The relevance of bacterial isoprenoid biosynthetic pathways for host-microbe interactions

This thesis was undertaken to investigate the relevance of two bacterial isoprenoid biosynthetic pathways (Mevalonate (MVAL) and 2-C-methyl-D-erythritol 4-phosphate (MEP)) for host-microbe interactions. We determined a significant reduction in microbial diversity in the murine gut microbiota (by next generation sequencing) following oral administration of a common anti-cholesterol drug Rosuvastatin (RSV) that targets mammalian and bacterial HMG-CoA reductase (HMG-R) for inhibition of MVAL formation. In tandem we identified significant hepatic and intestinal off-target alterations to the murine metabolome indicating alterations in inflammation, bile acid profiles and antimicrobial peptide synthesis with implications on community structure of the gastrointestinal microbiota in statin-treated animals. However we found no effect on local Short Chain Fatty Acid biosynthesis (metabolic health marker in our model). We demonstrated direct inhibition of bacterial growth in-vitro by RSV which correlated with reductions in bacterial MVAL formation. However this was only at high doses of RSV. Our observations demonstrate a significant RSV-associated impact on the gut microbiota prompting similar human analysis. Successful deletion of another MVAL pathway enzyme (HMG-CoA synthase (mvaS)) involved in Listeria monocytogenes EGDe isoprenoid biosynthesis determined that the enzyme is non-essential for normal growth and in-vivo pathogenesis of this pathogen. We highlight potential evidence for alternative means of synthesis of the HMG-CoA substrate that could render mvaS activity redundant under our test conditions. Finally, we showed by global gene expression analysis (Massive Analysis of cDNA Ends (MACE RNA-seq) a significant role for the penultimate MEP pathway metabolite (E)-4-hydroxy-3-methyl-2-but-2-enyl pyrophosphate (HMBPP) in significant up regulation of genes of immunity and antigen presentation in THP-1 cells at nanomolar levels. We infected THP-1 cells with wild type or HMBPP under/over-producing L. monoctyogenes EGDe mutants and determined subtle effects of HMBPP upon overall host responses to Listeria infection. Overall our findings provide greater insights regarding bacterial isoprenoid biosynthetic pathways for host-microbe/microbe-host dialogue.

Molecular characterisation of the mechanisms of compatible solute accumulation in Listeria monocytogenes

The ability of the Gram-positive foodborne pathogen Listeria monocytogenes to survive and grow in environments of elevated osmolarity can be attributed, at least in part, to the accumulation of a restricted range of low molecular mass solutes compatible with cellular function. Accumulated to high internal concentrations in hyper-saline environments, compatible solutes, either transported into the cell or synthesized de novo, play a dual role: helping to stabilize protein structure and function while also counterbalancing external osmotic strength, thus preventing water loss from the cell and plasmolysis. While previous physiological investigations identified glycine betaine, carnitine, and proline as the principal compatible solutes in the listerial osmostress response, genetic alanysis of the uptake/synthesis systems governing the accumulation of these compounds has, until now, remained largely unexplored. Representing the first genetic analysis of compatible solute accumulation in L. monocytogenes, this thesis describes the molecular characterization of BetL; a highly specific secondary glycine betaine transport system, OpuC; a multicomponent carnitine/glycine betaine transporter, and finally proBA; a two-gene operon encoding the first two enzymes of the listerial proline piosynthesis pathway. In addition to their role in osmotolerance, the potential of each system in contributing to listerial pathogenesis was investigated. While mutations in each gene cluster exhibited dramatic reductions in listerial osmotolerance, OpuC- mutants were additionally shown to exhibit reduced virulence when admisistered via the oral route. This represents the first direct link between the salt stress response and virulence in L. monocytogenes.

Edmund Burke and the heritage of oral culture

The dissertation proposes that one of the more fruitful ways of interpreting Burke's work is to evaluate him as an oral performer rather than a literary practitioner and it argues that in his voice can be heard the modulations of the genres and conventions of oral composition of eighteenth-century Gaelic Ireland. The first chapter situates Burke in the milieu of the Gaelic landed class of eighteenth-century Ireland. The next chapter examines how the rich oral culture of the Munster Gaelic gentry, where Burke spent his childhood days, was to provide a lasting influence on the form and content of Burke's work. His speeches on the British constitution are read in the context of the historical and literary culture of the Jacobites, specifically the speculum principis, Párliament na mBán. The third chapter surveys the tradition of Anglo-Irish theoretical writings on oratory and discusses how Burke is aligned with this school. The focus is on how Burke's thought and practice, his 'idioms', might be understood as being mediated through the criterion of orality rather than literature. The remaining chapters discuss Burke's politics and performance in the light of Gaelic cultural practices such as the rituals of the courts of poetry, the Warrant Poems or Barántas; the performance of funeral laments and elegies, Caoineadh, the laments for the fallen nobility, Marbhna na daoine uaisle, the satires and the political vision allegories of Munster, Aislingí na Mumhan; to show how they provide us with a remarkable context for discussing Burke's poetical-political performance. In hearing Burke's voice through the body of Gaelic culture our understanding of Burke's position in the wider world of the eighteenth century (and hence his meaning) is profoundly affected.

