Use of oxygen sensors for the non destructive measurement of oxygen in packaged food and beverage products and its impact on product quality and shelf life

The principal objective of this thesis was to investigate the ability of reversible optical O2 sensors to be incorporated into food/beverage packaging systems to continuously monitor O2 levels in a non-destructive manner immediately postpackaging and over time. Residual levels of O2 present in packs can negatively affect product quality and subsequently, product shelf-life, especially for O2-sensitive foods/beverages. Therefore, the ability of O2 sensors to continuously monitor O2 levels present within food/beverage packages was considered commercially relevant in terms of identifying the consequences of residual O2 on product safety and quality over time. Research commenced with the development of a novel range of O2 sensors based on phosphorescent platinum and palladium octaethylporphyrin-ketones (OEPk) in nano-porous high density polyethylene (HDPE), polypropylene (PP) polytetrafluoroethylene (PTFE) polymer supports. Sensors were calibrated over a temperature range of -10°C to +40°C and deemed suitable for food and beverage packaging applications. This sensor technology was used and demonstrated itself effective in determining failures in packaging containment. This was clearly demonstrated in the packaging of cheese string products. The sensor technology was also assessed across a wide range of packaged products; beer, ready-to-eat salad products, bread and convenience-style, muscle-based processed food products. The O2 sensor technology performed extremely well within all packaging systems. The sensor technology adequately detected O2 levels in; beer bottles prior to and following pasteurisation, modified atmosphere (MA) packs of ready-to-eat salad packs as respiration progressed during product storage and MA packs of bread and convenience-style muscle-based products as mycological growth occurred in food packs over time in the presence and absence of ethanol emitters. The use of the technology, in conjunction with standard food quality assessment techniques, showed remarkable usefulness in determining the impact of actual levels of O2 on specific quality attributes. The O2 sensing probe was modified, miniaturised and automated to screen for the determination of total aerobic viable counts (TVC) in several fish species samples. The test showed good correlation with conventional TVC test (ISO:4833:2003), analytical performance and ruggedness with respect to variation of key assay parameters (probe concentration and pipetting volume). Overall, the respirometric fish TVC test was simple to use, possessed a dynamic microbial range (104-107 cfu/g sample), had an accuracy of +/- one log(cfu/g sample) and was rapid. Its ability to assess highly perishable products such as fish for total microbial growth in <12 hr demonstrates commercial potential.

ARIA 2016: Care pathways implementing emerging technologies for predictive medicine in rhinitis and asthma across the life cycle

The Allergic Rhinitis and its Impact on Asthma (ARIA) initiative commenced during a World Health Organization workshop in 1999. The initial goals were (1) to propose a new allergic rhinitis classification, (2) to promote the concept of multi-morbidity in asthma and rhinitis and (3) to develop guidelines with all stakeholders that could be used globally for all countries and populations. ARIA—disseminated and implemented in over 70 countries globally—is now focusing on the implementation of emerging technologies for individualized and predictive medicine. MASK [MACVIA (Contre les Maladies Chroniques pour un Vieillissement Actif)-ARIA Sentinel NetworK] uses mobile technology to develop care pathways for the management of rhinitis and asthma by a multi-disciplinary group and by patients themselves. An app (Android and iOS) is available in 20 countries and 15 languages. It uses a visual analogue scale to assess symptom control and work productivity as well as a clinical decision support system. It is associated with an inter-operable tablet for physicians and other health care professionals. The scaling up strategy uses the recommendations of the European Innovation Partnership on Active and Healthy Ageing. The aim of the novel ARIA approach is to provide an active and healthy life to rhinitis sufferers, whatever their age, sex or socio-economic status, in order to reduce health and social inequalities incurred by the disease.

