The molecular basis of telomere-mediated chromosome pairing and genetic exchange during prophase I of meiosis

PhDProphase I encapsulates the unique and defining events of meiosis; chromosome pairing, homologous recombination, synapsis, and subsequent segregation, to produce genetically unique haploid germ cells. These essential processes depend on a variety of protein complexes including the meiotic telomere complex (MTC), the synaptonemal complex (SC) and the meiotic recombination machinery. To carry out homology searches chromosomes must be tethered to the nuclear envelope, this is achieved by interplay between the MTC proteins (MAJIN, TERB1, and TERB2) and the shelterin complex protein, TRF1. Once attached, chromosomes undergo rapid prophase movements to find their homologous partner and begin to synapse. This involves the formation of the universally conserved SC structure along the lengths of aligned homologues. The SC provides the essential structural framework for HR and the crossover (CO) pathway. CO formation is dependent on the pro-CO machinery, including the E3 ligase proteins, HEI10 and RNF212. The main focus of this thesis is to use biophysical and structural approaches to deepen our understanding of the roles and mechanisms of the proteins and protein complexes involved in these meiotic processes. Here, we report the structural basis of the mammalian MTC and provide a mechanistic insight into chromosome tethering at the inner nuclear membrane (INM) achieved by the MTC. We show that the MTC recruits telomere-bound TRF1, through the 2:1 TRF1:TERB1 interaction, and undergoes subsequent structural rearrangement to displace TRF1 allowing the MTC to directly bind telomeric DNA and subsequently stabilise telomere-INM connectivity. The core architecture of mammalian SC is provided through the self-assembly of the transverse filament (TF) protein, SYCP1. We provide the first structural analysis of the D. melanogaster SC, specifically the TF protein, C(3)G. Biophysical analysis reveals that the central α-helical domain of C(3)G form dimers in a side-by-side parallel arrangement, but has some propensity to tetramerise, which could serve as building blocks for the recruitment and assembly of the complete SC. We show that HEI10 forms an obligate tetrameric structure and RNF212:RNF212b for a highly stable 2:2 complex and propose a structural model for the human E3 ligase proteins based upon solution scattering studies. Together, these findings provide a solid foundation for elucidating the mechanisms of mammalian meiosis

Mechanisms of pulmonary inflammation in ageing and chronic lung disease

Ph. D. Thesis.The human respiratory tract is exposed to copious antigen over the course of the lifespan by virtue of its free communication with the external environment through the process of ventilation. The host immune system must therefore distinguish innocuous inhaled antigen in the respiratory tract from antigen potentially associated with infection, produce an inflammatory response with minimal collateral host damage if required, and allow a return to homeostasis once infection is cleared. Inadequacies of these processes can result in a predisposition to respiratory illnesses. Respiratory diseases are leading causes of morbidity and mortality worldwide. It is notable that the burden of respiratory disease disproportionately falls upon older adults, and disorders of inflammation arising with ageing may contribute to this disparity. The work in this thesis describes a viable platform for the assessment of pulmonary inflammation that could be adapted to facilitate experimental medicine studies characterising inflammation in advanced age or early phase trials of immunomodulatory drugs that might alter the course and resolution of inflammation. This thesis also describes a method to identify candidate immunomodulatory drugs using connectivity maps and puts forward Del-1 as a target for drugs that enhance the resolution of inflammation. In considering the role of inflammation in chronic lung disease, this thesis also presents an exploration of the mechanisms of inflammation in chronic hypersensitivity pneumonitis, using a systems biology approach to implicate tissue-resident memory T lymphocytes in the pathogenesis of the disease. This opens up the possibility of IL-15 signalling as a potential target for treatment of the disease where few treatments are currently proven to be effective.NIHR Newcastle BRC, the MRC SHIELD AMR Research Consortium and the Medical Research Foundation National PhD Training Programme in Antimicrobial Resistance Researc

