The role of bacterial interspecies communication in polymicrobial infection of the cystic fibrosis lung

There is an increasing appreciation of the polymicrobial nature of bacterial infections associated with Cystic Fibrosis (CF) and of the important role for interactions in influencing bacterial virulence and response to therapy. Patients with CF are co-infected with Pseudomonas aeruginosa, Burkholderia cenocepacia and Stenotrophomonas maltophilia. These latter bacteria produce signal molecules of the diffusible signal factor (DSF) family, which are cis-2-unsaturated fatty acids. Previous studies showed that DSF from S. maltophilia leads to altered biofilm formation and increased tolerance to antibiotics in P. aeruginosa and that these responses require the P. aeruginosa sensor kinase PA1396. The work in this thesis aims of further elucidate the influence and mechanism of DSF signalling on P. aeruginosa and examine the role that such interspecies signalling play in infection of the CF airway. Next generation sequencing technologies targeting the 16S ribosomal RNA gene were applied to DNA and RNA isolated from sputum taken from cohorts of CF and non-CF subjects to characterise the bacterial community. In parallel, metabolomics analysis of sputum provided insight into the environment of the CF airway. This analysis revealed a number of observations including; that differences in metabolites occur in sputum taken from clinically stable CF patients and those with exacerbation and DNA- and RNA-based methods suggested that a strong relationship existed between the abundance of specific strict anaerobes and fluctuations in the level of metabolites during exacerbation. DSF family signals were also detected in the sputum and a correlation with the presence of DSFproducing organisms was observed. To examine the signal transduction mechanisms used by P. aeruginosa, bioinformatics with site directed mutagenesis were employed to identify signalling partners for PA1396. A pathway suggesting a role for a number of proteins in the regulation of several factors following DSF recognition by PA1396 were observed.

Leadership, fairness and gender: a practitioner's perspective

This Portfolio of Exploration outlines the course of learning by a practitioner on a personal leadership journey. It constructs a functional examination of ideas around leadership. It explores the belief system which underpins leadership practice and it also explores to what extent the increased participation of women can lead to a qualitatively different type of leadership. Different models of leadership are explored to find the model which can best fit with the author’s perception of leadership. The Women’s Intercultural Leadership Model is discussed. This model conceptualises leadership as the envisioning of oneself and others as potential leaders. It seeks to promote that recognition whilst at the same time encouraging personal transformation. The promotion of a values based leadership is examined. The value of fairness is examined as an element of functional leadership. The extent to which increasing the number of women in leadership can lead to a qualitatively different type of leadership is explored. Drucker’s assertion that every practice rests on theory is used to unearth the underlying assumptions of this reflective practitioner doctorate. Kegan’s Theory of Adult Mental Development and Subject-Object separation is used to explicitly examine knowledge construction. Myers Briggs Type Indicator (MBTI) and Assumption/Commitment/Behaviour/Outcome (ACBO) template are used to promote practice change.

Assessment of dietary background exposure of the Irish adult population to dioxins and PCBs particularly taking into account additional exposure due to the 2008 Irish dioxin food contamination incident

