Towards in silico IBV vaccine design: defining the role of polymorphism in viral attenuation

The gammacoronavirus, Infectious Bronchitis Virus (IBV), is a respiratory pathogen of chickens. IBV is a constant threat to poultry production as established vaccines are often ineffective against emerging strains. This requires constant and rapid vaccine production by a process of viral attenuation by egg passage, but the essential forces leading to attenuation in the virus have not yet been characterised. Knowledge of these factors will lead to the development of more effective, rationally attenuated, live vaccines and reduction of the mortality and morbidity caused by this pathogen. M41 CK strain was egg passaged four times many years ago at Houghton Poultry Research Station and stored as M41-CK EP4 (stock virus at The Pirbright Institute since 1992). It was the first egg passage to have its genome pyrosequenced and was therefore used as the baseline reference. The overall aim of this project was to analyse deep sequence data obtained from four IBV isolates (called A, A1, C and D) each originating from the common M41-CK EP4 (ep4) and independently passaged multiple times in embryonated chicken eggs (figure 1.1). Highly polymorphic encoding regions of the IBV genome were then identified which are likely involved in the attenuation process through the formation of independent SNPs and/or SNP clusters. This was then used to direct targeted investigation of SNPs during the attenuation process of the four IBV passages. A previously generated deep sequence dataset was used as a preliminary map of attenuation for one virulent strain of IBV. This investigation showed the nucleocapsid and spike as two highly polymorphic encoding regions within the IBV genome with the highest proportion of SNPs compared to encoding region size. This analysis then led to more focussed studies of the nucleocapsid and spike encoding region with the ultimate aim of mapping key attenuating regions and nucleotide positions. The 454 pyrosequencing data and further investigation of nucleocapsid and spike encoding regions have identified the SNPs present at the same nucleotide positions within analysed A, A1, C and D isolates. These SNPs probably play a crucial role in viral attenuation and universal vaccine production but it is not clear if independent SNPs are also involved in loss of virulence. The majority of SNPs accumulated at different nucleotide positions without further continuation in Sanger sequenced egg passages presenting S2 subunit (spike) and nucleocapsid as polymorphic encoding regions which in nature remain highly conserved.

An investigation into the properties of non-digestible carbohydrates that selectively promote colonic propionate production

Short chain fatty acids (SCFA), including propionate, are produced by the bacterial fermentation of carbohydrates in the colon. Propionate has many potential roles in health, including inhibiting cholesterol synthesis, de novo lipogenesis and increasing satiety. The profile of SCFA produced is determined by both the substrate available and the bacteria present and may be influenced by environmental conditions within the lumen of the colon. Whilst it may be beneficial to increase colonic propionate production, dietary strategies to achieve this are unproven. Adding propionate to food leads to poorer organoleptic properties, and oral propionate is absorbed in the small intestine. The optimum way to selectively increase colonic propionate would be to select fermentable carbohydrates that selectively promote propionate production. To date, few studies have undertaken a systematic assessment of the factors leading to increased colonic propionate production making the selection of propiogenic carbohydrates challenging. The aim of this thesis was to identify the best carbohydrates for selectively increasing propionate production, and to explore the factors which control propionate production. This work started with a systematic review of the literature for evidence of candidate carbohydrates, which led to a screen of ‘propiogenic’ substrates using in vitro batch fermentations and mechanistic analysis of the impact of pH, bond linkage and orientation using a range of sugars, polysaccharides and fibre sources. A new unit for SCFA production was developed to allow comparison of results from in vitro studies encompassing a range different methodologies found in the literature. The systematic review found that rhamnose yielded the highest rate and proportion of propionate production whereas, for polysaccharides, β-glucan ranked highest for rate and guar gum ranked highest for molar production, but this was not replicated across all studies. Thus, no single NDC was established as highly propiogenic. Some substrates appeared more propiogenic than others and when these were screened in vitro. Laminarin, and other β-glucans ranked highest for propionate production. Legume fibre and mycoprotein fibre were also propiogenic. A full complement of glucose disaccharides were tested to examine the role glycosidic bond orientation and position on propionate production. Of the glucose disaccharides tested, β(1-4) bonding was associated with increased proportion of propionate and α(1-1) and β(1-4) increased the rate and proportion of butyrate production. In conclusion, it appears that for fibre to affect satiety, high intakes of fibre are needed, and which a major mechanism is thought to occur via propionate. Within this thesis it was identified that rather than selecting specific fibres, increasing overall intakes of highly fermentable carbohydrates is as effective at increasing propionate production. Selecting carbohydrates with beta-bonding, particularly laminarin and other β(1-4) fermentable carbohydrates leads to marginal increases in propionate production. Compared with targeted delivery of propionate to the colon, fermentable carbohydrates examined in this thesis have lesser and variable effects on propionate production. A more complete understanding of the impact of bond configurations in polysaccharides, rather than disaccharides, may help selection or design of dietary carbohydrates which selectively promote colonic propionate production substrates for inclusion in functional foods. Overall this study has concluded that few substrates are selectively propiogenic and the evidence suggests that similar changes in propionate production may be achieved by modest changes in dietary fibre intake