Mergers and Acquisitions in Sin Industries

Ph. D. ThesisMergers and acquisitions (M&A) have the potential to generate value for firms and their shareholders by gaining synergy from targets. However, the empirical evidence suggests M&A destroy firms’ value and shareholders’ wealth instead. The reason is that the acquirers are overwhelmingly motivated by value-decreasing motives (e.g., market-timing, empire building). The sin industries (e.g., tobacco, alcohol, and casino) are different from other industries due to their harmfulness and devastative consequences to society. Because of this characteristic, sin industries are stigmatized and neglected by society and investors. This negative attitude towards sin industries poses a significant negative impact on sin businesses (e.g., elevating the cost of capital, see Hong and Kacperczyk, 2009). Accordingly, it is essential for sin firms to improve their images. Shedding light on this behaviour, this thesis examines performance and motives of sin M&As in the G20 countries from 1993 to 2017. We show that sin firms try to improve their images by making value-increasing acquisitions. In relative terms, the sin acquirer market returns are more favourable than non-sin acquirer returns. Moreover, prior literature shows evidence that societal attitudes towards sin industries differ across countries. Classifying the G20 sample into high and low social norm countries, we extended prior literature by examining how social norms impact sin and non-sin firm M&As. We explore three angles of sin mergers and acquisitions: short-term market reaction to M&A announcements, long-term performance after acquisitions, and the motives behind M&A decisions. In the first empirical chapter, we find that the sin acquirer cumulative abnormal returns (CAR) at M&A announcements are more favourable than non-sin acquirer CARs. The difference in CARs across sin and non-sin acquirers is further elevated in high relative to lowsocial-norm countries, where people are less concerned about the negative consequences of sin industries than other countries. In the second empirical chapter, we find that the long-term operating performance of sin acquirers are not improved. However, the sin acquirer’s shareholders gain significantly positive returns in the long-term after acquisitions. Moreover, the sin acquirer returns are more favourable than non-sin acquirer returns. Interestingly, the difference in returns across sin and non-sin acquirers is further elevated in high relative to low-social-norm countries. In the last empirical chapter, we find that sin acquirers are inspired by market-timing and synergy motives. However, sin acquirers are less motivated by market-timing than non-sin acquirers. The difference in market-timing motive between sin acquirers and non-sin acquirers iii is greater in high-social-norm countries, where people are more concerned about the negative effect of the sin industries In conclusion, we find evidence that the sin firms improve their image by involving in better M&A deals than non-sin acquirers. As a result, the market reactions to M&A announcements of sin acquirers are more favourable than for non-sin acquirers. As there is no differential impact on operating performance, the more favourable return of sin acquirers likely derives from their better motives (i.e., less market-timing). Interestingly, the difference in market performance and motives across sin and non-sin acquirers is further elevated in high relative to low-social norm countries

The effect of intrinsic and extrinsic influences on skin ageing within associated demographics

Ph. D. ThesisThe skin ages because of intrinsic and extrinsic influences, resulting in damage to mitochondrial DNA (mtDNA). Intrinsic ageing occurs chronologically and cannot be controlled; however, extrinsic skin ageing results from exposure to environmental factors such as ultraviolet radiation (UVR). Although only reported in a small number of publications, previous studies have used a skin swab technique to detect differences in mtDNA damage as a result of UVR exposure. Limited repair mechanisms make mtDNA an effective biomarker of ageing, pioneered predominantly by the Birch-Machin laboratory. A plasmid containing a mitochondrial region of interest was developed to improve normalisation methodology for mtDNA damage comparison. A VISIA® Skin Analysis system was also used to investigate UV spot variation, which was used alongside the swab technique to determine whether differences in mtDNA damage following recent UVR exposure and lifestyle factors can be detected using a skin swab, including a large seasonal study (n=87). Although forskolin and caffeine are natural compounds frequently used in the cosmetic industry, their combined effect has not been investigated; therefore, their protective effects against complete solar light in human dermal neonatal fibroblasts (HDFn) was investigated using cell viability assays. We built upon previous research involving the skin swab by investigating differences in mtDNA damage between individuals. Results did not show a consistent increase in damage immediately following high intensity UVR exposure and significant correlations were not observed with sun exposure and protection behaviours. A seasonal study showed the greatest level of mtDNA damage in spring, in comparison to summer and autumn and a significant positive corelation was seen between protection behaviours and mtDNA damage in swabs collected from the left cheek in summer (p=0.02). UV spot %Area increased during summer and decreased during winter, and trends were observed with age and skin type. A trending correlation was observed between mtDNA damage and UV spots in samples collected from the right side of the face in spring (p=0.09). A combination of caffeine and forskolin was found to have protective effects against 4.32 standard erythemal dose (SED) complete solar light. Although mtDNA damage observed did not reflect perceived recent UVR exposure under our experimental study protocol, facial imaging analysis showed some correlations; however, further studies are necessary. Future studies would employ an objective measure of sunscreen use which would enable a clearer conclusion. Facial imaging analysis could not only prove effective at measuring damage, but could also be useful in the screening of protective skincare compounds such as forskolin and caffeine.European Regional Development Fun

An investigation of the driving factors affecting children’s water, sanitation and hygiene (WASH) behaviours in East New Delhi primary schools