Irish monitoring data on PCDD/Fs, DL-PCBs and Marker PCBs were collated and combined with Irish Adult Food Consumption Data, to estimate dietary background exposure of Irish adults to dioxins and PCBs. Furthermore, all available information on the 2008 Irish pork dioxin food contamination incident was collated and analysed with a view to evaluate any potential impact the incident may have had on general dioxin and PCB background exposure levels estimated for the adult population in Ireland. The average upperbound daily intake of Irish adults to dioxins Total WHO TEQ (2005) (PCDD/Fs & DLPCBs) from environmental background contamination, was estimated at 0.3 pg/kg bw/d and at the 95th percentile at 1 pg/kg bw/d. The average upperbound daily intake of Irish adults to the sum of 6 Marker PCBs from environmental background contamination ubiquitous in the environment was estimated at 1.6 ng/kg bw/d and at the 95th percentile at 6.8 ng/kg bw/d. Dietary background exposure estimates for both dioxins and PCBs indicate that the Irish adult population has exposures below the European average, a finding which is also supported by the levels detected in breast milk of Irish mothers. Exposure levels are below health based guidance values and/or Body Burdens associated with the TWI (for dioxins) or associated with a NOAEL (for PCBs). Given the current toxicological knowledge, based on biomarker data and estimated dietary exposure, general background exposure of the Irish adult population to dioxins and PCBs is of no human health concern. In 2008, a porcine fat sample taken as part of the national residues monitoring programme led to the detection of a major feed contamination incidence in the Republic of Ireland. The source of the contamination was traced back to the use of contaminated oil in a direct-drying feed operation system. Congener profiles in animal fat and feed samples showed a high level of consistency and pinpointed the likely source of fuel contamination to be a highly chlorinated commercial PCB mixture. To estimate additional exposure to dioxins and PCBs due to the contamination of pig and cattle herds, collection and a systematic review of all data associated with the contamination incident was conducted. A model was devised that took into account the proportion of contaminated product reaching the final consumer during the 90 day contamination incident window. For a 90 day period, the total additional exposure to Total TEQ (PCDD/F &DL-PCB) WHO (2005) amounted to 407 pg/kg bw/90d at the 95th percentile and 1911 pg/kg bw/90d at the 99th percentile. Exposure estimates derived for both dioxins and PCBs showed that the Body Burden of the general population remained largely unaffected by the contamination incident and approximately 10 % of the adult population in Ireland was exposed to elevated levels of dioxins and PCBs. Whilst people in this 10 % cohort experienced quite a significant additional load to the existing body burden, the estimated exposure values do not indicate approximation of body burdens associated with adverse health effects, based on current knowledge. The exposure period was also limited in time to approximately 3 months, following the FSAI recall of contaminated meat immediately on detection of the contamination. A follow up breast milk study on Irish first time mothers conducted in 2009/2010 did not show any increase in concentrations compared to the study conducted in 2002. The latter supports the conclusion that the majority of the Irish adult population was not affected by the contamination incident.

Lower extremity amputation in people with diabetes: Trends and determinants

Introduction: The prevalence of diabetes is rising rapidly. Assessing quality of diabetes care is difficult. Lower Extremity Amputation (LEA) is recognised as a marker of the quality of diabetes care. The focus of this thesis was first to describe the trends in LEA rates in people with and without diabetes in the Republic of Ireland (RoI) in recent years and then, to explore the determinants of LEA in people with diabetes. While clinical and socio-demographic determinants have been well-established, the role of service-related factors has been less well-explored. Methods: Using hospital discharge data, trends in LEA rates in people with and without diabetes were described and compared to other countries. Background work included concordance studies exploring the reliability of hospital discharge data for recording LEA and diabetes and estimation of diabetes prevalence rates in the RoI from a nationally representative study (SLAN 2007). To explore determinants, a systematic review and meta-analysis assessed the effect of contact with a podiatrist on the outcome of LEA in people with diabetes. Finally, a case-control study using hospital discharge data explored determinants of LEA in people with diabetes with a particular focus on the timing of access to secondary healthcare services as a risk factor. Results: There are high levels of agreement between hospital discharge data and medical records for LEA and diabetes. Thus, hospital discharge data was deemed sufficiently reliable for use in this PhD thesis. A decrease in major diabetes-related LEA rates in people with diabetes was observed in the RoI from 2005-2012. In 2012, the relative risk of a person with diabetes undergoing a major LEA was 6.2 times (95% CI 4.8-8.1) that of a person without diabetes. Based on the systematic review and meta-analysis, contact with a podiatrist did not significantly affect the relative risk (RR) of LEA in people with diabetes. Results from the case-control study identified being single, documented CKD and documented hypertension as significant risk factors for LEA in people with diabetes whilst documented retinopathy was protective. Within the seven year time window included in the study, no association was detected between LEA in patients with diabetes and timing of patient access to secondary healthcare for diabetes management. Discussion: Many countries have reported reduced major LEA rates in people with diabetes coinciding with improved organisation of healthcare systems. Reassuringly, these first national estimates in people with diabetes in the RoI from 2005 to 2012 demonstrated reducing trends in major LEA rates. This may be attributable to changes in diabetes care and also, secular trends in smoking, dyslipidaemia and hypertension. Consistent with international practice, LEA trends data in Ireland can be used to monitor quality of care. Quantifying this improvement precisely, though, is problematic without robust denominator data on the prevalence of diabetes. However, a reduction in major diabetes-related LEA rates suggests improved quality of diabetes care. Much controversy exists around the reliability of hospital discharge data in the RoI. This thesis includes the first multi-site study to explore this issue and found hospital discharge data reliable for the reporting of the procedure of LEA and diagnosis of diabetes. This project did not detect protective effects of access to services including podiatry and secondary healthcare for LEA in people with diabetes. A major limitation of the systematic review and meta-analysis was the design and quality of the included studies. The data available in the area of effect of contact with a podiatrist on LEA risk are too sparse to say anything definitive about the efficacy of podiatry on LEA. Limitations of the case-control study include lack of a diabetes register in Ireland, restricted information from secondary healthcare and lack of data available from primary healthcare. Due to these issues, duration of disease could not be accounted for in the study which limits the conclusions that can be drawn from the results. The model of diabetes care in the RoI is currently undergoing a re-configuration with plans to introduce integrated care. In the future, trends in LEA rates should be continuously monitored to evaluate the effectiveness of changes to the healthcare system. Efforts are already underway to improve the availability of routine data from primary healthcare with the recent development of the iPCRN (Irish Primary Care Research Network). Linkage of primary and secondary healthcare records with a unique patient identifier should be the goal for the future.

