Constructive alignment (CA) describes an approach to education where teaching, learning and assessment are aligned to allow the learner to achieve the intended learning outcomes (ILOs) of the course. Assessment has a strong influence on learning and therefore the potential to have either a positive or negative impact on CA. The aim of the research in this thesis is to explore the effects of assessment on CA. The context for the research is the final year of study within the School of Veterinary Medicine and Science (SVMS), at the University of Nottingham. Five mixed methods studies were conducted utilising questionnaires, semi-structured interviews and focus groups. In study one the ILOs of the course were defined and subsequently used in study two as a framework for an alumni survey to determine how well prepared graduates feel for clinical practice. Studies three and four investigated the impact of assessments on learning behaviour, namely multiple-choice questions (MCQ), directly observed procedural skills (DOPS) and the script concordance test (SCT). Finally in study five the influence of the transition to practice on learning behaviour during final year was explored. Graduates felt well prepared by the SVMS curriculum for a career in practice with respect to all ILOs. However, assessments were not rated so highly when considered alone. DOPS and to some extent the SCT are considered to be authentic assessment formats and encourage a deep approach to learning. The MCQ in this context results in surface learning strategies being adopted. The imminent transition to practice has a positive effect on learning behaviour, however this conflicts with the preparation required for final year examinations. Elements of the assessment strategy that have a positive and negative impact on CA are identified and discussed. Changes to the curriculum are proposed to enhance CA and ease the transition to practice.

Fusarium head blight (FHB) is a devastating fungal disease of wheat and other small grain cereals worldwide caused by a complex of toxigenic Fusarium spp. and non-toxigenic Microdochium spp. Infection leads to a reduction of grain yield, loss of grain quality and the production of harmful mycotoxins. Control methods for FHB include both cultural and chemical strategies, however the development of cultivars with improved FHB resistance is considered as the most sustainable method for controlling the impact of this disease. Resistance to FHB is a polygenic trait and can be improved by stacking multiple resistance genes together, however there are currently no highly FHB resistant genotypes with acceptable agronomic characteristics available, therefore passive disease resistance can potentially make significant contributions to improved FHB resistance. The aim of this study was to identify novel physiological traits in wheat conferring passive resistance to FHB using ground inoculated field experiments to enable disease escape mechanisms to be expressed, and spray inoculated glasshouse experiments to test if the identified traits were associated with genetic resistance. The most consistent traits relating to FHB were flag leaf length, plant height and awn length. Since these relationships were present in both field and glasshouse experiments, they are likely caused by a genetic linkage or pleiotropy, with genes conferring FHB resistance or susceptibility. Remaining leaf area was less consistently related to FHB, however, since canopy leaf area showed a positive relationship with the development of FHB in ground inoculated field experiments, there is a basis to support the role of reduced canopy leaf area as conferring passive resistance to FHB. In general, relationships were poor between visual FHB symptoms and both pathogen DNA and grain mycotoxin contamination. This was theorised to be due to the use of a mixed species inoculation which introduced antagonism between FHB species and which included more than one producer of several mycotoxins quantified. Therefore the use of visual FHB assessments under mixed species inoculation is concluded to be a poor indicator of both pathogen infection and mycotoxin contamination.

Routinely collected herd management data in a variety of formats were collated from 468 dairy herds, and novel objective measures of data recording quality were developed and applied. This revealed that there was a substantial amount of variation in data quality between herds, and the vast majority of herds failed to meet the threshold level for at least one of the data quality measures used. Analysis of trends in reproductive performance across the herds with good quality fertility event recording suggested that their fertility was generally declining through the first half of the 2000s, but there was some evidence that improvements in submission rate were beginning to reverse this decline in the later years studied (up to 2007). Associations between reproduction and two endemic diseases common in dairy cattle (mastitis and lameness) were explored using multilevel discrete time survival modelling, and probabilistic sensitivity analysis (PSA) used to contextualise and illustrate the results. In both cases, statistical modelling revealed significant and sizeable associations between disease events and reproductive outcomes at lactation level. However, simulation and application of PSA showed that a herd’s incidence rate of either disease was highly unlikely to influence its overall reproductive performance to a clinically relevant degree when other inputs to herd fertility were also considered. Factors associated with the proportion of serves leading to a pregnancy (pregnancy rate) were explored using multilevel logistic regression modelling. This revealed that relatively little of the variation in herd pregnancy rate is explainable by routinely recorded milk recording data (including constituent concentration in early lactation as well as daily and lactation yields). A large amount of the unexplained variation was revealed to be at herd level and very little at cow level, suggesting that investigation of herd management practices associated with pregnancy rate would be rewarding.

