The biodiversity, control and genetic characterisation of the lactococcal 936 group phages

Phages belonging to the 936 group represent one of the most prevalent and frequently isolated phages in dairy fermentation processes using Lactococcus lactis as the primary starter culture. In recent years extensive research has been carried out to characterise this phage group at a genomic level in an effort to understand how the 936 group phages dominate this particular niche and cause regular problems during large scale milk fermentations. This thesis describes a large scale screening of industrial whey samples, leading to the isolation of forty three genetically different lactococcal phages. Using multiplex PCR, all phages were identified as members of the 936 group. The complete genome of thirty eight of these phages was determined using next generation sequencing technologies which identified several regions of divergence. These included the structural region surrounding the major tail protein, the replication region as well as the genes involved in phage DNA packing. For a number of phages the latter genomic region was found to harbour genes encoding putative orphan methyltransferases. Using small molecule real time (SMRT) sequencing and heterologous gene expression, the target motifs for several of these MTases were determined and subsequently shown to actively protect phage DNA from restriction endonuclease activity. Comparative analysis of the thirty eight phages with fifty two previously sequenced members of this group showed that the core genome consists of 28 genes, while the non-core genome was found to fluctuate irrespective of geographical location or time of isolation. This study highlights the continued need to perform large scale characterisation of the bacteriophage populations infecting industrial fermentation facilities in effort to further our understanding dairy phages and ways to control their proliferation.

Engineering design of a bioprocess for the production of natural red colourants by submerged fermentation of the thermophilic fungus Penicillium purpurogenum GH2

The development of a new bioprocess requires several steps from initial concept to a practical and feasible application. Industrial applications of fungal pigments will depend on: (i) safety of consumption, (ii) stability of the pigments to the food processing conditions required by the products where they will be incorporated and (iii) high production yields so that production costs are reasonable. Of these requirements the first involves the highest research costs and the practical application of this type of processes may face several hurdles until final regulatory approval as a new food ingredient. Therefore, before going through expensive research to have them accepted as new products, the process potential should be assessed early on, and this brings forward pigment stability studies and process optimisation goals. Only ingredients that are usable in economically feasible conditions should progress to regulatory approval. This thesis covers these two aspects, stability and process optimisation, for a potential new ingredient; natural red colour, produced by microbial fermentation. The main goal was to design, optimise and scale-up the production process of red pigments by Penicillium purpurogenum GH2. The approach followed to reach this objective was first to establish that pigments produced by Penicillium purpurogenum GH2 are sufficiently stable under different processing conditions (thermal and non-thermal) that can be found in food and textile industries. Once defined that pigments were stable enough, the work progressed towards process optimisation, aiming for the highest productivity using submerged fermentation as production culture. Optimum production conditions defined at flask scale were used to scale up the pigment production process to a pilot reactor scale. Finally, the potential applications of the pigments were assessed. Based on this sequence of specific targets, the thesis was structured in six parts, containing a total of nine chapters. Engineering design of a bioprocess for the production of natural red colourants by submerged fermentation of the thermophilic fungus Penicillium purpurogenum GH2.

Conversion as transformative experience: a sociological study of identity formation and transformation processes

This thesis contributes to the understanding of the processes involved in the formation and transformation of identities. It achieves this goal by establishing the critical importance of ‘background’ and ‘liminality’ in the shaping of identity. Drawing mainly from the work of cultural anthropology and philosophical hermeneutics a theoretical framework is constructed from which transformative experiences can be analysed. The particular experience at the heart of this study is the phenomenon of conversion and the dynamics involved in the construction of that process. Establishing the axial age as the horizon from which the process of conversion emerged will be the main theme of the first part of the study. Identifying the ‘birth’ of conversion allows a deeper understanding of the historical dynamics that make up the process. From these fundamental dynamics a theoretical framework is constructed in order to analyse the conversion process. Applying this theoretical framework to a number of case-studies will be the central focus of this study. The transformative experiences of Saint Augustine, the fourteenth century nun Margaret Ebner, the communist revolutionary Karl Marx and the literary figure of Arthur Koestler will provide the material onto which the theoretical framework can be applied. A synthesis of the Judaic religious and the Greek philosophical traditions will be the main findings for the shaping of Augustine’s conversion experience. The dissolution of political order coupled with the institutionalisation of the conversion process will illuminate the mystical experiences of Margaret Ebner at a time when empathetic conversion reached its fullest expression. The final case-studies examine two modern ‘conversions’ that seem to have an ideological rather than a religious basis to them. On closer examination it will be found that the German tradition of Biblical Criticism played a most influential role in the ‘conversion’ of Marx and mythology the best medium to understand the experiences of Koestler. The main ideas emerging from this study highlight the fluidity of identity and the important role of ‘background’ in its transformation. The theoretical framework, as constructed for this study, is found to be a useful methodological tool that can offer insights into experiences, such as conversion, that otherwise would remain hidden from our enquiries.

