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Infectious disease is an important issue for animal breeders, farmers and governments. Solutions to control infectious disease are needed and research focused on the genetic loci determining variation in immune-related traits has the potential to deliver solutions. The primary aim of this thesis is to discover regions of the bovine genome which influence the immune response post immunisation. To accomplish this two types of immunising agents, a Foot-and-Mouth Disease Virus (FMDV) peptide (FMDV15) and a commercial vaccine for Bovine Respiratory Syncytial Virus (BRSV), were used to immunise the second generation (F2 and backcrosses) of the Roslin Bovine Genome (RoBoGen) herd, a Charolais Holstein cross population. The FMDV15 peptide consisted of two sections of the VP1 protein located on the FMDV capsid, together encompassing the major neutralising antibody sites that are known to be immunogenic. Protection against FMDV is generally believed to relate to the levels of neutralising antibody and has been correlated with IgG1 and IgG2 levels as well as interferon- . In addition it has been shown that T cell responses also play a role in protection against FMDV. Thus all of these were used as phenotypic measurements post immunisation to the FMDV15 peptide. The BRSV vaccine used was an attenuated live vaccine. Protective mechanisms against BRSV infection include IgA, IgG1, IgG2 and IgM BRSV-specific antibodies and antibody titres particularly those of the IgG isotypes are considered to be correlates of protection. Thus, IgG1 and IgG2 antibody levels were measured post vaccination with the BRSV vaccine. All phenotypes were measured across time, and allowed analysis of the primary and secondary adaptive immune responses. Both agents caused considerable variation in the phenotypes measured post immunisation, with significant responses detected two weeks post immunisation. REstricted Maximum Likelihood (REML) analysis attributed much of this variation to sire, highlighting the heritable component, and environmental effects. Significant positive correlations were detected across time within each trait for both the FMDV and BRSV responses. The FMDV and BRSV antibody levels also correlated with each other at later time points, suggesting that there may be animals which are genetically predisposed to be high or low responders in general. Initially a linkage mappingapproach was followed using 165 microsatellite markers, which detected 77 QTL in response to the FMDV peptide and 27 QTL in response to the BRSV vaccine. There were some overlapping QTL, for example QTL which spanned the Major Histocompatibility Complex. Further analysis was conducted by developing a Perl scripted program which genotyped the RoBoGen herd in two ways; 1) Single Nucleotide Polymorphism(s) (SNP) were genotyped within the confidence intervals of the previously discovered QTL and 2) SNP were genotyped via a candidate gene approach. Association study methodology, accounting for relationship stratification via principal components of the genetic relationship matrix, was used to detect significant SNP, in response to both the FMDV peptide and the BRSV vaccine. Twenty significant SNP associations were discovered across 19 traits, with some SNP located in genes with known biological relevance to an immune response, such as the Toll-Like Receptors (TLR), TLR4 and TLR8. This thesis has detected regions of the genome which are significantly associated with the immune responses elicited by two different agents, suggesting similar pathway(s)/gene(s) may be used in defence of multiple pathogens. Once regions of significance were detected, further analysis using SNP markers identified significant, non-synonymous SNP that were associated with the immunising agents. The novel markers discovered in this study may aid breeding for resistance to disease via marker assisted selection. In addition, they may also have highlighted new targets for vaccinologists to develop ‘next generation’ vaccines.