Groundnut, Arachis hypogaea (L.), can be attacked by a range of pathogens, including Aspergillus species, which can cause accumulation of the mycotoxin aflatoxin. Although some success in controlling this pathogen has been achieved with application of fungicides, their use is not always feasible in developing nations like Nigeria. The aim of this study was, therefore, to evaluate naturally-occurring plant oils and BCAs with a past history of efficacy as alternatives to fungicides for reduction of Aspergillus infection and aflatoxin accumulation in groundnut. Aspergillus strains and thirteen different plant essential oils were tested. The oils were derived from clove, camphor, vanilla, garlic, galangal, green oregano, lemon grass, neem, ginger, basil, tea tree, thyme and onion. The biocontrol agents used were fungi Trichoderma harzianum strain T-22, T. asperellum and T. viride from a commercial biocontrol product, TUSAL, and bacteria Pseudomonas chlororaphis ssp. aureofaciens and Bacillus amyloliquefaciens (strains MBI600, 62P, and 66P). The identities of a strain of A. niger, isolated from Nigerian groundnut samples, and of T. asperellum and T. viride were confirmed by PCR amplification of DNA and sequence comparison to reference isolates in the GenBank database. Some of the plant oils (clove, camphor and vanilla) and biocontrol agents (Trichoderma strains) tested proved effective in inhibiting the A. flavus and A. niger strains used in the research, in both in vitro and in planta experiments. Improved seedling emergence in pathogen-contaminated compost and reduced post-harvest pod infection were observed. Combinations of the most active BCAs and EOs also provided disease suppression. ELISA analysis of aflatoxin B1 in treated, A. flavus-inoculated groundnut pods showed a reduction in toxin concentrations, to a level below that recommended by the European Commission of 15 ppb. Of the control agents tested, the most effective were T. harzianum T-22 as a BCA and probably clove oil as a plant extract. Commercial products based on Trichoderma are used world-wide. EOs, have, to date, had little use in control of Aspergillus infection of groundnut. It was also demonstrated that detection of asymptomatic A. flavus pod infection could be achieved by the traditional method of surface sterilisation and plating out, and by use of a LAMP assay to detect pathogen DNA. The latter could provide a rapid, portable method for A. flavus detection in harvested groundnut pods and could have application in both developed and developing nations. Since low resource growers in nations like Nigeria need alternative, low-cost methods for protecting groundnut from Aspergillus infection, to produce a nutritionally-valuable, high protein foodstuff low in toxin contamination, such alternative methods of disease control may have a future role to play in global food security. It may prove possible to extract antifungal components from appropriate, locally-sourced plant material in a cost-effective manner. However, whether the level of disease control and suppression of aflatoxin accumulation reported here was adequate for possible commercial application is unclear. Further evaluation, including field experiments, is required.

A substantial increase in wheat yield is needed for global food security. This requires a comprehensive understanding of the physiological and genetic basis of yield determination. The present study aimed to dissect yield physiologically and genetically in a recombinant inbred line mapping population derived from bread wheat × spelt. A total of 201 traits were investigated in the field and glasshouse across three years, and these traits formed five themes: genetic variation in yield and yield components, and the usefulness of spelt as a genetic resource; tillering dynamics; biomass accumulation; flowering time and subsequent leaf senescence; and grain filling processes. Large genetic variation in all traits was found, and spelt showed many desirable traits and alleles independent of low threshability, so it can be used to broaden genetic diversity for yield improvement in bread wheat, while maintaining the free-threshing habit. Quantitative trait loci for tiller production and survival were identified, which were also affected by light environment under the canopy: low red:far red ratio (R:FR) led to early tillering cessation, few total shoots, high infertile shoot number and shoot abortion, probably resulting from an assimilate shortage due to early and enhanced stem growth induced by low R:FR. More fertile tillers normally contributed to plant yield and grain number, but reduced individual grain weight, partly because of smaller carpels and fewer stem water soluble carbohydrates at anthesis. In addition, preanthesis biomass accumulation increased yield and yield components. For grain weight, slightly early anthesis and delayed but fast leaf senescence were associated with larger grains. Carpel size at anthesis, grain dry matter and water accumulation, as well as grain morphological expansion, determined final grain weight, because of pleiotropy or tight gene linkages. These findings provide deeper insight into yield determination in wheat, and facilitate trait-based physiological and molecular breeding.