Optimisation of chemoenzymatic processes in asymmetric synthesis

This thesis describes the optimisation of chemoenzymatic methods in asymmetric synthesis. Modern synthetic organic chemistry has experienced an enormous growth in biocatalytic methodologies; enzymatic transformations and whole cell bioconversions have become generally accepted synthetic tools for asymmetric synthesis. Biocatalysts are exceptional catalysts, combining broad substrate scope with high regio-, enantio- and chemoselectivities enabling the resolution of organic substrates with superb efficiency and selectivity. In this study three biocatalytic applications in enantioselective synthesis were explored and perhaps the most significant outcome of this work is the excellent enantioselectivity achieved through optimisation of reaction conditions improving the synthetic utility of the biotransformations. In the first chapter a summary of literature discussing the stereochemical control of baker’s yeast (Saccharomyces Cerevisae) mediated reduction of ketones by the introduction of sulfur moieties is presented, and sets the work of Chapter 2 in context. The focus of the second chapter was the synthesis and biocatalytic resolution of (±)-trans-2-benzenesulfonyl-3-n-butylcyclopentanone. For the first time the practical limitations of this resolution have been addressed providing synthetically useful quantities of enantiopure synthons for application in the total synthesis of both enantiomers of 4-methyloctanoic acid, the aggregation pheromone of the rhinoceros beetles of the genus Oryctes. The unique aspect of this enantioselective synthesis was the overall regio- and enantioselective introduction of the methyl group to the octanoic acid chain. This work is part of an ongoing research programme in our group focussed on baker’s yeast mediated kinetic resolution of 2-keto sulfones. The third chapter describes hydrolase-catalysed kinetic resolutions leading to a series of 3-aryl alkanoic acids. Hydrolysis of the ethyl esters with a series of hydrolases was undertaken to identify biocatalysts that yield the corresponding acids in highly enantioenriched form. Contrary to literature reports where a complete disappearance of efficiency and, accordingly enantioselection, was described upon kinetic resolution of sterically demanding 3-arylalkanoic acids, the highest reported enantiopurities of these acids was achieved (up to >98% ee) in this study through optimisation of reaction conditions. Steric and electronic effects on the efficiency and enantioselectivity of the biocatalytic transformation were also explored. Furthermore, a novel approach to determine the absolute stereochemistry of the enantiopure 3-aryl alkanoic acids was investigated through combination of co-crystallisation and X-ray diffraction linked with chiral HPLC analysis. The fourth chapter was focused on the development of a biocatalytic protocol for the asymmetric Henry reaction. Efficient kinetic resolution in hydrolase-mediated transesterification of cis- and trans- β-nitrocyclohexanol derivatives was achieved. Combination of a base-catalysed intramolecular Henry reaction coupled with the hydrolase-mediated kinetic resolution with the view to selective acetylation of a single stereoisomer was investigated. While dynamic kinetic resolution in the intramolecular Henry was not achieved, significant progress in each of the individual elements was made and significantly the feasibility of this process has been demonstrated. The final chapter contains the full experimental details, including spectroscopic and analytical data of all compounds synthesised in this project, while details of chiral HPLC analysis are included in the appendix. The data for the crystal structures are contained in the attached CD.