Molecular and cellular aspects of the SREBP pathway

The SREBP (sterol response element binding proteins) transcription factors are central to regulating de novo biosynthesis of cholesterol and fatty acids. The SREBPs are regulated by retention or escape from the ER to the Golgi where they are proteolytically cleaved into active forms. The SREBP cleavage activating protein (SCAP) and the INSIG proteins are essential in this regulatory process. The aim of this thesis is to further characterise the molecular and cellular aspects surrounding regulation of SREBP processing. SREBP and SCAP are known to interact via their carboxy-terminal regulatory domains (CTDs) but this interaction is poorly characterised. Significant steps were achieved in this thesis towards specific mapping of the interaction site. These included cloning and over expression and partial purification of tagged SREBP1 and SREBP2 CTDs and probing of a SCAP peptide array with the CTDs. Results from the SREBP2 probing were difficult to interpret due to insolubility issues with the protein, however, probing with SREBP1 revealed five potential binding sites which were detected reproducibly. Further research is necessary to overcome SREBP2 insolubility issues and to confirm the identified SREBP1 interaction site(s) on SCAP. INSIG1 has a central role in regulating SREBP processing and in regulating stability of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR), a rate limiting enzyme in cholesterol biosynthesis. There are two protein isoforms of human INSIG1 produced through the use of two in-frame alternative start sites. Bioinformatic analysis indicated that the presence of two in-frame start sites within the 5-prime region of INSIG1 mRNA is highly conserved and that production of two isoforms of INSIG1is likely a conserved event. Functional differences between these two isoforms were explored. No difference in either the regulation of SREBP processing or HMGCR degradation between the INSIG1 isoforms was observed and the functional significance of the two isoforms is as yet unclear. The final part of this thesis focused on enhancing the cytotoxicity of statins by targeted inhibition of SREBP processing by oxysterols. Statins have significant potential as anti-cancer agents as they inhibit the activity of HMGCR leading to a deficiency in mevalonate which is essential for cell survival. The levels of HMGCR fluctuate widely due to cholesterol feedback of SREBP processing. The relationship between sterol feedback and statin mediated cell death was investigated in depth in HeLa cells. Down regulation of SREBP processing by sterols significantly enhanced the efficacy of statin mediated cell death. Investigation of sterol feedback in additional cancer cell lines showed that sterol feedback was absent in cell lines A- 498, DU-145, MCF-7 and MeWo but was present in cell lines HT-29, HepG2 and KYSE-70. In the latter inhibition of SREBP processing using oxysterols significantly enhanced statin cytotoxicity. The results indicate that this approach is valid to enhance statin cytotoxicity in cancer cells, but may be limited by deregulation of SREBP processing and off target effects of statins, which were observed for some of the cancer cell lines screened.