The small East African shorthorn zebu (EASZ) is an indigenous stable zebu x taurine admixed cattle population highly adapted to the local African environment, i.e. disease resistance, thermotolerance, sustain themselves on poor feed quality, in comparison to the exotic productive cattle. Understanding the genetic control of their adaptations will help sustainable breeding improvement programs, both within populations and through crossbreeding. In this thesis, genome-wide SNP data, from two commercially available SNP arrays; the Illumina BovineSNP50 BeadChip v.1 and the Illumina BovineHD BeadChip, and full genome sequence of 10 pooled EASZ samples were used to define candidate regions with signatures of positive selection in the genome of EASZ. In chapter 2, the low-density SNP chip has defined 24 candidate regions (21 in the autosomes and three in the sex chromosome X (BTA X)) by two Extended Haplotype Homozygosity (EHH)-based (intra-population iHS and inter-population Rsb) analyses and an inter-population FST approach. Characterising the EASZ genome with high-density genome-wide SNP analyses (meta-SS, Rsb, iHS and ΔAF) and pooled heterozygosity (Hp) sequence analysis, in chapters 3 and 4, identified a total of 266 autosomal and 20 BTA X candidate regions. Analysing genome-wide SNP data of zebu cattle populations from Uganda and Nigeria classified some of these regions as East African zebu-sharing and East and West African zebu-sharing candidate regions. Genes and quantitative trait loci (QTL) associated with adaptive traits (e.g., reproduction, immunity and heat stress) were found within the identified candidate regions. Moreover, Nine non-synonymous variants were found in five candidate genes and considered as possible causative mutations under selection. Finally, the mitochondrial DNA (mtDNA) of 13 EASZ were investigated and affiliated to T1a, T1b and T1b1 sub-haplogroups. No selective advantage was found to be associated with taurine mtDNA over the zebu type. Although purifying selection is the main selective factor influencing African cattle mtDNA, in Cox-2 gene of the T1b/T1b1 sub-haplogroups a non-synonymous mutation may confer a selective advantage. The results of this thesis are just the first milestone to define the valuable genetic material in EASZ, which should be conserved in future composite cattle upon informed selective crossbreeding and/or the recently introduced gene modification techniques (TALEN and CRISPER/Cas9).

Obesity is a growing problem for humans and their horses and ponies, yet emaciated animals still form an important part of the work of equine welfare charities. Non-invasive yet reliable methods of assessing equine body fat are required in order to promote management procedures to improve animal welfare. The overall objective of this work was to investigate the application of a horse-specific body condition scoring system in ponies in order to either validate or revise it, or even replace it with a novel system if necessary. Seasonal differences in appetite, body mass (BM) gain, body condition score (BCS) change and direct (ultrasound) and indirect (morphometry and D2O dilution) measures of body fat were explored in two relatively homogeneous groups of mature Welsh mountain pony mares, studied over summer (June –September 2007) and winter (January-April 2008). The ponies in each group were paired so that, at study outset, two ponies were ‘thin’ (BCS, 1-3/9); two were ‘moderate’ (BCS, 4-6/9); and two were ‘obese’ (BCS, 7-9/9). The greatest appetites (peak 4.6% BM as DMI), increases in body mass (~60kg) and in BCS (~3 points) were recorded for ponies of non-obese outset condition in summer (non-ObS, n=4). For ponies of non-obese outset condition in winter (non-ObW, n=3), appetites peaked at 3.5% BM as DMI, BM increased by a mean of 50kg and BCS increased by ~2 points over the 3 month study period. Appetites for all obese (Ob, n=4) ponies remained almost constant (~2% BM as DMI; peak 2.3% BM as DMI) and minimal changes in BM (n=3) and BCS (n=4) were recorded, regardless of season. All measures of body fat increased for non-Ob ponies (non-ObS>non-ObW). An exponential relationship was determined between body fat content and BCS and for values > 6, BCS was not a useful predictor of actual body fat content. The endogenous circannual mechanisms to encourage winter weight loss were insufficient to prevent the development of obesity in ad libitum fed ponies. The effects of dietary restriction to 1% BM as DMI were studied in a group of 5 overweight or obese mature pony mares (BCS 5.6-8/9). Those measures outlined above were likewise recorded. All ponies remained healthy throughout the 12 week trial. Overall, BM reduced by 1% of outset BM per week. Approximately half the lost BM comprised fat, but fatter animals lost relatively more fat. Despite an average loss of ~30 kg BM, BCS did not change appreciably suggesting that BCS was a relatively poor indicator of early weight/fat loss in obese ponies. The relationships between BCS, direct (ultrasonic) and indirect (morphometric and D2O dilution derived) measures of body fat and actual body fat content determined by both physical dissection and chemical cadaver analysis were explored using 7 donated mature Welsh pony mares (BCS 1.25 to 7/9). Body ‘fat’ content (dissected white adipose tissue or chemically-extracted lipid fractions) was the most variable constituent of the cadavers (up to 1/3rd body mass), and was non-linearly related to BCS. From these studies, it was also possible to validate the D2O dilution technique for the measurement of total body water and fat in ponies. Contemporaneously gathered data for BCS and body fat (D2O dilution) from 48 separate observations were explored statistically. A non-linear association between body fat content and BCS was confirmed, with a cut off value of BCS 7/9, above which BCS was less useful for determining body fat content. A novel BCS system was created and is undergoing field trials.

