitive transmission routes or infection reservoirs of DD in either cattle or sheep had thus far been delineated, with only a single study finding a potential reservoir site of DD treponemes in the dairy cattle gastrointestinal (GI) tract. Using molecular bacteriological studies it was found that CODD and beef cattle BDD, as in dairy cattle BDD, show a high association with the three DD treponeme phylogroups. All CODD and beef BDD lesions investigated had at least one of the three DD treponeme phylogroups present in the lesions and these treponemes were also isolated from a high proportion of lesions. No DD treponemes were detected in healthy sheep or beef cattle foot tissue. Upon 16S rRNA gene sequence analysis all isolates showed a high similarity, if not 100% identity, to representatives of each treponeme phylogroup isolated from dairy cattle BDD lesions, indicating a shared aetiology between DD in all three animals. Additionally, the same treponeme bacteria were detected and isolated from a new undefined foot disease in dairy goats in the UK indicating that cross-species transmission of DD may have occurred causing DD infection in a previously unaffected domestic livestock species. To understand potential transmission routes and infection reservoirs of DD, the host GI tract and hoof trimming equipment were investigated. Of the sheep gingival (n= 40) and rectal tissues (n= 40), 1/40 gingival tissues were positive for DD- associated treponemes (T. pedis), and 3/40 rectal tissues (one containing T. medium- like and two tissues containing T. pedis). No DD- associated treponeme DNA was amplified from beef cattle rectal tissues (n= 40), however 4/40 beef gingival tissues were positive for DD- associated treponemes (all containing T. phagedenis- like). A T. phagedenis- like DD treponeme was isolated from the rectal tissue of a CODD symptomatic sheep. Beef cattle (n= 41) and sheep (n= 79) faeces failed to amplify DD- associated Treponema DNA. Twenty two treponemes were isolated from sheep faeces; however, upon phylogenetic analysis these clustered with considered non-pathogenic treponemes, which interestingly exhibited farm specific diversity in their 16S rRNA gene. Trimming equipment was tested after being used to trim cattle and sheep hooves, and subsequently after disinfection of equipment. Of the blades used to trim DD symptomatic animals (n= 26, cattle and sheep combined), 25/26 were found to be positive for at least one of the DD Treponema phylotypes. This figure was reduced to 10/26 (38%) after disinfection of the blades. Following culture of a swab, an isolate belonging to the T. phagedenis- like spirochaetes was isolated from a knife sample after trimming a DD positive cow. Beef cattle sera from DD positive and negative farms were investigated to understand whether beef cattle’s perceived lower prevalence of BDD in the UK is due to a lack of exposure to treponemes, or a protective immune response. Beef cattle from DD positive farms appeared to produce a strong immunological response to treponemes, compared with DD negative farm animal sera. Therefore the perceived lower prevalence of DD in beef cattle does not appear to be due to a protective response in these animals, but more likely due to a lack of exposure to DD treponemes. In conclusion, these studies have produced vital information describing DD in beef cattle and sheep and their respective aetiological agents allowing for more appropriate treatments in the future. Additionally, given the two potential transmission routes delineated from the data, effective actions can be taken to prevent the spread of DD within current hosts and to limit emergence into yet unknown additional host species.