Anticipatory vigilance: A classic grounded theory of risk reduction and management in the perioperative setting

This research aimed to investigate the main concern facing nurses in minimising risk within the perioperative setting and to generate an explanatory substantive theory of how they resolve this through anticipatory vigilance. In the context of the perioperative setting, nurses encounter challenges in minimising risks for their patients on a continuous basis. Current explanations of minimising risk in the perioperative setting offers insights into how perioperative nurses undertake their work. Currently research in minimising risk is broadly related to dealing with errors as opposed to preventing them. To date, little is known about how perioperative nurses practice and maintain safety. This study was guided by the principles of classic grounded theory as described by Glaser (1978, 1998, 2001). Data was collected through individual unstructured interviews with thirty seven perioperative nurses (with varying lengths of experiences of working in the area) and thirty three hours of non-participant observation within eight different perioperative settings in the Republic of Ireland. Data was simultaneously collected and analysed. The theory of anticipatory vigilance emerged as the pattern of behaviour through which nurse’s deal with their main concern of minimising risk in a high risk setting. Anticipatory vigilance is enacted through orchestrating, routinising and momentary adapting within a spirit of trusting relations within the substantive area of the perioperative setting. This theory of offers an explanation on how nurses resolve their main concern of minimising risk within the perioperative setting. The theory of anticipatory vigilance will be useful to nurses in providing a comprehensive framework of explanation and understanding on how nurses deal with minimising risk in the perioperative setting. The theory links perioperative nursing, risk and vigilance together. Clinical improvements through understanding and awareness of the theory of anticipatory vigilance will result in an improved quality environment, leading to safe patient outcomes.

Moral shielding: A grounded theory of integrity maintenance in multidisciplinary teams

Using a classic grounded theory methodology (CGT), this study explores the phenomenon of moral shielding within mental health multidisciplinary teams (MDTS). The study was located within three catchment areas engaged in acute mental health service practice. The main concern identified was the maintenance of a sense of personal integrity during situational binds. Through theoretical sampling thirty two practitioners, including; doctors, nurses, social workers, occupational therapists, counsellors and psychologists, where interviewed face to face. In addition, emergent concepts were identified through observation of MDTs in clinical and research practice. Following a classic grounded theory methodology, data collection and analysis occurred simultaneously. A constant comparative approach was adopted and resulted in the immergence of three sub- core categories; moral abdication, moral hinting and pseudo-compliance. Moral abdication seeks to re-position within an event in order to avoid or deflect the initial obligation to act, it is a strategy used to remove or reduce moral ownership. Moral gauging represents the monitoring of an event with the goal of judging the congruence of personal principles and commitments with that of other practitioners. This strategy is enacted in a bid to seek allies for the support of a given moral position. Pseudo-compliance represents behaviour that hides desired principles and commitments in order to shield them from challenge. This strategy portrays agreement with the dominant position within the MDT, whilst holding a contrary position. It seeks to preserve a reservoir of emotional energy required to maintain a sense of personal integrity. Practitioners who were successful in enacting moral shielding were found to not experience significant emotional distress associated with the phenomenon of moral distress; suggesting that these practitioners had found mechanisms to manage situational binds that threatened their sense of personal integrity.

Landscapes of kingship in early medieval Ireland, AD 400–1150

This thesis explores the evolution of kingship in early medieval Ireland (AD 400–1150) through a kingdom based and multi-scalar approach to royal landscapes. Through exploring the role of place and landscape in the construction of early medieval Irish kingship, this study will assess the relationship between the social, economic and ideological roles of the king in Irish society. Kingship in Ireland was vested in places, such that royal landscapes were the pre-eminent symbol of regality and authority. As such, an interdisciplinary study of kingship grounded in archaeological methodologies has a unique potential to contribute to our knowledge of the practice of kingship. Consequently, this research considers the material apparatus of different scales of kingships and explores the role of landscape in the construction of kingship and the evolution of kingdoms. It takes two major case studies; (i) Cashel, Munster and the Éoganachta federation; and (ii) the Uí Néill, Tara and the Síl nÁedo Sláine kingdom of Brega. Through interdisciplinary methodologies it charts the genesis and development of political federations, focusing specifically on the role that royal landscapes’ played in their evolution. Similarly, this thesis engages critically with the nature of assembly places and practices in Ireland, and focuses specifically on issues pertaining to the nature of assembly and the archaeological manifestation of such practices. It includes a list of 115 landscapes identified as assembly places, and through the analysis of this material, this thesis examines the ways in which different types of royal sites articulated together to create royal landscapes implicated in the exercise of kingship, and the construction and maintenance of authority. Moreover, through the analysis of assembly places within the context of the development of kingdoms, and structures of jurisdiction and administration, it also investigates the evolution of supra-regional scales of identity and community associated with the emergence of major political federations in early medieval Ireland.