Synecology in soft sediment bivalves: the influence of parasites, physiological processes, and environmental stressors on health and disease

Ecosystem goods and services provided by estuarine and near coastal regions are being increasingly recognised for their immense value, as is the biodiversity in these areas and these near coastal communities have been identified as sentinels of climate change also. Population structure and reproductive biology of two bivalve molluscs, Cerastoderma edule and, Mytilus edulis were assessed at two study sites over a 16-month study period. Following an anomalously harsh winter, advancement of spawning time was observed in both species. Throughout Ireland and Europe the cockle has experienced mass surfacings in geographically distinct regions, and a concurrent study of cockles was undertaken to explore this phenomenon. Surfaced and buried cockles were collected on a monthly basis and their health compared. Age was highlighted as a source of variation between dying and healthy animals with a parasite threshold being reached possibly around age three. Local factors dominated when looking at the cause of surfacing at each site. The health of mussels was explored too on a temporal and seasonal basis in an attempt to assess what constitutes a healthy organism. In essence external drivers can tip the balance between “acceptable” levels of infection where the mussel can still function physiologically and “unacceptable” where prevalence and intensity of infection can result in physiological impairment at the individual and population level. Synecological studies of intertidal ecosystems are lacking, so all bivalves encountered during the sampling were assessed in terms of population structure, reproduction, and health. It became clear, that some parasites might specialize on one host species while others are not so specific in host choice. Furthermore the population genetics of the cockle, its parasite Meiogymnophallus minutus, and its hyperparasite Unikaryon legeri were examined too. A small nucleotide polymorphism was detected upon comparison of Ireland and Morocco.

Exploring processes of indeterminate determinism in music composition, programming and improvisation

This portfolio consists of 15 original musical works. Taking the form of electronic and acousmatic music, multimedia, and scores, these chamber works serve as a result of experimentation and improvisation with individually built computer interfaces. The accompanying commentary provides discourse on the conceptual practice of these interfaces becoming a compositional entity that present a multi-interpretative opportunity to explore, engage, and personalise. Following this, the commentary examines the path of creative decisions and musical choices that formed both these interfaces and the resulting musical and visual works. This portfolio is accompanied by interfaces used, transcoded interfacing behavioural information, and documented improvisational findings.

The musical enculturation of Irish traditional musicians: An ethnographic study of learning processes

The enculturation of Irish traditional musicians involves informal, non-formal, and sometimes formal learning processes in a number of different settings, including traditional music sessions, workshops, festivals, and classes. Irish traditional musicians also learn directly from family, peers, and mentors and by using various forms of technology. Each experience contributes to the enculturation process in meaningful and complementary ways. The ethnographic research discussed in this dissertation suggests that within Irish traditional music culture, enculturation occurs most effectively when learners experience a multitude of learning practices. A variety of experiences insures that novices receive multiple opportunities for engagement and learning. If a learner finds one learning practice ineffective, there are other avenues of enculturation. This thesis explores the musical enculturation of Irish traditional musicians. It focuses on the process of becoming a musician by drawing on methodologies and theories from ethnomusicology, education, and Irish traditional music studies. Data was gathered through multiple ethnographic methodologies. Fieldwork based on participant-observation was carried out in a variety of learning contexts, including traditional music sessions, festivals, workshops, and weekly classes. Additionally, interviews with twenty accomplished Irish traditional musicians provide diverse narratives and firsthand insight into musical development and enculturation. These and other methodologies are discussed in Chapter 1. The three main chapters of the thesis explore various common learning experiences. Chapter 2 explores how Irish traditional musicians learn during social and musical interactions between peers, mentors, and family members, and focuses on live music-making which occurs in private homes, sessions, and concerts. These informal and non-formal learning experiences primarily take place outside of organizations and institutions. The interview data suggests these learning experiences are perhaps the most pervasive and influential in terms of musical enculturation. Chapter 3 discusses learning experience in more organized settings, such as traditional music classes, workshops, summer schools, and festivals. The role of organizations such as Comhaltas Ceoltóirí Éireann and pipers’ clubs are discussed from the point of view of the learner. Many of the learning experiences explored in this chapter are informal, non-formal, and sometimes formal in nature, depending on the philosophy of the organization, institution, and individual teacher. The interview data and field observations indicate that learning in these contexts is common and plays a significant role in enculturation, particularly for traditional musicians who were born during and after the 1970s. Chapter 4 explores the ways Irish traditional musicians use technology, including written sources, phonography, videography, websites, and emerging technologies, during the enculturation process. Each type of technology presents different educational implications, and traditional musicians use these technologies in diverse ways and some more than others. For this, and other reasons, technology plays a complex role during the process of musical enculturation. Drawing on themes which emerge during Chapter 2, 3, and 4, the final chapter of this dissertation explores overarching patterns of enculturation within Irish traditional music culture. This ethnographic work suggests that longevity of participation and engagement in multiple learning and performance opportunities foster the enculturation of Irish traditional musicians. Through numerous and prolonged participation in music-making, novices become accustomed to and learn musical, social, and cultural behaviours. The final chapter also explores interconnections between learning experiences and also proposes directions for future research.