PhD ThesisSustainable Development Goal 6 (Clean Water and Sanitation) addresses gaps that persist in Water, Sanitation and Hygiene (WASH) access worldwide, particularly affecting poor communities’ opportunity to live healthy, hygienic lives. According to the ‘Capability, Opportunity, Motivation Behaviour Model’, these three domains must be addressed for WASH interventions to achieve sustained adoption of targeted behaviours. Numerous factors pertaining to these three domains enable or obstruct East New Delhi primary school children’s WASH behaviours and therefore progress towards SDG 6. This thesis investigates these driving factors, analysing mixed methods data gathered in three government schools and one low-fee private (LFP) school, as well as in the communities surrounding them. The main findings indicate that: - Children attending the LFP school practise positive WASH behaviours more frequently than government school children and have access to superior school WASH provision. Children at schools with higher-quality WASH facilities are more likely to practise positive WASH behaviours. - School principals face challenges in providing adequate school WASH facilities and ensuring that children have the capability, opportunity and motivation to practise positive WASH behaviours. These include insufficient funding, teachers’ obligatory non-school commitments, unexplained teacher absenteeism and a high turnover of students. Schools-based WASH interventions can mitigate these, particularly by motivating school staff. - Socio-economic status affects children’s opportunity to adopt positive WASH behaviours. Children from lower-income backgrounds practise positive WASH behaviours less often. Schools-based WASH interventions could mitigate this through outreach to parents and children transferring learning into the household. These findings reveal the driving factors affecting children’s capability, opportunity and motivation to practise positive WASH behaviours in East New Delhi primary schools. Secondly, they highlight action which could be taken to support children’s sustained adoption of these behaviours, securing progress towards SDG 6 for the next generatio

A Conceptualization of the Role of Economic Characteristics in Resources Conservation: An Application to the Study of Work Engagement

Ph. D. Thesis.This thesis examines the resources conservational effect of two economic life experiences, namely, economic life demands and organisational experiences of economic adversities on work engagement. Despite the acknowledgement of the relevance of economic resources in the acquisition and sustainment of emotional resources, little is known regarding whether and through what mechanism do economic life experiences relate with work engagement. Having a conceptual account that highlights the theoretical underpinnings of economic life experiences in relation to work engagement is crucial for the development of workplace interventions that can help sustain work engagement particularly during periods of economic constraints at both the individual and organisational level. To address this gap, two empirical studies were conducted. Specifically, it was examined whether i) economic life demands and ii) organisation experiences of economic adversities relate adversely with work engagement, and if yes, why and under what conditions will this relation be salient. In addressing these questions, this thesis drew from the conservation of resources theory. Using a three-wave (approximately one week apart) panel data set (N= 145), this thesis finds that i) employees’ economic life demands and ii) organisational experiences of economic adversities relates negatively to work engagement. Moreover, analyses of mediation relationship showed that economic life demands relate negatively and indirectly with work engagement through the mediating effects of emotional distress. Likewise, it was found that organisational experiences of economic adversities relate negatively and indirectly with work engagement through (i) role ambiguity and (ii) organisational support for strength use. Analysis of moderation-mediation relationship elucidated that that off-job detachment mitigated the detrimental influence of economic life demands on work engagement through emotional distress such that the strength of the adverse influence was less under conditions of high economic life demands and high off-job detachment. Furthermore, results of moderation-mediation analysis revealed that detachment buffered the indirect negative influence of organisational experiences of economic adversities on work engagement. Specifically, it was discovered that the mediating influence of role ambiguity and organisational support for strength use was less salient under conditions of high organisational experiences of economic adversities and high detachment. The thesis’s findings that economic life demands relate negatively with work engagement through emotional distress help substantiate the desperation and resource loss spiral principle iv of the conservation of resources theory. Likewise, findings of this thesis, in particular, the conditioning influence of detachment in the indirect relation between economic life demands and work engagement provides support for the resource passageways principle of the conservation of resources theory. Furthermore, the negative indirect influence of organisational experiences of economic adversities on work engagement through role ambiguity and organisational support for strength use substantiate that the desperation principle of the conservation of resources theory at the level of the organisation. From a practitioner perspective, findings of this thesis demonstrate that intervention measures that are centred towards the promotion of off-job detachment is a core medium through which organisations can promote employee work engagement