Introduction: Obesity and related cardio-metabolic complications have acquired global epidemic proportions. Suboptimal nutritional environment in early life induces adaptations in energy homeostasis, metabolism and adipose tissue development that may confer short-term survival advantages but are detrimental in later life, particularly if nutrient supply is restored. Brown adipose tissue (BAT) has a unique role in energy homeostasis because it can provide a potential compensatory mechanism against excess weight gain via cold or diet-induced adaptive thermogenesis. Brown adipocytes also have a potential role in lipid and glucose metabolism and BAT activation can increase clearance of lipids and glucose from the circulation. Pericardial fat, particularly epicardial adipose tissue (fat present between the myocardium and the visceral layer of the pericardium), is anatomically and clinically related to cardiac morphology and function and is believed to be a metabolically active organ that affects cardiac function and the evolution of cardiac pathologies. High expression of mRNA for uncoupling protein (UCP) 1 in adult human epicardial adipose tissue suggests that this may be a depot of BAT. Hypotheses: In my thesis, I hypothesised that pericardial adipose tissue is a depot of brown fat in humans and sheep. I also hypothesised that suboptimal nutrition in early life will affect adiposity and development of BAT in this depot. Methods: UCP1 mRNA expression and protein abundance and other BAT and white adipose tissue related genes were studied in pericardial adipose tissue. In the first study, pericardial fat was sampled from newborn and 30 day old sheep born to mothers fed with 100% or 60% of their total metabolisable energy (ME) requirement from 110 day gestation to term. In the second study, pericardial fat was sampled from near-term (140 day gestation) fetuses delivered to mothers fed 100% or 60% of total ME requirement from 28 to 80 days and then fed ad libitum. Gene expression was measured by reverse transcription-polymerase chain reaction and protein abundance by Western blotting and immunohistochemistry. To confirm the presence of BAT in the human epicardial fat depot, relative abundance of UCP1 was measured by Western Blotting in epicardial, paracardial, and subcutaneous fat samples taken from adults. In the final study, epicardial fat samples were collected from 63 children (0-18 years of age) undergoing cardiac surgery and gene expression of UCP1 and other BAT and WAT related genes identified by microarray. The presence of UCP1 was confirmed by immunohistochemistry. Results: Pericardial adipose tissue is a depot of BAT in fetal and newborn sheep. Suboptimal maternal nutrition in late gestation reduces the abundance of UCP1 and downregulates other BAT related genes whilst suboptimal maternal nutrition in early-to-mid gestation followed by ad libitum feeding to term, increases adiposity, enhances UCP1 abundance and upregulates genes involved in brown and white adipogenesis. Epicardial fat from newborn infants, children, adolescents and older adults contains UCP1 confirming that it is a BAT depot in humans. UCP1 gene expression in infancy and early childhood in humans is downregulated in children with poor nutritional states. Conclusions: I have shown that adipose tissue depots present around the heart are a repository of brown fat, at least in humans and sheep. In view of the potential role of BAT in regulation of lipid and glucose metabolism, this may have therapeutic implications for treatment of cardiovascular complications of obesity. Suboptimal nutrition in utero and during early life compromises BAT development. Although the exact mechanism of how these changes affect the propensity towards obesity and metabolic dysregulation remains to be elucidated, a reduction in thermogenesis presents a plausible mechanism for the increased metabolic efficiency associated with nutritional deprivation in early life. BAT persists beyond the neonatal period in to adult life and, therefore, presents a potential target for long lasting nutritional manipulations to promote better health.

Salmonella enterica infection affects a wide range of animals including humans. The avian specific serotype S. Pullorum infection produces systemic disease followed by a persistent carrier state in convalescence birds. Vaccination and other control strategies require an improved understanding of the immunity in response to S. Pullorum infection. This study compared the different immune dynamics following infection with (persistent) S. Pullorum and related (non-persistent) serovars S. Enteritidis and S. Gallinarum using co-culture of Salmonella-infected macrophages and CD4+ T lymphocytes in vitro and 2-day-old chickens in vivo. In comparison with S. Enteritidis, macrophages infected with S. Pullorum had a reduced gene expression of pro-inflammatory cytokines CXCLi2, IL-6, iNOS, IFN-γ, IL-12α and IL-18 and lower level of nitrite production. S. Pullorum-infected macrophages were found to be less effective than S. Enteritidis in stimulating the CD4+ lymphocytes to proliferate in vitro. CD4+ lymphocytes in co-culture with Salmonella-infected macrophages also produced lower levels of IFN-γ and IL-17F mRNA in response to S. Pullorum compared with S. Enteritidis. S. Pullorum infection in 2-day-old chickens stimulated proliferation of Th2-like lymphocytes with reduced IFN-γ and IL-17F but increased IL-4, IL-13 and IL-10 in the caecal tonsils and spleens when compared to S. Enteritidis. However, the modulation by S. Pullorum is not likely to be related to its large virulence plasmid, although the virulence plasmid of S. Gallinarum was shown to reduce nitrite production and gene expression of IL-1β and iNOS in infected HD11 cells. Our data showed no evidence of clonal anergy or immune suppression induced by S. Pullorum in vitro. The experimental work thus shows that the response to S. Pullorum infection was characterised by a modulation on host immunity from a dominant IFN-γ-producing Th17 response towards a Th2-like response which may promote persistent infection in chickens. This study provides insights into mechanisms by which S. Pullorum evades host immunity and produces the persistent carrier state. This opens the possibility for therapeutic application of cytokines to restore the host protective immune response to eliminate infection.