Investigation of lactic acid bacteria mediated bioprotection with applications in cereal industry. Case-study: malting process

Antifungal compounds produced by Lactic acid bacteria (LAB) metabolites can be natural and reliable alternative for reducing fungal infections pre- and post-harvest with a multitude of additional advantages for cereal-base products. Toxigenic and spoilage fungi are responsible for numerous diseases and economic losses. This thesis includes an overview of the impact fungi have on aspects of the cereal food chain. The applicability of LAB in plant protection and cereal industry is discussed in detail. Specific case studies include Fusarium head blight, and the impact of fungi in the malting and baking industry. The impact of Fusarium culmorum infected raw barley on the final malt quality was part of the investigation. In vitro infected barley grains were fully characterized. The study showed that the germinative energy of infected barley grains decreased by 45% and grains accumulated 199 μg.kg-1 of deoxynivalenol (DON). Barley grains were subsequently malted and fully characterized. Fungal biomass increased during all stages of malting. Infected malt accumulated 8-times its DON concentration during malting. Infected malt grains revealed extreme structural changes due to proteolytic, (hemi)-cellulolytic and starch degrading activity of the fungi, this led to increased friability and fragmentation. Infected grains also had higher protease and β-glucanase activities, lower amylase activity, a greater proportion of free amino and soluble nitrogen, and a lower β-glucan content. Malt loss was over 27% higher in infected malt when compared to the control. The protein compositional changes and respective enzymatic activity of infected barley and respective malt were characterized using a wide range of methods. F. culmorum infected barley grains showed an increase in proteolytic activity and protein extractability. Several metabolic proteins decreased and increased at different rates during infection and malting, showing a complex F. culmorum infection interdependence. In vitro F. culmorum infected malt was used to produce lager beer to investigate changes caused by the fungi during the brewing processes and their effect on beer quality attributes. It was found, that the wort containing infected malt had a lower pH, a higher FAN, higher β-glucan and a 45% increase in the purging rate, and led to premature yeast flocculation. The beer produced with infected malt (IB) had also a significantly different amino acid profile. IB flavour characterization revealed a higher concentration of esters, fusel alcohols, fatty acids, ketones, and dimethylsulfide, and in particular, acetaldehyde, when compared to the control. IB had a greater proportion of Strecker aldehydes and Maillard products contributing to an increased beer staling character. IB resulted in a 67% darker colour with a trend to better foam stability. It was also found that 78% of the accumulated mycotoxin deoxynivalenol in the malt was transferred into beer. A LAB cell-freesupernatant (cfs), produced in wort-base substrate, was investigated for its ability to inhibit Fusarium growth during malting. Wort was a suitable substrate for LAB exhibiting antifungal activity. Lactobacillus amylovorus DSM19280 inhibited 104 spores.mL-1 for 7 days, after 120 h of fermentation, while Lactobacillus reuteri R29 inhibited 105 spores.mL-1 for 7 days, after 48 h of fermentation. Both LAB cfs had significant different organic acid profiles. Acid-base antifungal compounds were identified and, phenyllactic, hydroxy-phenyllactic, and benzoic acids were present in higher concentrations when compared to the control. A 3 °P wort substrate inoculated With L. reuteri R29 (cfs) was applied in malting and successfully inhibited Fusarium growth by 23%, and mycotoxin DON by 80%. Malt attributes resulted in highly modified grains, lower pH, higher colouration, and higher extract yield. The implementation of selected LAB producing antifungal compounds can be used successfully in the malting process to reduce mould growth and mycotoxin production.