Plasmid biology of natural Lactococcus lactis strains and molecular mechanisms of bacteriophage-host interaction

Lacticin 3147, enterocin AS-48, lacticin 481, variacin, and sakacin P are bacteriocins offering promising perspectives in terms of preservation and shelf-life extension of food products and should find commercial application in the near future. The studies detailing their characterization and bio-preservative applications are reviewed. Transcriptomic analyses showed a cell wall-targeted response of Lactococcus lactis IL1403 during the early stages of infection with the lytic bacteriophage c2, which is probably orchestrated by a number of membrane stress proteins and involves D-alanylation of membrane lipoteichoic acids, restoration of the physiological proton motive force disrupted following bacteriophage infection, and energy conservation. Sequencing of the eight plasmids of L. lactis subsp. cremoris DPC3758 from raw milk cheese revealed three anti-phage restriction/modification (R/M) systems, immunity/resistance to nisin, lacticin 481, cadmium and copper, and six conjugative/mobilization regions. A food-grade derivative strain with enhanced bacteriophage resistance was generated via stacking of R/M plasmids. Sequencing and functional analysis of the four plasmids of L. lactis subsp. lactis biovar. diacetylactis DPC3901 from raw milk cheese revealed genes novel to Lactococcus and typical of bacteria associated with plants, in addition to genes associated with plant-derived lactococcal strains. The functionality of a novel high-affinity regulated system for cobalt uptake was demonstrated. The bacteriophage resistant and bacteriocin-producing plasmid pMRC01 places a metabolic burden on lactococcal hosts resulting in lowered growth rates and increased cell permeability and autolysis. The magnitude of these effects is strain dependent but not related to bacteriocin production. Starters’ acidification capacity is not significantly affected. Transcriptomic analyses showed that pMRC01 abortive infection (Abi) system is probably subjected to a complex regulatory control by Rgg-like ORF51 and CopG-like ORF58 proteins. These regulators are suggested to modulate the activity of the putative Abi effectors ORF50 and ORF49 exhibiting topology and functional similarities to the Rex system aborting bacteriophage λ lytic growth.

An investigation of innovation and knowledge creation in virtual worlds

The Internet and World Wide Web have had, and continue to have, an incredible impact on our civilization. These technologies have radically influenced the way that society is organised and the manner in which people around the world communicate and interact. The structure and function of individual, social, organisational, economic and political life begin to resemble the digital network architectures upon which they are increasingly reliant. It is increasingly difficult to imagine how our ‘offline’ world would look or function without the ‘online’ world; it is becoming less meaningful to distinguish between the ‘actual’ and the ‘virtual’. Thus, the major architectural project of the twenty-first century is to “imagine, build, and enhance an interactive and ever changing cyberspace” (Lévy, 1997, p. 10). Virtual worlds are at the forefront of this evolving digital landscape. Virtual worlds have “critical implications for business, education, social sciences, and our society at large” (Messinger et al., 2009, p. 204). This study focuses on the possibilities of virtual worlds in terms of communication, collaboration, innovation and creativity. The concept of knowledge creation is at the core of this research. The study shows that scholars increasingly recognise that knowledge creation, as a socially enacted process, goes to the very heart of innovation. However, efforts to build upon these insights have struggled to escape the influence of the information processing paradigm of old and have failed to move beyond the persistent but problematic conceptualisation of knowledge creation in terms of tacit and explicit knowledge. Based on these insights, the study leverages extant research to develop the conceptual apparatus necessary to carry out an investigation of innovation and knowledge creation in virtual worlds. The study derives and articulates a set of definitions (of virtual worlds, innovation, knowledge and knowledge creation) to guide research. The study also leverages a number of extant theories in order to develop a preliminary framework to model knowledge creation in virtual worlds. Using a combination of participant observation and six case studies of innovative educational projects in Second Life, the study yields a range of insights into the process of knowledge creation in virtual worlds and into the factors that affect it. The study’s contributions to theory are expressed as a series of propositions and findings and are represented as a revised and empirically grounded theoretical framework of knowledge creation in virtual worlds. These findings highlight the importance of prior related knowledge and intrinsic motivation in terms of shaping and stimulating knowledge creation in virtual worlds. At the same time, they highlight the importance of meta-knowledge (knowledge about knowledge) in terms of guiding the knowledge creation process whilst revealing the diversity of behavioural approaches actually used to create knowledge in virtual worlds and. This theoretical framework is itself one of the chief contributions of the study and the analysis explores how it can be used to guide further research in virtual worlds and on knowledge creation. The study’s contributions to practice are presented as actionable guide to simulate knowledge creation in virtual worlds. This guide utilises a theoretically based classification of four knowledge-creator archetypes (the sage, the lore master, the artisan, and the apprentice) and derives an actionable set of behavioural prescriptions for each archetype. The study concludes with a discussion of the study’s implications in terms of future research.