The utility of survey and administrative data to generate information for research and outcomes-based oral health services development

The aim of this research, which focused on the Irish adult population, was to generate information for policymakers by applying statistical analyses and current technologies to oral health administrative and survey databases. Objectives included identifying socio-demographic influences on oral health and utilisation of dental services, comparing epidemiologically-estimated dental treatment need with treatment provided, and investigating the potential of a dental administrative database to provide information on utilisation of services and the volume and types of treatment provided over time. Information was extracted from the claims databases for the Dental Treatment Benefit Scheme (DTBS) for employed adults and the Dental Treatment Services Scheme (DTSS) for less-well-off adults, the National Surveys of Adult Oral Health, and the 2007 Survey of Lifestyle Attitudes and Nutrition in Ireland. Factors associated with utilisation and retention of natural teeth were analysed using count data models and logistic regression. The chi-square test and the student’s t-test were used to compare epidemiologically-estimated need in a representative sample of adults with treatment provided. Differences were found in dental care utilisation and tooth retention by Socio-Economic Status. An analysis of the five-year utilisation behaviour of a 2003 cohort of DTBS dental attendees revealed that age and being female were positively associated with visiting annually and number of treatments. Number of adults using the DTBS increased, and mean number of treatments per patient decreased, between 1997 and 2008. As a percentage of overall treatments, restorations, dentures, and extractions decreased, while prophylaxis increased. Differences were found between epidemiologically-estimated treatment need and treatment provided for those using the DTBS and DTSS. This research confirms the utility of survey and administrative data to generate knowledge for policymakers. Public administrative databases have not been designed for research purposes, but they have the potential to provide a wealth of knowledge on treatments provided and utilisation patterns.

Genetic analysis of bacteriophages from clinical and environmental samples

Bacteriophages, viruses infecting bacteria, are uniformly present in any location where there are high numbers of bacteria, both in the external environment and the human body. Knowledge of their diversity is limited by the difficulty to culture the host species and by the lack of the universal marker gene present in all viruses. Metagenomics is a powerful tool that can be used to analyse viral communities in their natural environments. The aim of this study was to investigate diverse populations of uncultured viruses from clinical (a sputum of patient with cystic fibrosis, CF) and environmental samples (a sludge from a dairy food wastewater treatment plant) containing rich bacterial populations using genetic and metagenomic analyses. Metagenomic sequencing of viruses obtained from these samples revealed that the majority of the metagenomic reads (97-99%) were novel when compared to the NCBI protein database using BLAST. A large proportion of assembled contigs were assignable as novel phages or uncharacterised prophages, the next largest assignable group being single-stranded eukaryotic virus genomes. Sputum from a cystic fibrosis patient contained DNA typical of phages of bacteria that are traditionally involved in CF lung infections and other bacteria that are part of the normal oral flora. The only eukaryotic virus detected in the CF sputum was Torque Teno virus (TTV). A substantial number of assigned sequences from dairy wastewater could be affiliated with phages of bacteria that are typically found in the soil and aquatic environments, including wastewater. Eukaryotic viral sequences were dominated by plant pathogens from the Geminiviridae and Nanoviridae families, and animal pathogens from the Circoviridae family. Antibiotic resistance genes were detected in both metagenomes suggesting phages could be a source for transmissible antimicrobial resistance. Overall, diversity of viruses in the CF sputum was low, with 89 distinct viral genotypes predicted, and higher (409 genotypes) in the wastewater. Function-based screening of a metagenomic library constructed from DNA extracted from dairy food wastewater viruses revealed candidate promoter sequences that have ability to drive expression of GFP in a promoter-trap vector in Escherichia coli. The majority of the cloned DNA sequences selected by the assay were related to ssDNA circular eukaryotic viruses and phages which formed a minority of the metagenome assembly, and many lacked any significant homology to known database sequences. Natural diversity of bacteriophages in wastewater samples was also examined by PCR amplification of the major capsid protein sequences, conserved within T4-type bacteriophages from Myoviridae family. Phylogenetic analysis of capsid sequences revealed that dairy wastewater contained mainly diverse and uncharacterized phages, while some showed a high level of similarity with phages from geographically distant environments.