Designing sustainable community interfaces

Ph. D. Thesis.This thesis explores the role of systems and processes to support inter-community communication and relations between communities and public service institutions. I explore two contexts, rural and urban, and the potential of technical systems to support communities organise, but also support better understanding and dialogues between services providers and beneficiaries. This potential depends on the contextual barriers and opportunities and the willingness of stakeholders to adopt systems and processes that inevitably effects change in day-to-day organisational cultures. Drawing from two longitudinal case studies in the NorthEast of England, I describe the requirements of these systems to be used effectively and sustainably by communities and public service institutions. The first case study developed with rural communities of Wooler and Rothbury where, over the course of three years, a communityrun pervasive display network was designed and deployed to bolster intra-community communication. I describe the development of a partnership with Glendale Gateway Trust and the design and deployment of simple hardware and bespoke software packaged alongside a suggested approach for its administration and governance. The study explores the implications of incorporating a governance model with particular focus on how this impacts ownership, moderation and maintenance as part of sustaining technical systems between self-organised configurations of communities. The second case study, developed with Northumbria Police’s Neighbourhood Policing team, involved the iterative design, implementation and evaluation of an approach to support police officers communicate more effectively with local communities and better understand local issues. The intervention aimed to strengthen communityinstitutional relations; it included training neighbourhood police officers in alternative modes of community engagement and ways to configure technical processes for public institutions’ specific needs and challenges. Learning from these two case studies is synthesized in a discussion of the different ways technical systems and processes can be designed and configured to meet stakeholders’ needs and organisational cultures; and to embody important values such as sustainability, scalability, moderation, governance and ownership

Optimisation of energy usage and carbon emissions for an advancedanaerobic digester plant

PhD ThesisIn this thesis Northumbrian Water Limited’s (NWL) Advanced Anaerobic Digester (AAD) plant at Howdon was used to investigate modelling and optimisation opportunities based on energy prices, demands and their new greenhouse gas emissions pledge. It is believed this site is the first in the UK with a mixed operational strategy for biogas and biomethane produced on site: to burn in Combined Heat and Power (CHP) engines to create electricity, burn in Steam Boilers for onsite steam use or inject the biomethane into the national grid - Natural Gas can be imported to make up shortfalls in biomethane if required. Initially, a realistic model for the gas distribution on site was developed using a novel mixed integer linear programming (MILP) approach. Retrospective Optimisation (RO) using historical plant data was performed, with results indicating the plant operated optimally within accepted tolerance 98% of the time. However, improving plant robustness (such as reducing unexpected breakdown incidents) could yield a significant increase in gas revenue of 7.8%. Next, the gas distribution model is developed further as a realistic MILP model for energy and carbon management where operators are provided with a visual daily operational schedule based on varying tariffs. The results indicate that biomethane injection should be maximised for the highest financial gain, with the driving force for optimising the remaining operations being the site electricity demand and whether the electricity purchased from the grid generates carbon emissions, based on the new carbon performance commitment. Using the developed energy and carbon model a sensitivity analysis was performed on electricity tariffs, natural gas prices, the volume of biogas production and the Biomethane Upgrade Plant (BUP) processing limits. The results reinforce the understanding that maximising biomethane injection into the national grid is the most cost-effective operational strategy. Second to this, the optimal operation of the CHP engines is subject to the available excess biogas available after BUP processing and the current daily energy prices. To ensure the site always maintains a positive revenue, operators should ensure that at least 20,000 Nm3 /day of raw biogas can be processed and injected into the national grid. Finally, an investigation into the unique modelling problem regarding the three on site Anaerobic Digesters (ADs) was performed. A key parameter used in the current optimisation model is the amount of biogas that is produced on site each day, however currently an average daily value is used based on historical data. To improve the optimisation, it would be better to provide a more accurate prediction based on current state of the ADs and the expected sludge processing volumes into the ADs. The lack of individual gas flow data for each AD posed an interesting challenge in predicting the total biogas flow produced on site. Multiple linear models of the onsite AD’s were investigated but were not accurate enough to be used on site. A NARX (Nonlinear autoregressive with external input) Neural Network was developed to model all three anaerobic digesters as a single process for the day ahead prediction of biogas production. The resulting optimal NARX model can accurately predict the biogas production on a day-ahead basis over 95% of the time

The influences of microstructural processes on concrete exposed to high temperatures