Genteel revolutionaries: the lives of Anna and Thomas Haslam

The lives of Thomas and Anna Haslam were dedicated to the attainment of women's equality. They were feminists before the word was coined. In an era when respectable women were not supposed to know of the existence of prostitutes, Anna became empowered to do the unthinkable, not only to speak in public but to discuss openly matters sexual and to attack the double standard of sexuality which was enshrined in the official treatment of prostitutes. Their life-long commitment to the cause of women's suffrage never faltered, despite the repeated discouragement of the fate of bills defeated in the House of Commons. The Haslams represented an Ireland which did not survive them. While they were dedicated to the union with Westminster, they worked happily with those who applied themselves to its destruction. Although in many ways they exemplified the virtues of their Quaker backgrounds, they did not subscribe to any organised religion. Despite living in straitened circumstances, they were part of an urban intellectual elite and participated in the social and cultural life of Dublin for over fifty years. It is tempting to speculate how the Haslams would have fared in post independence Ireland. Hanna Sheehy Skeffington who had impeccable nationalist credentials, was effectively marginalised. It is likely that they would have protested against discriminatory legislation in their usual law abiding manner but, in a country which quickly developed an overwhelmingly Roman Catholic ethos, would they have had a voice or a constituency? Ironically, Thomas's teaching on chastity would have found favour with the hierarchy; his message was disseminated in a simple and more pious manner in numerous Catholic Truth Society pamphlets. The Protestant minority never sought to subvert the institutions of the state, was careful not to criticise and kept its collective head down. Dáil Éireann was not bombarded with petitions for the restoration of divorce facilities or the unbanning of birth control. Those who sought such amenities obtained them quietly 'in another jurisdiction.' Fifty years were to pass before the condom wielding 'comely maidens' erupted on to the front pages of the Sunday papers. They were, one imagines, the spiritual descendants of the militant rather than the constitutional suffrage movement. "Once and for all we need to commit ourselves to the concept that women's rights are not factional or sectional privileges, bestowed on the few at the whim of the many. They are human rights. In a society in which the rights and potential of women are constrained no man can be truly free." These words spoken by Mary Robinson as President of Ireland are an echo of the principles to which the Haslams dedicated their lives and are, perhaps, a tribute to their efforts.

Monasticism and its limits: rematerialising monastic space in early medieval Ireland

This thesis creates a multi-faceted archaeological context for early Irish monasticism, so as to ‘rematerialise’ a phenomenon that has been neglected by recent archaeological scholarship. Following revision of earlier models of the early Irish Church, archaeologists are now faced with redefining monasticism and distinguishing it from other diverse forms of Christian lifestyle. This research addresses this challenge, exploring the ways in which material limits can be set on the monastic phenomenon. The evidence for early Irish monasticism does not always conform to modern expectations of its character, and monastic space must be examined as culturally unique in its own right - though this thesis demonstrates that early Irish monasticism was by no means as unorthodox in its contemporary European setting as has previously been suggested. The research is informed by theories of the body, habitus and space, drawing on a wide body of archaeological, religious, sociological and anthropological thought. The data-set comprises evidences gathered through field-survey, reassessment of archaeological scholarship, historical research and cartographic research, enabling consideration of the ways in which early Irish monastics engaged with their environments. A sample of thirty-one early Irish ecclesiastical sites plus Iona forms the basis for discussion of the location and layout of monastic space, the ways in which monastics used buildings and space in their daily lives, the relationship of monasticism and material culture, the setting of mental and physical limits on monastic space and monastic bodies, and the variety of monastic lifestyles that pertained in early medieval Ireland. The study then examines the Christian landscapes of two case-studies in mid-Western Ireland in order to illustrate how monasticism functioned on the ground in these areas. As this research shows, the material complexities of early Irish monastic life are capable of archaeological definition in terms of both communal and personal lived experience.