Resonant power conversion topologies for inductive charging of electrical vehicle batteries

This thesis is concerned with inductive charging of electric vehicle batteries. Rectified power form the 50/60 Hz utility feeds a dc-ac converter which delivers high-frequency ac power to the electric vehicle inductive coupling inlet. The inlet configuration has been defined by the Society of Automotive Engineers in Recommended Practice J-1773. This thesis studies converter topologies related to the series resonant converter. When coupled to the vehicle inlet, the frequency-controlled series-resonant converter results in a capacitively-filtered series-parallel LCLC (SP-LCLC) resonant converter topology with zero voltage switching and many other desirable features. A novel time-domain transformation analysis, termed Modal Analysis, is developed, using a state variable transformation, to analyze and characterize this multi-resonant fourth-orderconverter. Next, Fundamental Mode Approximation (FMA) Analysis, based on a voltage-source model of the load, and its novel extension, Rectifier-Compensated FMA (RCFMA) Analysis, are developed and applied to the SP-LCLC converter. The RCFMA Analysis is a simpler and more intuitive analysis than the Modal Analysis, and provides a relatively accurate closed-form solution for the converter behavior. Phase control of the SP-LCLC converter is investigated as a control option. FMA and RCFMA Analyses are used for detailed characterization. The analyses identify areas of operation, which are also validated experimentally, where it is advantageous to phase control the converter. A novel hybrid control scheme is proposed which integrates frequency and phase control and achieves reduced operating frequency range and improved partial-load efficiency. The phase-controlled SP-LCLC converter can also be configured with a parallel load and is an excellent option for the application. The resulting topology implements soft-switching over the entire load range and has high full-load and partial-load efficiencies. RCFMA Analysis is used to analyze and characterize the new converter topology, and good correlation is shown with experimental results. Finally, a novel single-stage power-factor-corrected ac-dc converter is introduced, which uses the current-source characteristic of the SP-LCLC topology to provide power factor correction over a wide output power range from zero to full load. This converter exhibits all the advantageous characteristics of its dc-dc counterpart, with a reduced parts count and cost. Simulation and experimental results verify the operation of the new converter.

Form-focused instruction in Irish-medium immersion education: a critical examination of teachers' perspectives and practices. A small-scale qualitative case study

It has been suggested that the less than optimal levels of students’ immersion language “persist in part because immersion teachers lack systematic approaches for integrating language into their content instruction” (Tedick, Christian and Fortune, 2011, p.7). I argue that our current lack of knowledge regarding what immersion teachers think, know and believe and what immersion teachers’ actual ‘lived’ experiences are in relation to form-focused instruction (FFI) prevents us from fully understanding the key issues at the core of experiential immersion pedagogy and form-focused integration. FFI refers to “any planned or incidental instructional activity that is intended to induce language learners to pay attention to linguistic form” (Ellis, 2001b, p.1). The central aim of this research study is to critically examine the perspectives and practices of Irish-medium immersion (IMI) teachers in relation to FFI. The study ‘taps’ into the lived experiences of three IMI teachers in three different IMI school contexts and explores FFI from a classroom-based, teacher-informed perspective. Philosophical underpinnings of the interpretive paradigm and critical hermeneutical principles inform and guide the study. A multi-case study approach was adopted and data was gathered through classroom observation, video-stimulated recall and semistructured interviews. Findings revealed that the journey of ‘becoming’ an IMI teacher is shaped by a vast array of intricate variables. IMI teacher identity, implicit theories, stated beliefs, educational biographies and experiences, IMI school cultures and contexts as well as teacher knowledge and competence impacted on IMI teachers’ FFI perspectives and practices. An IMI content teacher identity reflected the teachers’ priorities as shaped by pedagogical challenges and their educational backgrounds. While research participants had clearly defined instructional beliefs and goals, their roadmap of how to actually accomplish these goals was far from clear. IMI teachers described the multitude of choices and pedagogical dilemmas they faced in integrating FFI into experiential pedagogy. Significant gaps in IMI teachers’ declarative knowledge about and competence in the immersion language were also reported. This research study increases our understanding of the complexity of the processes underlying and shaping FFI pedagogy in IMI education. Innovative FFI opportunities for professional development across the continuum of teacher education are outlined, a comprehensive evaluation of IMI is called for and areas for further research are delineated.