Application of mesoporous silica for the oral delivery of poorly water-soluble drugs

The objective of this thesis was to improve the dissolution rate of the poorly waters-soluble drug, fenofibrate by processing it with a high surface area carrier, mesoporous silica. The subsequent properties of the drug – silica composite were studied in terms of drug distribution within the silica matrix, solid state and release properties. Prior to commencing any experimental work, the properties of unprocessed mesoporous silica and fenofibrate were characterised (chapter 3), this allowed for comparison with the processed samples studied in later chapters. Fenofibrate was a highly stable, crystalline drug that did not adsorb moisture, even under long term accelerated storage conditions. It maintained its crystallinity even after SC-CO2 processing. Its dissolution rate was limited and dependent on the characteristics of the particular in vitro media studied. Mesoporous silica had a large surface area and mesopore volume and readily picked up moisture when stored under long term accelerated storage conditions (75% RH, 40 oC). It maintained its mesopore character after SC-CO2 processing. A variety of methods were employed to process fenofibrate with mesoporous silica including physical mixing, melt method, solvent impregnation and novel methods such as liquid and supercritical carbon dioxide (SC-CO2) (chapter 4). It was found that it was important to break down the fenofibrate particulate structure to a molecular state to enable drug molecules enter into the silica mesopores. While all processing methods led to some increase in fenofibrate release properties; the impregnation, liquid and SC-CO2 methods produced the most rapid release rates. SC-CO2 processing was further studied with a view to optimising the processing parameters to achieve the highest drug-loading efficiency possible (chapter 5). In this thesis, it was that SC-CO2 processing pressure had a bearing on drug-loading efficiency. Neither pressure, duration or depressurisation rate affected drug solid state or release properties. The amount of drug that could be loaded onto to the mesoporous silica successfully was also investigated at different ratios of drug mass to silica surface area under constant SC-CO2 conditions; as the drug – silica ratio increased, the drug-loading efficiency decreased, while there was no effect on drug solid state or release properties. The influence of the number of drug-loading steps was investigated (chapter 6) with a view to increasing the drug-loading efficiency. This multiple step approach did not yield an increase in drug-loading efficiency compared to the single step approach. It was also an objective in this chapter to understand how much drug could be loaded into silica mesopores; a method based on the known volume of the mesopores and true density of drug was investigated. However, this approach led to serious repercussions in terms of the subsequent solid state nature of the drug and its release performance; there was significant drug crystallinity and reduced release extent. The impact of in vitro release media on fenofibrate release was also studied (chapter 6). Here it was seen that media containing HCl led to reduced drug release over time compared to equivalent media not containing HCl. The key findings of this thesis are discussed in chapter 7 and included: 1. Drug – silica processing method strongly influenced drug distribution within the silica matrix, drug solid state and release. 2. The silica surface area and mesopore volume also influenced how much drug could be loaded. It was shown that SC-CO2 processing variables such as processing pressure (13.79 – 41.37 MPa), duration time (4 – 24 h) and depressurisation rate (rapid or controlled) did not influence the drug distribution within the SBA- 15 matrix, drug solid state form or release. Possible avenues of research to be considered going forward include the development and application of high resolution imaging techniques to visualise drug molecules within the silica mesopores. Also, the issues surrounding SBA-15 usage in a pharmaceutical manufacturing environment should be addressed.

Identification of novel innate immune mechanisms regulating inflammation in the gastrointestinal tract