Fundamental studies of sourdoughs fermented with Weissella cibaria and Lactobacillus plantarum: influence on baking characteristics, sensory profiles and in vitro starch digestibility of gluten-free breads

The application of sourdough can improve texture, structure, nutritional value, staling rate and shelf life of wheat and gluten-free breads. These quality improvements are associated with the formation of organic acids, exopolysaccharides (EPS), aroma or antifungal compounds. Initially, the suitability of two lactic acid bacteria strains to serve as sourdough starters for buckwheat, oat, quinoa, sorghum and flours was investigated. Wheat flour was chosen as a reference. The obligate heterofermentative lactic acid bacterium (LAB) Weissella cibaria MG1 (Wc) formed the EPS dextran (a α-1,6-glucan) from sucrose in situ with a molecular size of 106 to 107 kDa. EPS formation in all breads was analysed using size exclusion chromatography and highest amounts were formed in buckwheat (4 g/ kg) and quinoa sourdough (3 g/ kg). The facultative heterofermentative Lactobacillus plantarum FST1.7 (Lp) was identified as strong acidifier and was chosen due to its ubiquitous presence in gluten-free as well as wheat sourdoughs (Vogelmann et al. 2009). Both Wc and Lp, showed highest total titratable acids in buckwheat (16.8 ml; 26.0 ml), teff (16.2 ml; 24.5 ml) and quinoa sourdoughs (26.4 ml; 35.3 ml) correlating with higher amounts of fermentable sugars and higher buffering capacities. Sourdough incorporation reduced the crumb hardness after five days of storage in buckwheat (Wc -111%), teff (Wc -39%) and wheat (Wc -206%; Lp -118%) sourdough breads. The rate of staling (N/ day) was reduced in buckwheat (Ctrl 8 N; Wc 3 N; Lp 6 N), teff (Ctrl 13 N; Wc 9 N; Lp 10 N) and wheat (Ctrl 5 N; Wc 1 N; Lp 2 N) sourdough breads. Bread dough softening upon Wc and Lp sourdough incorporation accounted for increased crumb porosity in buckwheat (+10.4%; +4.7), teff (+8.1%; +8.3%) and wheat sourdough breads (+8.7%; +6.4%). Weissella cibaria MG1 sourdough improved the aroma quality of wheat bread but had no impact on aroma of gluten-free breads. Microbial shelf life however, was not prolonged in any of the breads regardless of the starter culture used. Due to the high prevalence of insulin-dependent diabetes mellitus particular amongst coeliac patients, glycaemic control is of great (Berti et al. 2004). The in vitro starch digestibility of gluten-free breads with and without sourdough addition was analysed to predict the GI (pGI). Sourdough can decrease starch hydrolysis in vitro, due to formation of resistant starch and organic acids. Predicted GI of gluten-free control breads were significantly lower than for the reference white wheat bread (GI=100). Starch granule size was investigated with scanning electron microscopy and was significantly smaller in quinoa flour (<2 μm). This resulted in higher enzymatic susceptibility and hence higher pGI for quinoa bread (95). Lowest hydrolysis indexes for sorghum and teff control breads (72 and 74, respectively) correlate with higher gelatinisation peak temperatures (69°C and 71°C, respectively). Levels of resistant starch were not increased by addition of Weissella cibaria MG1 (weak acidifier) or Lactobacillus plantarum FST1.7 (strong acidifier). The pGI was significantly decreased for both wheat sourdough breads (Wc 85; Lp 76). Lactic acid can promote starch interactions with gluten hence decreasing starch susceptibility (Östman et al. 2002). For most gluten-free breads, the pGI was increased upon sourdough addition. Only sorghum and teff Lp sourdough breads (69 and 68, respectively) had significantly decreased pGI. Results suggest that the increase of starch hydrolysis in gluten-free breads was related to mechanism other than presence of organic acids and formation of resistant starch.