Between respectability and disgrace: schismogenesis and the regeneration of inequality, stigma and social exclusion in Limerick

The thesis examines cultural processes underpinning the emergence, institutionalisation and reproduction of class boundaries in Limerick city. The research aims to bring a new understanding to the contemporary context of the city’s urban regeneration programme. Acknowledging and recognising other contemporary studies of division and exclusion, the thesis creates a distinctive approach which focuses on uncovering the cultural roots of inequality, educational disadvantage, stigma and social exclusion and the dynamics of their social reproduction. Using Bateson’s concept of schismogenesis (1953), the thesis looks to the persistent, but fragmented culture of community and develops a heuristic ‘symbolic order of the city’. This is defined as “…a cultural structure, the meaning making aspect of hierarchy, the categorical structures of world understanding, the way Limerick people understand themselves, their local and larger world” (p. 37). This provides a very different departure point for exploring the basis for urban regeneration in Limerick (and everywhere). The central argument is that if we want to understand the present (multiple) crises in Limerick we need to understand the historical, anthropological and recursive processes underpinning ‘generalised patterns of rivalry and conflict’. In addition to exploring the historical roots of status and stigma in Limerick, the thesis explores the mythopoesis of persistent, recurrent narratives and labels that mark the boundaries of the city’s identities. The thesis examines the cultural and social function of ‘slagging’ as a vernacular and highly particularised form of ironic, ritualised and, often, ‘cruel’ medium of communication (often exclusion). This is combined with an etymology of the vocabulary of Limerick slang and its mythological base. By tracing the origins of many normalised patterns of Limerick speech ‘sayings’, which have long since forgotten their roots, the thesis demonstrates how they perform a significant contemporary function in maintaining and reinforcing symbolic mechanisms of inclusion/exclusion. The thesis combines historical and archival data with biographical interviews, ethnographic data married to a deep historical hermeneutic analysis of this political community.

Cryptographic coprocessors for embedded systems

In the field of embedded systems design, coprocessors play an important role as a component to increase performance. Many embedded systems are built around a small General Purpose Processor (GPP). If the GPP cannot meet the performance requirements for a certain operation, a coprocessor can be included in the design. The GPP can then offload the computationally intensive operation to the coprocessor; thus increasing the performance of the overall system. A common application of coprocessors is the acceleration of cryptographic algorithms. The work presented in this thesis discusses coprocessor architectures for various cryptographic algorithms that are found in many cryptographic protocols. Their performance is then analysed on a Field Programmable Gate Array (FPGA) platform. Firstly, the acceleration of Elliptic Curve Cryptography (ECC) algorithms is investigated through the use of instruction set extension of a GPP. The performance of these algorithms in a full hardware implementation is then investigated, and an architecture for the acceleration the ECC based digital signature algorithm is developed. Hash functions are also an important component of a cryptographic system. The FPGA implementation of recent hash function designs from the SHA-3 competition are discussed and a fair comparison methodology for hash functions presented. Many cryptographic protocols involve the generation of random data, for keys or nonces. This requires a True Random Number Generator (TRNG) to be present in the system. Various TRNG designs are discussed and a secure implementation, including post-processing and failure detection, is introduced. Finally, a coprocessor for the acceleration of operations at the protocol level will be discussed, where, a novel aspect of the design is the secure method in which private-key data is handled

Composition portfolio and commentaries

In an attempt to provide an analytical entry point into my compositional practice, I have identified eight themes which are significantly recurrent: reduction – the selection of a small number of elements; imperfection – a damaged or warped characteristic of sound; hierarchy – a concern with the roles of instruments with regard to their relative prominence; motion – apparently static sound masses consist of fine internal movement; listener perception – expectations for change influence the experience of affect; translation – the transitioning of electronic sounds to the acoustic realm, and vice versa; immersion – the creation of an accommodating soundscape; blurring – smearing and overlapping sounds or genres. Each of these eight factors is associated with relevant precedents in the history and theory of music that have been influential on my work. These include the minimalist compositions of Steve Reich and Arvo Pärt; the lo-fi aesthetic of Boards of Canada and My Bloody Valentine; concerns with political hierarchy in the work of Louis Andriessen; the variations of dynamics and microtonal shifts of Giacinto Scelsi; Leonard B. Meyer's account of expectation in music; cross-fertilisation of the acoustic and electronic in pieces by Gérard Grisey and Gyorgy Ligeti; the immersive technique of Brian Eno's ambient music; and the overlapping sounds of Aphex Twin. These eight factors are variously applicable to the eleven submitted pieces, which are individually analysed with reference to the most significant of the categories. Together they form a musical language that sustains the interaction of a variety of techniques, concepts and genres.