Degradation of terrestrial habitats with high conservation value has resulted in strategic efforts to cease or reverse their declines. Broad habitat management can restore ecological processes and large herbivores can provide ecological function in some terrestrial systems. Following years of decline and fragmentation, owing to factors such as cessation of traditional practices, lowland heathland has become an internationally important habitat with strategic protection. Free-ranging grazing aims to assist in mitigating such losses to habitat and vegetation communities, but quantifying the grazing regime and its associated impacts is necessary to ensure protection of these vulnerable systems. Reviews of herbivore impacts on lowland heath provide detailed evaluations and recognise the absence of experimental assessments and baseline monitoring. This research aimed to assess ecological activity and impacts (herbage removal, trampling and dunging) of horses and cattle on a lowland heath system to determine their influence on changing vegetation and to inform grazing management. This mixed regime is commonly adopted for restoration of semi-natural habitats but a failure to understand the separate vegetation impacts can be detrimental for the system as a whole. Behavioural activity was quantified using scan-sampling assessing spatial and temporal variation in behaviour, habitat selection and niche overlap, spatial occupancy and diet. A factorial design was set up to quantify the impacts of herbage removal, trampling and dunging to vegetation separately. Assessments vegetation community composition and architecture in treatment and control areas were undertaken. Analyses incorporated non-parametric and general linear models. Animals utilised their environments in different ways, varying for feeding and showed high habitat selectivity, based on physiology and foraging strategy primarily. Herbage removal strongly influenced vegetation architecture and heterogeneity owing to selection for graminoids and the plants’ competitive traits; effects on other plants were not as well defined due to minimal abundance. Trampling modified the vegetation structure due to reduced canopy density maintaining colonising gaps, but increased graminaceous cover and showed a capacity for lateral expansion. Dunging regime was highly influential for enhancing plant architecture and modified vegetation composition based on nutrient availability and competition. Worming regime was influential on architectural parameters and may be due to retarded dung degradation; further research is required. The findings contributed knowledge to lowland heath grazing management, validating the use of mixed regimes at low densities, for generating vegetation heterogeneity, for the control of dominating plants and for understanding the impacts of different animal-management practices. Expanding the reach of this research to comparable systems is necessary to develop the knowledge of grazing-management impacts. The work addressed an absence of experimental evaluation on these systems and also illustrated the importance of separately quantifying the impacts of large herbivores.

Feline Osteoarthritis (OA) is a pathological change of a diarthrodial articulation which primarily occurs in older cats. The aims of this study were:- 1) to define the radiographic features of OA in the cat for each individual appendicular joint; 2) to relate the radiographic features to the gross pathologic and histopathologic features; 3) to explore underlying causes of OA in cats, 4) to identify the presence of Protease Activated Receptor-2 (PAR-2) and matriptase in feline articular cartilage and synovial membrane and to determine their role in OA pathogenesis. The present study has defined five radiographic features of OA for each appendicular joint:- presence of osteophytes, enthesiophytes, areas of abnormal mineralisation,synovial effusion and joint remodelling. The study furthermore suggested that increases in radio-opacity beneath the semilunar notch, along the femoral trochlea, beneath the tibial plateau and on the femoral head/neck are also important radiographic features. The radiographic prevalence was highest in the elbow (23.9%, 93/389) and stifle (23.9%,93/389) joints, followed by the hip (21.1%, 82/389), tarsal (17.7%, 69/389), shoulder(6.7%, 27/389) and carpal (6.4%, 25/389) joints. The results from this study demonstrate that the presence of a radiographically apparent supinator sesamoid bone(SSB), meniscal mineralisation (MM) and two fabellae are related to cartilage pathology and can be indicators of OA. Prevalence rates for gross pathology changes were highest in the elbow (20.2%,102/506) joint, followed by the stifle (19.6%, 99/506), hip (18.4%, 93/506), shoulder (17.8%, 90/506), tarsal (15.0%, 76/506), and carpal (9.1%, 46/506) joints. Eight key gross pathologic features were identified- cartilage discolouration, cartilage fibrillation,cartilage ulceration, cartilage erosion, osteophytes, thickening of joint capsule, synovium discolouration and joint remodelling. The radiographic and gross pathologic total scores were positively correlated in each appendicular joint and the joint most likely to have cartilage damage without radiographic evidence of OA is the shoulder (71.1%, 64/90) followed by the elbow (39.1%, 9/23), hip (32.4%, 11/34), stifle (26.1%,6/23), carpal (23.1%, 21/91) and tarsal (14.9%, 7/47) joints. Four possible underlying conditions that lead to secondary OA were identified:- radioulnar incongruity, hip dysplasia (HD), cranial cruciate ligament (CCL) disease and primary meniscal mineralisation. The identification of PAR-2 and matriptase proteins and gene expression in feline articular tissues is a novel and important finding supporting the hypothesis that serine proteases are involved in the articular cartilage degradation seen in feline OA.