Mutational and molecular analyses of lactococcal bacteriophages TP901-1 and Tuc2009

Bacteriophages belonging to the Siphoviridae family represent viruses with a noncontractile tail that function as extremely efficient bacterium-infecting nanomachines. The Siphoviridae phages TP901-1 and Tuc2009 infect Lactococcus lactis, and both belong to the so-called P335 species. As P335 phages are typically capable of a lytic and lysogenic life cycle, a number of molecular tools are available to analyse their virions. This doctoral thesis describes mutational and molecular analyses of TP901-1 and Tuc2009, with emphasis on the role of their tail-associated structural proteins. Several novel and intriguing findings discovered during the course of this study on the nature of Siphoviridae phages furthers a basic molecular understanding of their virions, and the role of their virion proteins, during the initial stages of infection. While Siphoviridae virions represent complex quaternary structures of multiple proteins and subunits thereof, mutagenic analysis represents an efficient mechanism to discretely characterize the function of individual proteins, and constituent amino acids, in the assembly of the phage structure and their biological function. However, as always, more research is required to delve deeper into the mechanisms by which phages commence infection. This is important to advance our understanding of this intricate process and to facilitate application of such findings to manipulate phage infections. On the one hand, we may want to prevent phages from infecting starter cultures used in the dairy industry, while on the other hand it may be desirable to optimize viral infection for the application of phages as bacterial parasites and therapeutic agents.

Ecology of frontier populations of the invasive grey squirrel (Sciurus carolinensis) in Ireland

The rise in invasive species, together with habitat destruction, is associated with worldwide declines in biodiversity and ecosystem functioning. Management of invasive species, as well as amelioration of invasion impacts, provide challenges to species and ecosystem ecologists and conservation managers. Although any species can become invasive if it is transported to, establishes in and spreads in a new environment outside of its native range, rodents are a particularly frequent invader. Rodent introductions are often inadvertent but are also commonly intentional as these animals are traded and transported as pets and may escape from captivity. Tree squirrel species are attractive to humans and are able to establish populations with only a few founding individuals, making them a group well suited to performing the role of biological invaders. The eastern grey squirrel (Sciurus carolinensis) is the most commonly introduced squirrel species worldwide. This research addressed the grey squirrel invasion and frontier population biology. Novel results were generated through diverse research techniques. Public sighting surveys and hairtube surveys were used to locate the southern frontier of grey squirrel range expansion in Ireland. A 22-month intensive live trapping study of two frontier populations facilitated the collection of personality and demographic data from squirrels in increasing populations. A systematic literature search on grey squirrel demography provided context for the studied populations, among frontier and established introduced populations, as well as those in the native range. Advanced spatially explicit population modeling techniques predicted future range expansion and objectively compared the outcomes of 12 grey squirrel management strategies. The methods and results are discussed in both a basic scientific and applied invasion management context. An improved understanding of the behaviour, population dynamics, and future scenarios at the frontier of species invasions is crucial for managers worldwide and this is provided here for the grey squirrel in Ireland.