An exploration of treatment burden and patient capacity in people with stroke

Background and aims: Advances in modern medicine have led to improved outcomes after stroke, yet an increased treatment burden has been placed on patients. Treatment burden is the workload of health care for people with chronic illness and the impact that this has on functioning and well-being. Those with comorbidities are likely to be particularly burdened. Excessive treatment burden can negatively affect outcomes. Individuals are likely to differ in their ability to manage health problems and follow treatments, defined as patient capacity. The aim of this thesis was to explore the experience of treatment burden for people who have had a stroke and the factors that influence patient capacity. Methods: There were four phases of research. 1) A systematic review of the qualitative literature that explored the experience of treatment burden for those with stroke. Data were analysed using framework synthesis, underpinned by Normalisation Process Theory (NPT). 2) A cross-sectional study of 1,424,378 participants >18 years, demographically representative of the Scottish population. Binary logistic regression was used to analyse the relationship between stroke and the presence of comorbidities and prescribed medications. 3) Interviews with twenty-nine individuals with stroke, fifteen analysed by framework analysis underpinned by NPT and fourteen by thematic analysis. The experience of treatment burden was explored in depth along with factors that influence patient capacity. 4) Integration of findings in order to create a conceptual model of treatment burden and patient capacity in stroke. Results: Phase 1) A taxonomy of treatment burden in stroke was created. The following broad areas of treatment burden were identified: making sense of stroke management and planning care; interacting with others including health professionals, family and other stroke patients; enacting management strategies; and reflecting on management. Phase 2) 35,690 people (2.5%) had a diagnosis of stroke and of the 39 co-morbidities examined, 35 were significantly more common in those with stroke. The proportion of those with stroke that had >1 additional morbidities present (94.2%) was almost twice that of controls (48%) (odds ratio (OR) adjusted for age, gender and socioeconomic deprivation; 95% confidence interval: 5.18; 4.95-5.43) and 34.5% had 4-6 comorbidities compared to 7.2% of controls (8.59; 8.17-9.04). In the stroke group, 12.6% of people had a record of >11 repeat prescriptions compared to only 1.5% of the control group (OR adjusted for age, gender, deprivation and morbidity count: 15.84; 14.86-16.88). Phase 3) The taxonomy of treatment burden from Phase 1 was verified and expanded. Additionally, treatment burdens were identified as arising from either: the workload of healthcare; or the endurance of care deficiencies. A taxonomy of patient capacity was created. Six factors were identified that influence patient capacity: personal attributes and skills; physical and cognitive abilities; support network; financial status; life workload, and environment. A conceptual model of treatment burden was created. Healthcare workload and the presence of care deficiencies can influence and be influenced by patient capacity. The quality and configuration of health and social care services influences healthcare workload, care deficiencies and patient capacity. Conclusions: This thesis provides important insights into the considerable treatment burden experienced by people who have had a stroke and the factors that affect their capacity to manage health. Multimorbidity and polypharmacy are common in those with stroke and levels of these are high. Findings have important implications for the design of clinical guidelines and healthcare delivery, for example co-ordination of care should be improved, shared decision-making enhanced, and patients better supported following discharge from hospital.