This thesis explores, develops and implements modelling strategies for studying relationships between childhood growth and later health, focusing primarily on the relationship between the development of body mass index (BMI) in childhood and later obesity. Existing growth models are explored, though found to be inflexible and potentially inadequate. Alternative approaches using parametric and nonparametric modelling are investigated. A distinction between balanced and unbalanced data structure is made because of the ways in which missing data can be addressed. A dataset of each type is used for illustration: the Stockholm Weight Development Study (SWEDES) and the Uppsala Family Study (UFS). The focus in each application is obesity, with the first examining how the adiposity rebound (AR), and the second how the adiposity peak (AP) in infancy, relate to later adiposity. In each case a two-stage approach is used. Subject-specific cubic smoothing splines are used in SWEDES to model childhood BMI and estimate the AR for each subject. As childhood BMI data are balanced, missingness can be dealt with via mUltiple imputation. The relationship between the AR and late-adolescent adiposity is then explored via linear and logistic regression, with both the age and BMI at AR found to be strongly and independently associated with late-adolescent adiposity. In the UFS, where childhood BMI data are unbalanced, penalised regression splines are used within a mixed model framework to model childhood BMI and estimate the AP for each subject. The data correlations induced by the family structure of the observations are addressed by fitting multilevel models in the second stage. Both age and BMI at AP are found to be positively associated with later adiposity. The two nonparametric modelling approaches are found to be effective and flexible. Whilst the thesis concentrates on BMI development in childhood and later adiposity, the techniques employed, both in terms the modelling of growth and the relating of the derived features to the outcomes, are far more widely applicable.

Heterotetrameric sarcosine oxidase (TSOX; EC. 1.5.3.1) from Arthrobacter sp. 1-IN is a complex flavoprotein that catalyses the oxidative demethylation of sarcosine to produce glycine, formaldehyde and hydrogen peroxide. TSOX is composed of four subunits with approximate molecular weights of 106, 43, 24 and 15 kDa the genes for which have been cloned and the recombinant protein expressed at low levels. The Arthrobacter sp. 1-IN genomic DNA containing the sox operon was sequenced and, as well as the four TSOX genes, contains genes for a serine hydroxylmethyltransferase and a formyl-tetrahydrofolate deformylase. Native and recombinant TSOX were expressed, purified and characterised. Cofactor analysis showed that TSOX contains 1 mol each of non-covalently bound FAD and NAD+ and also 1 mol of covalent flavin. The reductive half-reaction of TSOX was studied using stopped-flow spectroscopy. pH dependence of flavin reduction by sarcosine indicated no kinetically influential ionisations in the enzyme-substrate complex. Two ionisations with pKa values of 7.4 0.1 and 10.4 0.2 were identified from a klim/Kd versus pH plot. Kinetic isotope effects studies of the rate of C-H bond breakage in sarcosine indicated a ground-state quantum tunnelling mechanism for H-transfer assisted by the thermal fluctuations of the protein molecule. Anaerobic reduction experiments indicated that the two flavins of TSOX were reducible and that two electrons were required per flavin for complete reduction. The redox potentials for the two flavins were determined and indicated that one flavin had an unusually high redox potential. The inter-flavin electron transfer rate was measured using a pH jump technique between pH 7 and 9. The pH jump experiments and redox potential measurements indicated that the intramolecular electron transfer in TSOX was an endergonic process.

Treatment of Escherichia coli DNA gyrase A protein with trypsin generates two large, stable fragments of molecular masses 64 kDa and 33 kDa which are derived respectively from the N-and C-terminus of GyrA. The trypsin-cleaved A protein (A'), can support DNA supercoiling, relaxation and other reactions of gyrase. The isolated 64 kDa fragment will also catalyse DNA supercoiling but the 33 kDa fragment shows no enzymic activity. An amber mutation, introduced into gyrA near the point which corresponds to the tryptic cleavage site, yields GyrA(1-573) which shares the same properties as the 64 kDa tryptic fragment. Using genetic engineering, large numbers of 3'-gyrA deletion mutants have been produced; those encoding a protein smaller than 58 kDa (GyrA(1-523)) did not obviously overproduce truncated GyrA. GyrA(1-523) shows similar enzymic properties to GyrA(1-573) but cannot perform DNA supercoiling. Deletion of fifty C-terminal residues from GyrA(1-573) has the effect of disrupting part of the protein essential for supercoiling. I propose that the N-terminal 64 kDa represents the DNA breakage/reunion domain of the A protein, while the 33 kDa fragment contributes to gyrase-DNA complex stability. Certain N-terminal deletion mutants of the GyrA protein were also constructed. Removal of the N-terminal 6 amino acids had no effect on the properties compared to GyrA. Removal of the N-terminal 69 amino acids yields a protein with no supercoiling or cleavage ability. The start of the N-terminal breakage-reunion domain is probably located within this 63 amino acid region. The domains of GyrA were investigated by microcalorimetry. GyrA yields two unfolding transitions. GyrA(1-573) and GyrA(1-523) both yield a single unfolding transition corresponding to one of the GyrA transitions. Therefore GyrA contains two structural domains that can be assigned to the functional moieties described above. GyrA(1-573) has been crystallized, and four crystal forms identified. A diffraction pattern to 7 A has been obtained.