Ph. D. ThesisConcrete is the most widely used construction material across the world. It is a heterogeneous material consisting of cement paste, fine and coarse aggregates, and it is a multi-phase porous media with dry air, liquid water, vapour and other kinds of fluids filling the pores. The hygro-thermo-chemo-mechanical behaviours of concrete under elevated temperature have been investigated for decades at the macroscale level using experimental methods and numerical simulations, including material strength, material properties, variables (e.g. pore pressure) and even microstructural properties. However, the findings are generally empirically in nature, and the mechanisms underneath all these macroscopic behaviours are still not clear. The objective of this thesis is to contribute to the understanding of the influences of microstructural processes on the macro-level behaviour of concrete at elevated temperatures through a combined numerical and experimental study. The work uses finite element analysis with a fully coupled hygro-thermo-chemo-mechanical model in combination with water vapour sorption isotherms measurements using the ‘Dynamic Vapour Sorption’ method. Numerical parametric studies have been conducted for nine properties rooted in the micro-scale. These have confirmed that: permeability is key to the development of gas pressures; the description of the heat and mass boundary conditions can have a considerable effect on the predicted results; the amount of water introduced into the system as a result of dehydration of the cement paste, the influence of micro-scale gas flow behaviour and the evolution of capillary pressures are all found to have a considerable effect on the development of macro-scale behaviours. Furthermore, the transient behaviour of moisture under elevated temperatures are found to be significantly affected by the formulation of the sorption isotherm, especially where that relates to microstructural behaviour. To further investigate this and potential contradictions between theoretical or observed microstructural behaviour and macro-scale model formulations, a series of experiments were conducted to measure water vapour sorption isotherms using the ‘Dynamic Vapour Sorption (DVS)’ method. Investigations were carried out to determine the potential microstructural changes of hardened cement pastes (CEMI with water to cement ratio of 0.4) subjected to different relative humidity ranges. The results indicate that the microstructure of cement paste is not affected by elevated temperatures until 80°C, after removing confounding effects from irreversible changes upon first drying and harsh drying. The only microstructural changes consistent with the presented results, during desorption and adsorption, appear to be reversible. The temperature dependency of sorption isotherms was investigated as well. The results confirm and extend the interpretation that the adsorption isotherm is near-equilibrium, and the desorption isotherm is not. These results are qualitatively confirmed by classical Density Functional Theory (DFT) theory. It is also confirmed that the adsorption isotherm is weakly temperature-dependent and desorption is much less temperature-dependent than from desiccator tests, where a marked increase of cavitation pressure is observed in the desorption branch with increased temperature. Additionally, the mechanism of interlayer water was investigated in this project by drying the samples to nominal RH=0%, instead of drying at 5% RH. The results suggested that the interlayer water play a significant role in the desorption range below 5% RH and the hysteresis in isotherms suggested that until the interlayer water was evaporated sufficiently, the interlayer spaces were never filled even when re-wetting to full saturation. All these results and their implications indicate the need for a revision of the models linking water content with humidity at high temperature, with possibly important implications for the understanding and prediction of temperature-induced damage in concrete. All these results indicated that microstructural processes have significant influences on the behaviours of concrete at the macroscale level when exposed to high temperature. However, these microstructural processes are still vague, which are strongly affected by the pore size distribution that needs to be explored and clarified further

Using audit and feedback to improve colonic polyp detection, qualitative studies within the national endoscopy database automated performance reports to improve quality outcomes trial (NED APRIQOT)

M.D ThesisColorectal cancer (CRC) arises from polyps, and polyp detection and resection at colonoscopy is pivotal in preventing CRC. Colonoscopists with a low polyp detection rate have a higher rate of CRC after colonoscopy. The National Endoscopy Database Automated Performance Reports to Improve Quality Outcomes Trial (NED-APRIQOT) is a randomised cluster control trial of electronic audit and feedback (A&F) in English endoscopy centres. This MD aimed to (1) assess the acceptability of colonoscopy key performance indicators (KPIs); (2) develop an evidence-based and theoretically informed behaviour change intervention (BCI), an A&F endoscopist performance report, for implementation in the trial; and (3) explore pre-trial experiences of endoscopy A&F. A narrative review of A&F and KPIs in the colonoscopy literature was undertaken. This informed selection of KPIs for a Delphi consensus, to determine the clinical acceptability of KPIs available through the NED. A panel of UK experts in colonoscopy, reflecting the varied professional backgrounds performing endoscopy, undertook three rounds rating statements and provided free-text comments. A case-mix adjusted mean number of polyps (MNP) was chosen for the trial. An A&F behavioural theory review informed the design of a draft BCI. Interviews were undertaken with 19 endoscopists from six English NHS endoscopy centres, purposively sampled for clinical background and professional experience. The BCI was iteratively refined through rounds of cognitive interviews in which participants interacted with and ‘talked aloud’ about the BCI. The finalised BCI was implemented in the NED-APRIQOT. These participants also undertook semi-structured interviews exploring current colonoscopy A&F practices. A framework thematic analysis mapped themes to Feedback Intervention Theory (FIT) and the Theory of Planned Behaviour. A FIT-based model described A&F’s intended and paradoxical effects on endoscopist behaviour. Detection and patient safety were dependent on coaching, team behaviours and unit-leads managing underperformance. Future endoscopy A&F interventions should consider targeting behaviours using theoretical models