Generation and characterisation of biologically active milk-derived protein and peptide fractions

In recent years, extensive research has been carried out on the health benefits of milk proteins and peptides. Biologically active peptides are defined as specific protein fragments which have a positive impact on the physiological functions of the body; such peptides are produced naturally in vivo, but can also be generated by physical and/or chemical processes, enzymatic hydrolysis and/or microbial fermentation. The aims of this thesis were to investigate not only the traditional methods used for the generation of bioactive peptides, but also novel processes such as heat treatment, and the role of indigenous milk proteases, e.g., in mastitic milk, in the production of such peptides. In addition, colostrum was characterised as a source of bioactive proteins and peptides. Firstly, a comprehensive study was carried out on the composition and physical properties of colostrum throughout the early-lactation period. Marked differences in the physico-chemical properties of colostrum compared with milk were observed. Various fractions of colostrum were also tested for their effect on the secretion of pro- and anti-inflammatory cytokines from a macrophage cell line and bone marrow dendritic cells, as well as insulin secretion from a pancreatic beta cell line. A significant reduction in the secretion of the pro-inflammatory cytokines, TNF-α, IL-6, IL-1β and IL-12, a significant increase in the secretion of the anti-inflammatory cytokine, IL-10, as well as a significant increase in insulin secretion were observed for various colostrum fractions. Another study examined the early proteomic changes in the milk of 8 cows in response to infusion with the endotoxin lipopolysaccharide (LPS) at quarter level in a model mastitic system; marked differences in the protein and peptide profile of milk from LPS challenged cows were observed, and a pH 4.6-soluble fraction of this milk was found to cause a substantial induction in the secretion of IL-10 from a murine macrophage cell line. Heat-induced hydrolysis of sodium caseinate was investigated from the dual viewpoints of protein breakdown and peptide formation, and, a peptide fraction produced in this manner was found to cause a significant increase in the secretion of the anti-inflammatory cytokine, IL-10, from a murine macrophage cell line. The effects of sodium caseinate hydrolysed by chymosin on the gut-derived satiety hormone glucagon-like peptide-1 (GLP-1) were investigated; the resulting casein-derived peptides displayed good in vitro and in vivo secretion of GLP-1. Overall, the studies described in this thesis expand on current knowledge and provide good evidence for the use of novel methods for the isolation, generation and characterisation of bioactive proteins and/or peptides.

Novel processes, test structures and characterisation for future germanium technologies

In order to widely use Ge and III-V materials instead of Si in advanced CMOS technology, the process and integration of these materials has to be well established so that their high mobility benefit is not swamped by imperfect manufacturing procedures. In this dissertation number of key bottlenecks in realization of Ge devices are investigated; We address the challenge of the formation of low resistivity contacts on n-type Ge, comparing conventional and advanced rapid thermal annealing (RTA) and laser thermal annealing (LTA) techniques respectively. LTA appears to be a feasible approach for realization of low resistivity contacts with an incredibly sharp germanide-substrate interface and contact resistivity in the order of 10 -7 Ω.cm2. Furthermore the influence of RTA and LTA on dopant activation and leakage current suppression in n+/p Ge junction were compared. Providing very high active carrier concentration > 1020 cm-3, LTA resulted in higher leakage current compared to RTA which provided lower carrier concentration ~1019 cm-3. This is an indication of a trade-off between high activation level and junction leakage current. High ION/IOFF ratio ~ 107 was obtained, which to the best of our knowledge is the best reported value for n-type Ge so far. Simulations were carried out to investigate how target sputtering, dose retention, and damage formation is generated in thin-body semiconductors by means of energetic ion impacts and how they are dependent on the target physical material properties. Solid phase epitaxy studies in wide and thin Ge fins confirmed the formation of twin boundary defects and random nucleation growth, like in Si, but here 600 °C annealing temperature was found to be effective to reduce these defects. Finally, a non-destructive doping technique was successfully implemented to dope Ge nanowires, where nanowire resistivity was reduced by 5 orders of magnitude using PH3 based in-diffusion process.

Activity patterns in design processes of IT standards

Contemporary IT standards are designed, not selected. Their design enacts a complex process that brings together a coalition of players. We examine the design of the SOAP standard to discover activity patterns in this design process. The paper reports these patterns as a precursor to developing a micro-level process theory for designing IT standards.