Analysis of military campaigns through the use of computational models and simulations, is one of the fundamental methods used within defence Operational Analysis at the Defence Science and Technology Laboratory. It helps to develop understanding behind the value of investment so that an agile defence capability can be built and maintained; in order to face the challenges of an ever-changing world. However, many of these models have been used and adapted continuously over decades, resulting in code-bases that have become unmaintainable in the face of constrained budgets. To address this problem, a number of software modelling framework, based upon the reuse of code and concepts have been developed. However, many of these ultimately did not achieve their full potential, because they merely iterated upon the same software patterns which had been used to produce models to-date. The most recent attempt however, known as the Generic Aggregator Model Valuator, was very different in this regard, due to its exploitation of the emerging Object-Functional design paradigm. As an emerging design paradigm, Object-Functional is still to be more formally understood. There is currently a lack of widely accepted design patterns for the paradigm and explicitly acknowledged examples of its use in projects. This thesis examines the Object-Functional paradigm in greater detail, by performing a qualitative evaluation of defence models built using the paradigm compared to extant models that use other approaches such as Object-Orientation. The evaluation aims to answer two key questions: what benefits does the exploitation of this paradigm bring to defence modelling? But also, what challenges? The Generic Aggregator Model Valuator framework’s implementation of the paradigm is also presented in detail, illustrating the patterns it uses, standing as an example that can contribute to the further refinement of this paradigm in the future.

The purpose of this study was to test a theoretical model which suggests that cognitive, intrapsychic, and family factors interact to facilitate or impede the adolescent separation-individuation process. It was hypothesized that adolescents whose families "cognitively bind" them--i.e. restrict the autonomy of their thinking--would demonstrate generally less effectiveness in thinking about "social topics" (represented in this study by separation-individuation and friendship) than would "non-bound" adolescents. It was also hypothesized that specifically, thinking about separation-individuation would be more adversely affected by cognitive binding than would thinking about friendship. Adolescents who rated their families high in cohesion were also expected to achieve higher cognitive scores than low cohesion subjects in both social domains, but again a more salient effect was expected in the separation-individuation domain. In addition, high cohesion and /or "non-bound" adolescents were expected to show more mature feelings concerning separation-individuation than were low cohesion and /or cognitively bound adolescents. Videotaped interactions of fifty-six fifteen and sixteen year old adolescents and their parents were coded for cognitive binding using the Cognitive Binding Assessment Measure (CBAM) designed for this research. Family cohesion was assessed with the FACES III questionnaire. Adolescents' feelings about separation were measured by the Psychological Separation Inventory questionnaire. The ability to apply their thinking to two social domains, separation-individuation and friendship, was assessed by the This I Believe (TIB) measure, a timed, written test and the Interpersonal Negotiation Strategy (INS), a semistructured interview. General cognitive abilities were measured by the WISC-R Similarities subtest and the Plant Problem which tests the ability to isolate variables. As predicted, high cohesion/non-cognitively bound adolescents outscored low cohesion/cognitively bound adolescents in both domains of social thinking, but not in general, non-interpersonal cognition. Also, CBAM correlated more negatively with separation-individuation than with friendship as predicted, but only for girls and only on the TIB test. Girls' but not boys' FACES III scores correlated with PSI in a number of ways which had not been predicted. Implications of these results for the conceptual model and the significance of the gender differences were discussed.

