Tropical forested peatlands are a major carbon store and are a significant source of global carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) emissions. While the role of environmental variables, including temperature and water table depth have been relatively well studied, uncertainty remains in the extent to which plant roots regulate greenhouse gas (GHG) fluxes and peat biogeochemistry. This study examined the role of roots, and root inputs of carbon and oxygen in regulating fluxes from peat under two dominant plant species, Campnosperma panamensis and Raphia taedigera, a broadleaved evergreen tree and canopy palm, in San San Pond Sak wetland, in Bocas del Toro Province, Panama. A combination of in situ and ex situ experiments were performed between February 2015 and August 2017. Small scale variation in GHG fluxes and peat biogeochemistry was measured at two distances within the rooting zones of C. panamensis and R. taedigera. Peat organic matter properties were assessed using Rock-Eval 6 pyrolysis. Results indicated significant variation in CH4 but not CO2 fluxes at different distances within the rooting zone, with CH4 fluxes subsequently linked to measures of the overall size of the available organic carbon pool (S2). Rock-Eval pyrolysis data was used to construct a three-pool model of organic matter thermostability which indicated significant differences in organic matter composition between peats derived from different botanical origins, in addition to a high level of heterogeneity within the rooting zone. Changes in GHG production and peat biogeochemical properties in response to the addition of root exudate analogues were assessed in an ex situ anoxic incubation experiment. A combination of organic acids and sugars, identified as common forest plant root exudate components, were added over a two week period to peats derived from C. panamensis and R. taedigera. GHG fluxes varied significantly between treatments but not by peat botanical origin, and were associated with significant changes in soil properties including, pH and redox potential, thereby demonstrating a link between plant root carbon inputs, peat properties and GHG fluxes. In situ mesocosms were used to assess the effects of root exclusion on peat biogeochemistry and GHG fluxes. Partial and full root exclusion significantly reduced dissolved oxygen concentrations and was associated with greater root necromass. Full root exclusion increased CH4 fluxes five-six fold compared to partial root exclusion, equivalent to an 86 - 90% reduction in CH4 oxidation, demonstrating the important role of root inputs of oxygen in mitigating CH4 efflux from tropical peat. A 13CO2 pulse labelling experiment was conducted using both R. taedigera, C. panamensis, and Symphonia globulifera, a second broadleaved evergreen tree species, to demonstrate a direct link between plant photosynthesis and CH4 fluxes, and identify aspects of the bacterial and fungal community associated with the turnover of labile carbon. The extent of 13C enrichment of CH4 differed significantly between plant types (palms vs broadleaved evergreen trees), as did the extent of net CH4 efflux. Phospholipid fatty acid (PLFA) biomarker analysis indicated both peat types were dominated by Gram negative bacteria. There was strong 13C enrichment of Gram negative bacteria, supporting their previously proposed role as important decomposers of labile carbon. Collectively, these results demonstrate that root inputs of carbon and oxygen can strongly regulate tropical peatland GHG fluxes, and that the extent of regulation can vary significantly between tropical wetland plant species from contrasting dominant plant types. This is particularly important in understanding regulatory processes in a globally significant carbon store and understanding possible consequences of land use change in the tropics.

Weaning is a stressful period in the early life of a pig. This stress manifests as immediate weight loss coinciding with increases in intestinal transepithelial resistance. This study aims to identify the transcriptional differences in the colon between suckling and weaned animals over this period using RNA-seq. This approach identified the maximal transcriptional differences at one-day post-weaning with 353 transcripts differentially expressed compared to 78 and three transcripts at four and fourteen days post weaning respectively (q < 0.1, FC > 2). This work identified increased transcription of pro-inflammatory cytokine genes including IL1A (FC=2.63) and IL1B2 (FC = 2.98) in the colon of weaned animals at one-day post weaning, suggesting activation of the immune system. The same time points at one, four and 14 days post weaning was used to assess the transcriptional effect of supplementation with probiotic Saccharomyces cerevisiae boulardii (4.43 Log10 CFU per day from seven days of age) on the colon. A distinct effect of probiotic yeast supplementation on transcription in the colon was identified in both weaned and suckling pigs. One, 77 and one transcripts were affected by the probiotic in weaned animals at the three time points respectively compared to 197, six and two in suckling animals. However, evidence of an anti-inflammatory effect (including increased expression of IL10, FC = 2.88) was identified in weaned animals at four days post-weaning. The clear distinction between differential expression in weaned and suckling animals suggests that the transcriptional effect of Saccharomyces cerevisiae boulardii supplementation may depend on the physiological state of the host. These differences may be due to the interaction of the probiotic with the host immune system as a result of weaning related bowel disruption.