Despite the fact that urban regeneration has been practiced for more than 40 years, there is still a lack of rigorous research on what constitutes best practice in evaluating urban regeneration interventions. It can be argued that in the late 1970s and early 1980s, evaluations were mostly focused on assessing the feasibility of projects, while in the mid 1980s evaluations were mostly conducted to examine the outcomes of projects or programmes instead of their effectiveness. It was only after the late 1980s that programme evaluations were carried out to examine the effectiveness of a programme. However, in spite of this development, such assessments were still considered inadequate. In this research, for example, it was soon discovered that the evaluation of urban regeneration initiatives through a regional park programme was almost entirely performed in isolation without any attempt to compare them with other similar initiatives. The practice of a regional park programme in delivering urban regeneration initiatives is seen as an important programme in the UK given that it promotes a large area within a high urban population location. Additionally, a regional park provides the opportunities for recreational and leisure purposes especially for the locals and the region therefore plays a vital role as a visitor destination. Hence, in order to serve its purpose completely, the performance of this intervention is essential. The essence of this research therefore seeks to address the gaps and to inject a comparative dimension and find the appropriate tools to measure the performance of urban regeneration initiatives in contrast to the current standard evaluation procedures. The research has been designed with the aim of seeking practical and effective ways of applying the benchmarking method and realistic evaluation as a combined assessment tool in evaluating the performance of such initiatives. For this reason, the research focuses on the functioning of the urban regeneration schemes delivered through regional park programmes in the UK. In relation to this, a decision was taken to ‘benchmark’ the Mersey Waterfront Regional Park against the Lee Valley Regional Park and to examine both case studies by means of ‘realistic evaluation’. The rationale for choosing these particular regional parks was made based on the parks’ background. Both regional park programmes have placed emphasis on regeneration of their respective areas. The idea of this comparative exercise is therefore to explore the differences between the Mersey Waterfront and the Lee Valley in terms of programme implementation, project delivery, mechanisms for efficiency, outcomes of programme, the institutional arrangement, the key success factors and the key learning points. These areas of research were therefore justified for the purpose of measuring the performance of a regional park thus teasing out the practicality and potential of both evaluation methods. The end-result of this research discovered that there were various mechanisms affecting the performance of a regional park. Additionally, it was discovered that programme outcomes are influenced by programme settings and delivery mechanisms. The findings also reveal the key lessons to programme performance and the variations of work processes. Nevertheless, the most significant result is the practicality and benefits of using the benchmarking method and realistic evaluation as a combined assessment tool in examining urban regeneration initiatives delivered through regional parks.

Equine laminitis manifests as a painful condition of the foot and is characterised by disruption of the dermo-epidermal lamellar bond within the equine hoof. Chronic pain in laminitis leads to debilitation and if unchecked euthanasia of the horse and is therefore a significant welfare issue for horses worlwide. P2X receptors are shown to have a pivotal role in pain pathways as well as other tissue functions making them attractive candidates for research in naturally occurring diseases such as equine laminitis. In this study, the presence and distribution of P2X receptors in tissues of the equine digit and its associated vasculature and innervation was investigated. The investigation was extended to tissues from horses suffering from naturally occurring chronic active lamintis in an attempt to identify changes in distribution or expression of the receptors in these tissues. Finally, the functionality of the P2X receptors expressed in equine nervous tissue was investigated. Gene expression (mRNA) for all seven receptors was found in the studied tissues and protein expression for P2X1-3 and 7 receptor subtype proteins in these tissues was confirmed with Western blot analysis. Immunohistochemical analysis of P2X1-3 and 7 receptor subtypes distribution showed differential cellular distribution within normal equine tissue and differential distribution and expression between normal and diseased tissues too. In particular, in a horse with shorter duration of chronic laminitis (1 month), P2X3 receptor subtype immunostaining in DRG neurons presented a marked increase in large neurons which coincided with a decrease in the proportion of these neurons in the DRG. Also, horses suffering from chronic laminitis displayed expression of P2X3 receptor subtype in smooth muscle cells of the palmar digital artery which was absent in normal horses. In chronic laminitic hooves, P2X7 receptor subtype showed particularly strong staining in partially keratinised cells. Finally, intracellular calcium measurements provided evidence for the presence of functional purinergic and P2X receptors in equine spinal cord and DRG cells, respectively. The expression of P2X receptor subtypes in key equine tissues for laminitis and chronic pain in laminitis and their differential expression in laminitic tissues highlights a potential role in chronic laminitis molecular mechanisms. Further research in this area may provide insights into putative targets for disease modulation and pain management in chronic laminitis and other conditions of the horse associated with chronic pain.