Refugees and displaced people who have been affected by political instability face complex challenges to access government services. Digital (eGovernment) services perhaps have the greatest potential for overcoming these challenges, particularly in societies and developing countries with limited access to traditional infrastructure and resources. There are limited academic works covering the provision and efficacy of eServices for this need. This work addresses this gap by examining eService provision for three levels of instability (High, Medium and Low, derived from UN data), and focuses particularly on the high-level case of instability in Syria, and on Syrian refugees hosted by other countries. The topic was challenging to investigate, given the current geopolitical context and issues of access to relevant people and stakeholders, which are distributed across countries and involve multiple agencies. A combination of research methodologies has been adopted, in this research. We reviewed the literature that focused on factors affecting the adoption of eService during instability, in which an initial conceptual formwork emerged. We compared eService activities in countries that exhibit different levels of instability, isolating factors and behaviours that led to successful experiences in order to repeat those successes in countries that have high-level of instability. This identified a need for an insightful study within highly unstable countries, therefore, we conducted a questionnaire to capture inputs from groups of displaced people which applied to the Syrian refugees in Syria, Turkey, Jordan, Lebanon and some EU countries. We received 415 complete responses and 1634 partially completed responses to this study. The results indicate possible areas of good practice in the use of technology to support and engage refugees. To find the full set of these activities and good practices we conducted nineteen interviews with different stakeholders and experts from several case studies. In total, more than thirty hours of interview gathered using field-work and teleconference. This research provides a novel framework (Instability Framework) as the main contribution, in which we suggest technology-related strategies, barriers, and enablers that may assist in the effective adoption of eService delivery in unstable countries. Furthermore, Institutional Theory and examples of similar work in government support e.g. reinventing government principles by (Osborn &Gabler and Heeks in the information age) were extended to reflect the adoption of eService delivery in unstable society and used as theoretical lenses to comprehend our results.

Efficient public service delivery is a primary task of public administration within any governance model. The main theme of modern governance implies an integrated, effective and citizen centric practices of government and administration as a prerequisite for a long term positive development of the economy. Electronic public service delivery via e-government portal has become a convenient means for the customers – Citizens and Businesses- to fulfil their requirements. This thesis investigates public service integration practicality, technicality and applicability in Jordan, with special emphasis in applying a novel public service integration model to the Zaatari refugee camp in Jordan. The thesis has primarily identified areas of integration in the public service provision within the Zaatari refugee camp in Jordan. 168 hours of recorded interviews and focus groups resulted from an intensive four year field study has helped defining a very remarkable and rather agile service provision model with four identified stages, namely, manic phase, just in time bureaucracy phase, semi structured phase and structured and sustainable phase. Moreover, this thesis captures essential features of the dynamicity and versatility of service provision models in Zaatari refugee camp. It has also helped in identifying serious issues in the government services provided within the camp, especially in the context of medical and education services. The thesis also argues that humanitarian actors should develop a better provisional model for refugee assistance. The novel service integration model constructed within will contribute to wider range of humanitarian crisis applications, especially in the context of refugee camps. The research strongly suggests that Jordanian government must shift its response from emergency level service provision model represented by immediate humanitarian relief to a structured service provision model represented by self-sustainable and long-term development, and from building camps to supporting cities through a sustainable efficient service provision model. Public service integration within the camp is not only necessary but also critical and crucial to cope with the extensive and sever humanitarian crisis in Jordan. This thesis provides an interoperability integration framework that connects closely coordinated services based on Service Oriented Architecture, Enterprise Service Bus and Web services in an attempt to align the organizational structures and processes of different government departments. The suggested integration framework has been demonstrated on two realistic case examples of public service integration in the current electronic government project implementation in Jordan. The first example is integrating three services, namely, applying for a Tourism Agency License, applying for a Vocational License and applying for No Criminal Record Certificate in a highly interoperable manner and a high level of adaptability to existing government policies and priorities. The second example draws upon the existing dependency in the current public service structure, and it applies the integration framework to Custom Clearance Service, Vocational Licenses and No Criminal Certificate services. Finally, the thesis provides a set of recommendations on how to apply the suggested integration framework to the identified areas of integration in the refugee camp, education and medical services, within the Zaatari refugee camp, and use this as model for future crisis management scenarios such as refugee camps.