Examining patient records is a useful way to identify common conditions and treatment outcomes in veterinary practice and data gathered can be fed back to the profession to assist with clinical decision making. This research aimed to develop a method to extract clinical data from veterinary electronic patient records (EPRs) and to assess the value of the data extracted for use in practice-based research. The transfer of new research from continuing professional development (CPD) into practice was also considered. An extensible mark-up language (XML) schema was designed to extract information from a veterinary EPR. The analysis of free text was performed using a content analysis program and a clinical terms dictionary was created to mine the extracted data. Data collected by direct observation was compared to the extracted data. A review of research published in the proceedings of a popular veterinary CPD event, British Small Animal Veterinary Association (BSAVA) Congress, was appraised for evidence quality. All animal records were extracted and validation confirmed 100% accuracy. The content analysis produced results with a high specificity (100%) and the mined data analysis was successful in assessing the prevalence of a specific disease. On comparison, the data extracted from the EPR contained only 65% of all data recorded by direct observation. The review of BSAVA Congress abstracts found the majority of the clinical research abstracts (CRAs) presented to be case reports and case series, with differences in focus between CRAs and veterinary lecture stream abstracts. This study has demonstrated that data extraction using an XML schema is a viable method for the capture of patient data from veterinary EPRs. The next step will be to understand the differences found between data collected by observation and extraction, and to investigate how research presented as CPD is received, appraised and applied by the veterinary profession.

The selection for specific physical characteristics by dog breeders has resulted in the expression of undesirable phenotypes, either directly or indirectly related to the physical characteristic selected for. One conformation that was considered desirable is extreme brachycephalia, which is associated with secondary physical changes adversely affecting the airways, eyes and central nervous system. Using a large population of pet dogs having diagnostic magnetic resonance imaging (MRI) studies, I demonstrated that the most commonly used historical head phenotype indices (Stockard and Evans indices) can be determined on MR images. I furthermore conformed that olfactory bulb angulation can be used as an alternate for classification of dog into brachycephalic, mesaticephalic and dolichocephalic head shapes, with similar results to the historical indices. The advantages of olfactory bulb angulation are that it only requires a single midline MR image and inclusion of the entire nose is not required. Using the historical indices and olfactory bulb angulation I then examined the effect of increasing brachycephalia on the appearance and dimensions of the nasal and cranial cavity. I established that progressive ventral rotation of the olfactory bulb (increasing brachycephalia) resulted in an alteration in the shape and a reduction in cross-sectional area of the nasopharynx. Similarly, increasing brachycephalia resulted in a reduction in the dorsal area of the ethmoturbinates and a corresponding reduction in the midline area of the olfactory bulb, providing a potential explanation for reduced olfactory acuity in brachycephalic dogs. Finally, I examined the effect of head phenotype on the structures of the middle fossa, the 3rd ventricle, quadrigeminal cistern and interthalamic adhesion. Head phenotype had a lesser effect on these structures, while brain disease (in particular ventriculomegaly) has a substantial effect, the recognition of which I described. These results confirm the potential of olfactory bulb angulation and orientation for objectively determining head phenotype using in vivo MRI, in particular determining the degree of brachycephalia. The study also quantified the effect of brachycephalia on the nasal cavity and rostral and middle cranial fossae dimensions. The objective quantification of head phenotype provides a useful tool for selection of breeding animals to normalise extreme brachycephalia. This might reduce the incidence of the adverse effects associated with extreme brachycephalia.

Osteoarthritis (OA) is a degenerative disease of synovial joints with an inflammatory component, which affects humans and companion animals, including horses. Current pharmacotherapy for OA is associated with deleterious side effects. Therefore, plant-derived products with anti-inflammatory properties may provide safer natural alternatives. The project aimed to use in vitro models of equine cartilage to test the hypothesis that plant-derived extracts would reduce inflammation and degradation in an explant model of early OA. The anti-inflammatory polyphenol, curcumin, significantly reduced interleukin-1 beta (lL-1β)-stimulated glycosaminoglycan, matrix metalloproteinase-3 and prostaglandin E[subscript]2 release in the explant model. Using a cocktail of plant extracts illustrated how different effects were observed depending on the solvent used to dissolve the raw material. Chondrocyte monolayers were used to determine that counteraction of IL-1β- stimulated effects in the explant model occurred at non-cytotoxic concentrations. The explant model was adapted for proteomic studies of the cartilage secretome. Several proteins involved in matrix function and degradation were identified. This adaptation may further our understanding of the processes in the early OA explant model and may facilitate studying the effects of anti-inflammatory compounds on the secretome. A concurrent field trial showed that the plant extract cocktail did not significantly improve mobility in horses with chronic hindlimb stiffness. However, it illustrated the need for practical, more objective markers to help select animals of similar disease status and determine effects in the joints. Therefore, the proteomic study highlighted the potential for in vitro models to support field trials by identifying in vivo biomarkers for diagnosing early OA and assessing therapeutic responses. In conclusion, in vitro models of equine cartilage have considerable potential for assessing the ability of plant extracts to target inflammatory pathways and catabolic mediators in OA. The data presented suggests that nutritional intervention using plant-derived extracts with putative anti-inflammatory properties may support equine joint health.