The development and analysis of crop models of differing complexity is presented, ranging from a simple, static, empirical model, to more complex, dynamic, mechanistic models. Two models, an existing mechanistic model (Sirius) and a new mechanistic model of more intermediate complexity (Intermediate), were developed and analysed using relatively detailed field-level observations. In contrast, two new simpler models, an empirical and a mechanistic model, were developed using relatively coarse farm-level observations. Analysis of the existing mechanistic model (Sirius) revealed that a number of model variables and cultivar-specific parameters were redundant and did not contribute to model performance. The results of this analysis informed the development of mechanistic model of more intermediate complexity (Intermediate), although this was also indicated to contain redundant variables and parameters. Vernalisation simulation was one aspect of the models that was consistently identified as an area of redundancy. These reduced models are a product of the data used to generate the reduced model - in this work, simplified versions of the models were identified that were capable of maintaining the ability to predict differences in cultivar growth and development under different nitrogen treatments. Careful consideration needs to be given to the application of the reduced model, to inform the data used in the reduction. Automated, comprehensive model reduction techniques, such as the one employed here, have the potential to be important tools in reducing unnecessary model complexity, and associated uncertainty, for an application. This unnecessary complexity can act as a barrier to application, analysis and understanding. An empirical (Simple-EMP) and simple mechanistic (Simple-MECH) model were additionally developed to predict wheat yield at the farm-scale, using farm-level observations. The empirical model produced more accurate predictions of wheat yields than the mechanistic design, which was hindered by the monthly time step necessitated by the driving meteorological observations and the lack of traditional mechanistic model input observations. The farm-level survey data from which these models were developed is collected annually, and suggestions for further development of these models are made, including (i) incorporating newly available data on fertiliser application to replace the existing proxy, and (ii) exploring the potential to obtain additional data traditionally required by crop models, primarily the timing of important management decisions, for example, sowing and harvest dates.

Floriculture, a flourishing industry since the end of 1990s, is a source of livelihood for thousands of people in Ethiopia. Investment into the sector has been promoted with the objective of creating employment opportunities, foreign exchange earnings and links to the international market. Flowers are now among major export commodities along-side other agricultural products such as coffee and oil seeds. The sector’s contribution as a source of employment is considerable in terms of poverty reduction as poverty is a deep rooted problem in Ethiopia. However, there are challenges related to employment conditions and environmental externalities. This thesis examines into the problems of environmental protection and regulatory frameworks regarding the floriculture industry. It provides analysis on factors that affect the effective implementation of regulatory frameworks. The thesis addresses the main environmental challenges associated with flower production. The main analysis is that in Ethiopia the problem basically lies with excessive application of pesticides and fertilisers; the impact eventually extends to affecting water and soil quality. Concerns about excessive utilization of surface and ground water are also addressed. With case studies of two freshwater lakes, the thesis demonstrates how establishment of floriculture companies adjacent to lakes compromise water quality and quantity, and affects aquatic life. Focusing on each environmental problem, the thesis provides analysis on existing regulatory frameworks and identifies lack of effective implementation as the root of the problem leading to environmental degradation. The country’s level of development has been a restricting factor to channel resources necessary to employ expertise and infrastructure. At the same time, there are tendencies of prioritizing economic development, through attracting investment, than environmental protection driven by the belief that strict regulation obstructs investment. The thesis also highlights that absence of effective and adequate regulatory framework has been a challenge to the objectives of investment promotion in Ethiopia and the right to improved living standard and to sustainable development guaranteed in the Constitution. The thesis suggests that strict monitoring and inspection of flower production process is needed, and the primary response to regulate environmental impacts must rest on the government. It identifies a number of intervention areas, including strengthening pesticide registration and control system, putting in place water use and discharge permit systems, requiring Environmental Impact Assessment reports and supporting companies to implement sustainable flower production methods. Promoting good agricultural production methods, private environmental standards and certification schemes can play role in improving environmental standards. However, compliance expenses can restrict industry wide implementation of the standards. The analysis offered in the thesis provides an evaluation of the main challenges facing the Ethiopian flower industry at a time of increasing volatility in the market. This is the first legal analysis of the environmental impact of flower industry in Ethiopia.