Towards a cognitive neurobiology of brain-gut axis disorders

The past two decades have seen substantial gains in our understanding of the complex processes underlying disturbed brain-gut communication in disorders such as irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). Despite a growing understanding of the neurobiology of brain-gut axis dysfunction, there is a relative paucity of investigations into how the various factors involved in dysregulating the brain-gut axis, including stress, immune activation and pain, could impact on fundamental brain processes such as cognitive performance. To this end, we proposed a cognitive neurobiology of brain-gut axis dysfunction and took a novel approach to examine how disturbed brain-gut interactions may manifest as altered cognitive performance in IBS and IBD, both cross-sectionally and prospectively. We have demonstrated that, disorders of the brain-gut axis are characterised by stable deficits in specific cognitive domains. Specifically, patients with IBS exhibit a consistent hippocampal mediated visuospatial memory impairment. In addition we have found evidence to suggest a similar visuospatial impairment in IBD. However, our most consistent finding within this population was that patients with Crohn’s disease exhibit impaired selective attention/ response inhibition on the classic Stroop interference test. These cognitive deficits may serve to perpetuate and sustain brain-gut axis dysfunction. Furthermore, this research has shed light on some of the underlying neurobiological mechanisms that may be mediating cognitive dysfunction in IBS. Our findings may have significant implications for the individual who suffers from a brain-gut axis disorder and may also inform future treatment strategies. Taken together, these findings can be incorporated into existing neurobiological models of brain-gut axis dysfunction, to develop a more comprehensive model accounting for the cognitive-neurobiology of brain-gut axis disorders. This has furthered our understanding of disease pathophysiology and may ultimately aid in both the diagnosis and treatment of these highly prevalent, but poorly understood disorders.

Functional metagenomic analysis of the human gut microbiome to identify novel salt tolerance genes

The ability to adapt to and respond to increases in external osmolarity is an important characteristic that enables bacteria to survive and proliferate in different environmental niches. When challenged with increased osmolarity, due to sodium chloride (NaCl) for example, bacteria elicit a phased response; firstly via uptake of potassium (K+), which is known as the primary response. This primary response is followed by the secondary response which is characterised by the synthesis or uptake of compatible solutes (osmoprotectants). The overall osmotic stress response is much broader however, involving many diverse cellular systems and processes. These ancillary mechanisms are arguably more interesting and give a more complete view of the osmotic stress response. The aim of this thesis was to identify novel genetic loci from the human gut microbiota that confer increased tolerance to osmotic stress using a functional metagenomic approach. Functional metagenomics is a powerful tool that enables the identification of novel genes from as yet uncultured bacteria from diverse environments through cloning, heterologous expression and phenotypic identification of a desired trait. Functional metagenomics does not rely on any previous sequence information to known genes and can therefore enable the discovery of completely novel genes and assign functions to new or known genes. Using a functional metagenomic approach, we have assigned a novel function to previously annotated genes; murB, mazG and galE, as well as a putative brp/blh family beta-carotene 15,15’-monooxygenase. Finally, we report the identification of a completely novel salt tolerance determinant with no current known homologues in the databases. Overall the genes identified originate from diverse taxonomic and phylogenetic groups commonly found in the human gastrointestinal (GI) tract, such as Collinsella and Eggerthella, Akkermansia and Bacteroides from the phyla Actinobacteria, Verrucomicrobia and Bacteroidetes, respectively. In addition, a number of the genes appear to have been acquired via lateral gene transfer and/or encoded on a prophage. To our knowledge, this thesis represents the first investigation to identify novel genes from the human gut microbiota involved in the bacterial osmotic stress response.