In this thesis, the behavioral, electrographic and neurobiological effects of a period of kainic acid-induced status epilepticus (SE) on the C57BL/6J inbred mouse strain are characterised. The severity of epileptic behaviour was scored, used immunohistochemistry to investigate the anatomical distribution of c-Fos expression in the hippocampal formation following SE and recorded EEG during and after SE using an implantable, wireless telemetry device. Further to assessing the severity of SE, changes subsequent to seizures related to the emergence of chronic epilepsy were investigated, including reactive gliosis and synaptogenesis and epileptiform discharges in the EEG trace. I investigated the potential of a range of pharmacological agents for modulating the severity of induced seizures and disease progression. These included drugs targetting the NR2B subunit of the NMDA receptor (RO 25-6981), neuronal nitric oxide synthase (L-NPA), The post synaptic density protein 95 (Tat-NR2B9a) and inducible nitric oxide synthase (1400W). L-NPA, when administered prior to the induction of SE was found to profoundly suppress the emergence of epileptiform activity, including behavioural, electrographic and neurobiological indicators. Further, L-NPA’s modulation of the precipitating event lead to a decrease in neurobiological changes associated with epileptogenesis, such as reactive gliosis in the CA3 region of the hippocampus and 5 elevated synaptogenesis in th molecular layer of the hippocampus. This correlated with a marked decrease in epileptiform discharges in the EEG trace. A novel method of kainic acid administration was trialed, involving multiple small doses of the drug, titrated by the severity of behaviour. This method led to a decrease in mortality and an increase in the severity and inter-individual uniformity of SE, assessed by the analysis of behaviour, EEG and c-Fos expression in the hippocampus. Furthermore, this method induced neurobiological changes associated with epileptogenesis 3 days following SE and was associated with an increased frequency of epileptiform discharges for 7 days post SE.

The study of behaviour is vital for animal welfare assessment in animal husbandry systems, exploring mechanisms of underlying diverse forms of behaviours and animal physiological and ecological interaction. Understanding animal behaviour is used in a systematic way to unlock and explore underlying functionalities of the brain which is one of the biggest challenges to science. This thesis introduces four novel applications for computational intelligence in human and animal behaviours. The four applications are: horse transport stress prediction system, human activity recognition, fish behaviour tracking and detection, and intelligent interactive fish feeding system. In the first application of human gait recognition, a practical, accurate and novel supervised learning system is proposed to recognize human activities. The proposed system uses single accelerometer device which makes the system practical to use and capable of being integrated with many commercially available devices. This work proposes highly accurate and practical human gait recognition system. In the second application of horse transport, a novel system is proposed to predict horse stress episodes during transport which enables a potential solution of horse stress by interfering at a suitable time. Dynamic nonlinear neural network is trained to predict horse stress time series given travel route and driving style time series. Horse transport is one of the most routinely stressful procedures in equine industry. In the third application of horse transport, a novel system for automatic fish tracking and behaviour recognition system is proposed. Fish are the second most popular experimental model behind mice in pharmaceuticals and biological research. Fish anxious behaviour could confound experiment outcomes. Fish behaviour could also be affected by invasive or non-invasive experiments in addition to other possible causes of distress. The proposed system consists of 3d real-time fish tracking, behaviour quantifying and recognition algorithms. Fish behaviour is estimated through fish swimming patterns. The system showed high accuracy recognition of fish behaviour in experiment where fish were exposed to a variety of external stimuli. In the fourth application of horse transport, an innovative smart fish feeding system is proposed. The fourth application of computational intelligence techniques addresses one of the major challenges in the fastest growing food sector industry worldwide, aquaculture industry. Most conventional fish feeding techniques are inefficient, cause environmental damage and fish losses, raise concerns regarding fish welfare and lead to non-uniform fish growth. Addressing these problems is a necessity for this industry to continue its growth. The novel feeding system is built based on fish behaviour which recognises, and assesses fish behaviours and interacts with fish to optimise the feeding process. Fish showed quick adaptation to this novel low-cost feeding system which proves the feasibly of implementing this system. The proposed system is expected to reduce food competition and environmental impact because of its responsive nature. Through novel applications of computational intelligence, this thesis has provided successful solutions for human and animal behaviour analysis research problems.