Ovine footrot is an infectious cause of lameness in sheep that has significant economic impact for the UK sheep farming industry. It is also a major concern for animal health and welfare. The causal agent is Dichelobacter nodosus, and Fusobacterium necrophorum is an opportunistic secondary pathogen that increases disease severity. The primary reservoirs for F. necrophorum in sheep were believed to be sheep faeces and the environment, however, no studies had demonstrated the presence of F. necrophorum at either of these sites. Two longitudinal studies (Study A and Study B) were conducted to determine reservoir sites of F. necrophorum in ovine footrot. Study A included 10 sheep sampled on four occasions at two week intervals. Study B included 40 sheep sampled weekly for 20 weeks. Samples collected from sheep and their environment were foot swabs, mouth swabs, faeces, soil and grass. Quantitative PCR was used to detect and quantify F. necrophorum. A multiple locus variable number tandem repeat analysis (MLVA) community typing scheme for F. necrophorum was developed and validated, and used to analyse samples from Study A and Study B. Contrary to prior assumption, the environment was not a significant reservoir of F. necrophorum. F. necrophorum persisted in sheep, primarily on feet with footrot. MLVA indicated that the strains of F. necrophorum found on the feet of sheep were closely related, and they may therefore share characteristics that make them well adapted to feet and footrot. Mouths and faeces were an intermittent reservoir for the strains of F. necrophorum involved in footrot. Mouths and faeces may therefore facilitate persistence of F. necrophorum in the absence of footrot, or facilitate transmission of F. necrophorum between flocks. Mouths were a persistent reservoir for strains of F. necrophorum not involved in footrot.

The diamondback moth (DBM), Plutella xylostella L. (Lepidoptera: Plutellidae), is the most important global pest of Brassica crops. It is now prevalent wherever Brassicas are grown and costs the agricultural industry US$ 4-5 billion annually. Traditionally, DBM is controlled by the use of insecticide only applications which has led to wide spread insecticide resistance in DBM populations. As insecticide only control strategies are not viable in the long term, it is the opinion of many experts that integrated pest management (IPM) is the way forward for DBM control. A component of the IPM system which holds great potential is entomopathogenic fungi (EPF). Despite their promise, EPF are not currently routinely used by growers to control DBM. This is mainly because the efficacy of EPF biopesticides tends to vary from one application to the next. The aim of this project was to study interactions between EPF and other elements of the IPM system to understand and address sources of variability. Temperature is the most important determinant of EPF growth, virulence and DBM development. However, there are considerable knowledge gaps when it comes to understanding the effect of temperature on these processes. This is mainly because of the left-skewed nature of the physiological response to temperature. We assessed the suitability of five non-linear models to describe these interactions and found Briere-1 to be the most appropriate model. Cardinal temperatures taken from it were used to develop a day-degree (DD) model which could accurately predict the virulence of EPF against DBM at fluctuating, “field realistic”, temperatures. In an IPM system, EPF would be applied with synthetic insecticides. Consequently, it is important to know how co-application of these products would affect the survival of groups of DBM larvae. After applying low-concentrations of various insecticides with EPF we found there to be negligible evidence of antagonism, indicating the insecticides and EPF are compatible for use within an IPM system. Finally, the effect of the age structure of the DBM larval population on efficacy of EPF biopesticides was investigated. We found that, because larvae slough off conidia during ecdysis, time between treatment of EPF and moult had a significant effect on larval mortality. It is hoped that this study will improve growers’ confidence in EPF biopesticides, and expedite their use within IPM systems to control DBM.