Canine infections with antimicrobial resistant (AMR), particularly multi-drug resistant (MDR) bacteria are increasing, severely limiting therapeutic options, and representing an animal health issue. In addition, with potential transfer of AMR bacteria between dogs, their environment, humans and other animals, there may also be a public health risk. Commensal isolates can be a source of clinical infections and studies reporting the prevalence of AMR and risk factors for such isolates are important. Furthermore, one of the most significant impacts upon commensal bacterial populations is antimicrobial therapy that may select for pre-existing AMR organisms or transmission of resistance determinants. The aim of this work was to investigate AMR amongst canine commensal bacterial populations and the effects of five different antimicrobials, authorised to treat dogs in the UK, on these populations both during and after therapy. Three groups of dogs were enrolled: healthy non-antimicrobial treated, non-vet visiting dogs (n = 28), to investigate longitudinal carriage of faecal E. coli; healthy non-antimicrobial treated, non-vet visiting, dogs (n = 73) and antimicrobial treated, non-hospitalised dogs (n = 127) to investigate longitudinal carriage of mucosal staphylococci and faecal E. coli. Staphylococci and E. coli isolated from swabs (nose/perineum) and faecal samples respectively, were tested for phenotypic AMR and carriage of resistance genes by PCR assay. Staphylococci were assigned to species by PCR assay (nuc gene), MALDI-TOF-MS and sequencing (tuf gene). Healthy dog E. coli underwent phylo-typing, and a selection of longitudinal healthy dog E. coli isolates were genotyped. Questionnaire data were used to formulate independent variables. Statistical analysis included Pearson’s Chi-square, survival analysis and multivariable logistic regression; multilevel for clustered data. The prevalence of meticillin-resistant (MR; 42%) and MDR staphylococci (resistant to ≥ 3 antimicrobial classes; 34%) was high amongst healthy dogs, however MR-coagulase positive staphylococci were not detected. The most common species detected was S. epidermidis (52% of dogs), followed by S. pseudintermedius (44%). S. aureus was only detected in a small number of dogs (8%). Faecal E. coli with AMR to at least one tested drug (63%), MDR (30%) and AmpC-production (16%) were prevalent in healthy dogs, however ESBL-producers (1%) were rare. Healthy dogs carried a predominance of phylogenetic group B1; group B2 E. coli isolates were less likely to have AMR while group D isolates were more likely. Carriage of E. coli with AMR to at least one tested drug was common and persistent, whereas MDR, AmpC- and ESBL-types were intermittent or transient. Genotyping revealed high intra-dog diversity with frequent new genotypes and resistance phenotypes detected over time. AMR staphylococci and E. coli were detected in more dogs following antimicrobial treatment than baseline, but generally returned to pre-treatment levels within three months. Eating raw meat/animal stools, living with other dogs/in-contact humans or pets that had been hospitalised/in-contact humans working with farm animals were associated with the detection of AMR canine commensal bacteria. In particular, following treatment with beta-lactams or fluoroquinolones there was a significant increase in the detection of MDR and AmpC-producing E. coli or MR- and MDR staphylococci, respectively. However significant differences were not detected at one month after the end of treatment. Antimicrobial therapy is a risk factor for antimicrobial resistant commensal bacteria in dogs and recovery may take up to three months after the end of treatment. This highlights the importance of prudent antimicrobial use and prescribing guidelines. However other factors, such as diet, in-contacts, co-selection and bacterial fitness may be involved in the carriage of resistant bacteria and should be considered.