The Gastro-Intestinal (GI) tract is a unique region in the body. Our innate immune system retains a fine homeostatic balance between avoiding inappropriate inflammatory responses against the myriad commensal microbes residing in the gut while also remaining active enough to prevent invasive pathogenic attack. The intestinal epithelium represents the frontline of this interface. It has long been known to act as a physical barrier preventing the lumenal bacteria of the gastro-intestinal tract from activating an inflammatory immune response in the immune cells of the underlying mucosa. However, in recent years, an appreciation has grown surrounding the role played by the intestinal epithelium in regulating innate immune responses, both in the prevention of infection and in maintaining a homeostatic environment through modulation of innate immune signalling systems. The aim of this thesis was to identify novel innate immune mechanisms regulating inflammation in the GI tract. To achieve this aim, we chose several aspects of regulatory mechanisms utilised in this region by the innate immune system. We identified several commensal strains of bacteria expressing proteins containing signalling domains used by Pattern Recognition Receptors (PRRs) of the innate immune system. Three such bacterial proteins were studied for their potentially subversive roles in host innate immune signalling as a means of regulating homeostasis in the GI tract. We also examined differential responses to PRR activation depending on their sub-cellular localisation. This was investigated based on reports that apical Toll-Like Receptor (TLR) 9 activation resulted in abrogation of inflammatory responses mediated by other TLRs in Intestinal Epithelial Cells (IECs) such as basolateral TLR4 activation. Using the well-studied invasive intra-cellular pathogen Listeria monocytogenes as a model for infection, we also used a PRR siRNA library screening technique to identify novel PRRs used by IECs in both inhibition and activation of inflammatory responses. Many of the PRRs identified in this screen were previously believed not to be expressed in IECs. Furthermore, the same study has led to the identification of the previously uncharacterised TLR10 as a functional inflammatory receptor of IECs. Further analysis revealed a similar role in macrophages where it was shown to respond to intracellular and motile pathogens such as Gram-positive L.monocytogenes and Gram negative Salmonella typhimurium. TLR10 expression in IECs was predominantly intracellular. This is likely in order to avoid inappropriate inflammatory activation through the recognition of commensal microbial antigens on the apical cell surface of IECs. Moreover, these results have revealed a more complex network of innate immune signalling mechanisms involved in both activating and inhibiting inflammatory responses in IECs than was previously believed. This contribution to our understanding of innate immune regulation in this region has several direct and indirect benefits. The identification of several novel PRRs involved in activating and inhibiting inflammation in the GI tract may be used as novel therapeutic targets in the treatment of disease; both for inducing tolerance and reducing inflammation, or indeed, as targets for adjuvant activation in the development of oral vaccines against pathogenic attack.

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.

An exploration through interview and drawings of the experiences of patients diagnosed with oral cancer across their cancer trajectory

Background: The treatment of oral cancer is complex and lengthy. Curative treatment implies a combination of surgery, radiotherapy and chemotherapy. The main goal of treatment is to guarantee long-term tumour free survival with as little functional and cosmetic damage. Despite progress in developing these strategies, cancers of the oral cavity continue to have high mortality rates that have not improved dramatically over the past ten years. Aim: The aim of this study was to uniquely explore the dynamic changes in the physical, psychological, social and existential experiences of newly diagnosed patients with oral cancer at two points across their cancer illness trajectory i.e. at the time of diagnosis and at the end of treatment. Methodology: A qualitative prospective longitudinal design was employed. Non-probability purposive sampling allowed the recruitment of 10 participants. The principal data collection method used was a digital audio taped semi-structured interview along with drawings produced by the participants. Analysis: Data was analysed using latent content analyses. Summary: Three ‘dynamic’ themes, physical, psychosocial and existential experiences were revealed that interact and influence each other in a complex and compound whole. These experiences are present at different degrees and throughout the entire trajectory of care. Patients have a number of specific concerns and challenges that cannot be compartmentalised into unitary or discrete aspects of their daily lives. Conclusion & Implications: An understanding of the patient’s experience of their illness at all stages of the disease trajectory, is essential to inform service providers’ decision making if the delivery of care is to be client centred. Dynamic and fluctuating changes in the patient’s personal experience of the cancer journey require dynamic, energetic and timely input from health care professionals.

A corpus-driven error analysis of the oral and written production of Leaving Certificate Spanish learners

The Leaving Certificate (LC) is the national, standardised state examination in Ireland necessary for entry to third level education – this presents a massive, raw corpus of data with the potential to yield invaluable insight into the phenomena of learner interlanguage. With samples of official LC Spanish examination data, this project has compiled a digitised corpus of learner Spanish comprised of the written and oral production of 100 candidates. This corpus was then analysed using a specific investigative corpus technique, Computer-aided Error Analysis (CEA, Dagneaux et al, 1998). CEA is a powerful apparatus in that it greatly facilitates the quantification and analysis of a large learner corpus in digital format. The corpus was both compiled and analysed with the use of UAM Corpus Tool (O’Donnell 2013). This Tool allows for the recording of candidate-specific variables such as grade, examination level, task type and gender, therefore allowing for critical analysis of the corpus as one unit, as separate written and oral sub corpora and also of performance per task, level and gender. This is an interdisciplinary work combining aspects of Applied Linguistics, Learner Corpus Research and Foreign Language (FL) Learning. Beginning with a review of the context of FL learning in Ireland and Europe, I go on to discuss the disciplinary context and theoretical framework for this work and outline the methodology applied. I then perform detailed quantitative and qualitative analyses before going on to combine all research findings outlining principal conclusions. This investigation does not make a priori assumptions about the data set, the LC Spanish examination, the context of FLs or of any aspect of learner competence. It undertakes to provide the linguistic research community and the domain of Spanish language learning and pedagogy in Ireland with an empirical, descriptive profile of real learner performance, characterising learner difficulty.