Ovine footrot (FR) is an economically important disease that causes lameness and affects sheep flocks worldwide. It is characterized by interdigital skin inflammation (interdigital dermatitis [ID]) with, or without, separation of the hoof horn from the underlying tissue (severe footrot [SFR]). The primary causative agent is the gram-negative anaerobic bacterium Dichelobacter nodosus, which is present in diseased feet and thought to be transmitted via contaminated surfaces. Periods of apparent zero prevalence of FR in a flock can be followed by disease occurrence when the climate becomes favourable for pathogen transmission. This suggests that there are sites where D. nodosus persists in the absence of disease. These sites might include healthy feet, the gingival cavity and faeces of sheep and also the environment. The aim of this thesis was to investigate persistence of D. nodosus, by investigating possible sites of survival of D. nodosus over time. Prospective longitudinal studies were used to investigate persistence. Samples were collected from sheep and from the pasture in three studies (Studies 1 and 2: England, study 3: Spain). Quantitative PCR was used to detect and quantify D. nodosus and to investigate associations between D. nodosus presence in feet, in the gingival cavity and on pasture and a range of predictor variables including climate. A multiple locus variable number tandem repeat analysis (MLVA) suitable for use on mixed DNA and environmental samples was optimized and validated to investigate D. nodosus strains within and between sites. A novel approach to characterize individual strains in a sample was designed. D. nodosus was detected in all sample types in all studies but not on all occasions. The feet of sheep were the only site where D. nodosus was detected in loads exceeding 103 cells per swab. In study 1, D. nodosus was detected in amounts exceeding103 cells in samples collected from the pasture in week 1 only, when detection frequency of D. nodosus on feet was high and the weather was wet. A minimum of 14 strains of D. nodosus were detected on the feet of sheep by MLVA. A decline in detection of D. nodosus in the environment coincided with periods of dry weather, however, dry weather did not coincide with a decline in D. nodosus loads on feet or incidence of disease. D. nodosus was more likely to be detected in the gingival cavity when a sheep had FR. It was detected in 25 % of gingival cavity samples and strain types identified in the gingival cavity were the same as the dominant strain types on the feet of sheep. In study 2, disease prevalence and D. nodosus detection frequencies were lower than in study 1. When sheep from the study group were separated from the main flock in week 1 and moved onto pasture that had been unoccupied for 10 days, D. nodosus was transferred to the study group on healthy feet. One dominant strain of D. nodosus persisted throughout an episode of disease and this strain was present on the healthy feet of sheep until up to 5 weeks before the development of lesions in high bacterial loads. There was a reduction in lesion severity and reduced detection of D. nodosus in soil in a period of dry weather. Only 1 sample from the gingival cavity was positive for D. nodosus. Two faecal sample were positive for D. nodosus, indicating for the first time that faecal shedding is possible. In study 3, there were high loads of D. nodosus on healthy feet of a sheep that was classed as susceptible when there had been no cases of FR for at least 2 month. D. nodosus was still present in the flock during the long non-transmission period in the summer. We conclude that D. nodosus is more likely to persist on the feet of sheep, whereas long-term environmental reservoirs of D. nodosus are unlikely. Future research should focus on the feet of sheep and possibly faeces as possible sites of persistence of D. nodosus in the absence of disease.

Pesticides are vital for controlling agricultural pests and increasing crop yields; however, they can have detrimental effects on the environment and human health. Regulatory laboratory studies need to be carried out to assess the risks of a pesticide before it can be produced and sold. These regulatory studies tend to poorly predict pesticide fate and degradation in the field, likely due to specified test conditions not accurately representing the environment. This thesis focuses on the potential for adding greater environmental realism to regulatory-type tests, using the fungicide isopyrazam in OECD 308- and 309-type studies. Regulatory tests are carried out under dark conditions. Microcosm studies were conducted in the presence of non-UV light to minimise photolysis, yet include phototrophic transformation; there was significantly more biodegradation in illuminated microcosms compared to those carried out in the dark, in which there was little degradation. The effect was more pronounced in water-sediment microcosms compared to water-only microcosms, as the sediment provided a platform for phototrophic biofilm development. Regulatory tests do not consider temporal variation in the microbial composition of environmental inoculum. Experiments carried out over two years showed that the outcome of tests, in terms of both degradation and mineralisation, were variable with inocula collected at different time periods from the same river location. Regulatory tests are also carried out statically. Recirculating microflume experiments showed that flowing water increased dissipation compared to static systems, regardless of light treatment. This suggests regulatory tests are not properly representing flowing aquatic systems, e.g. rivers. Lastly, regulatory tests are carried out on a small scale. Although there was little effect on pesticide decline in different sized microcosms, in the larger microflumes, dissipation occurred even under dark conditions. A number of Operational Taxonomic Units were specific to the microflumes suggesting that, on a larger scale, there was a wider variety of microorganisms that better reflected the environment. This work provides evidence for potential modifications to regulatory tests and insight into non-standard tests that industry could include in regulatory submissions.

While culture is a widely accepted issue in therapy, current approaches are criticised as unfit for purpose in a postmodern, postcolonial world characterised by large scale migration, cheap air travel and instantaneous electronic communication. This study attempts to move beyond crude ethno-cultural categories to view culture as a universal human phenomenon. It is a conception that admits characteristics of volatility, plasticity, contextuality and intersectionality; virtually unlimited hierarchical distinctions and dimensions that frequently come to stand in for each other. In addition, it attempts to view culture in positive terms, rather than as an unwanted obstacle to approaches to therapy that are historically rooted in dominant cultural groups. Four participants were selected using purposive sampling, and data was collected using semi-structured interviews, which were recorded and transcribed. The transcripts were then analysed narratively and using thematic analysis, and reported against a common subset of superordinate metacultural themes. While the study is a small scale exercise with admitted limitations, it provides support for a more universal view of culture; and the idea that it is a powerful personal resource that can be used both consciously and unconsciously. Personal factors caused participants to emphasise certain aspects of their cultural background and de-emphasise or avoid others. Participants attempted to seek out or access additional resources that helped to represent aspects of their personal story. The study provides support for three theoretical ideas: culture as a resource, cultural identity and personal culture; and it suggests ways in which culture can be used in therapy as a diagnostic and therapeutic tool. Further work includes additional case studies employing a more comprehensive methodology, the use of discourse analysis to provide a degree of triangulation and investigate the discursive processes at work, and extension of the approach to areas beyond therapy.

Plants - including commercially important crops - are exposed to numerous pathogens often resulting in significant loss of yield. Understanding the underlying mechanisms of pathogen recognition and defence strategies is key in successfully ensuring food security. Research on plant-pathogen interactions has mainly focused on the gene networks after pathogen perception as well the identification of resistance genes. Latest research suggests that chromatin remodelling, including nucleosome displacement and DNA or histone-modifying enzymes are important in plant immunity. This thesis focuses on chromatin remodelling as the mechanism by which plants mount an effective immune response. The thesis also investigates the role of histone acetylation as one of several chromatin remodelling mechanisms. Histone acetyltransferases (HATs) and histone deacetylases (HDACs) are two classes of histone modifying enzymes that antagonistically govern the acetylation levels of histones in gene promoters and gene bodies ultimately affecting gene expression. HAG1 was identified as an important positive regulator of plant immunity in the interaction with Pst DC3000. A proteomic approach allowed the identification of TOPLESS family members as HAG1 interactors. Considering that chromatin remodelling is an important aspect of plant immunity, it was hypothesised that pathogens have evolved mechanisms to interfere with such processes. To this end, this thesis will present a comprehensive approach towards identifying Pst DC3000 Type-III effectors with the ability to interfere with chromatin remodelling. HopO1-1 was initially identified as an effector with chromatin binding properties, however, further experiments pointed more strongly towards this effector’s involvement in processes such as translation and photosynthesis. Overall, this thesis contributes towards a better understanding of the roles of histone acetylation and HAG1 histone acetyltransferase in plant immunity and sheds light into which Pst DC3000 effectors could be potentially involved in chromatin remodelling processes.