Caring for the Celtic cubs: Discursive constructions of mothers and mothering in the Irish childcare debate

Drawing on an understanding of the public sphere as a multiplicity of communicative and discursive spaces this paper examines the constructions of mothers, mothering and motherhood which emerged in recent debates about childcare in Ireland. Preliminary analysis of these discursive constructions suggest that they are often based on rhetoric, informed by stereotypical assumptions and rooted in frames of reference which mitigate against the emergence of alternative ways of understanding the issues of mothering and childcare. It will be argued that the reductionist and divisive nature of the childcare debate which ensued prior to the 2005 budget, stymied childcare policy development at a time when its unprecedented prominence on the political agenda and the strength of public finances could have underpinned a shift in policy approach. The paper concludes with an exploration of the ways in which feminist scholarship can challenge the Irish model of childcare policy, which continues to be premised on an understanding of childcare and the reconciliation of work and family life as the privatised responsibility of individual women.

Isolation and characterisation of antifungal compounds from lactic acid bacteria and their application in wheat and gluten-free bread

As part of the “free-from” trend, biopreservation for bread products has increasingly become important to prevent spoilage since artificial preservatives are more and more rejected by consumers. A literature review conducted as part of this thesis revealed that the evaluation of more suitable antifungal strains of lactic acid bacteria (LAB) is important. Moreover, increasing the knowledge about the origin of the antifungal effect is fundamental for further enhancement of biopreservation. This thesis addresses the investigation of Lactobacillus amylovorus DSM19280, Lb. brevis R2: and Lb. reuteri R29 for biopreservation using in vitro trials and in situ sourdough fermentations of quinoa, rice and wheat flours as biopreservatives in breads. Their contribution to quality and shelf life extension on bread was compared and related to their metabolic activity and substrate features. Moreover, the quantity of antifungal carboxylic acids produced during sourdough fermentation was analysed. Overall a specific profile of antifungal compounds was found in the sourdough samples which were strain and substrate dependently different. The best preservative effect in quinoa sourdough and wheat sourdough bread was achieved when Lb. amylovorus DSM19280 fermented sourdough was used. However, the concentration of the antifungal compounds found in these biopreservatives were much lower when compared with Lb. reuteri R29 as the highest producer. Nevertheless, the artificial application of the highest concentration of these antifungal compounds in chemically acidified wheat sourdough bread succeeded in a longer shelf life than achieved only by acidifying the dough. This evidences their partial contribution to the antifungal activity and their synergy. Additionally, a HRGC/MS method for the identification and quantification of the antifungal active compounds cyclo(Leu-Pro), cyclo(Pro-Pro), cyclo(Met-Pro) and cyclo(Phe-Pro) was successfully developed by using stable isotope dilutions assays with the deuterated counterparts. It was observed that the concentrations of cyclo(Leu-Pro), cyclo(Pro-Pro), and cyclo(Phe-Pro) increased only moderately in MRS-broth and wort fermentation by the activity of the selected microorganism, whereas the concentration of cyclo(Met-Pro) stayed unchanged.

An examination of the impact of dietary lipids on behaviour and neurochemistry

The molecular and cellular basis of stress pathology remains an important research question in biological science. A better understanding of this may enable the development of novel approaches for the treatment of stress-related disorders. There is a considerable body of scientific evidence suggesting that dietary lipids, phospholipids and omega-3 polyunsaturated fatty acids (n-3 PUFAs), have therapeutic potential for certain psychiatric disorders. Thus, we proposed n-3 PUFAs as a novel strategy for the prevention or amelioration of stress-related disorders. We hypothesised that these compounds would improve behavioural and neurobiological responses and alter gut microbial composition. Furthermore, we proposed a new mechanism of action exerted by n-3 PUFAs using an in vitro model of stress. Lastly, we explored the protective effects of both phospholipids and n-3 PUFAs against neuroinflammation, which has been shown to contribute to the development of stress-related disorders. We provide further evidence that glucocorticoids, inflammation and early-life stress induce vulnerability to psychopathologies. Specifically, we have demonstrated that corticosterone (CORT) alters cortical neuron and astrocyte percentage composition, reduces brain-derived-neuronal factor (BDNF) expression, and induces glucocorticoid receptor (GR) down-regulation in mixed cortical cultures. Interestingly, we found that lipopolysaccharide (LPS) treatment resulted in an over-expression of pro-inflammatory cytokines in cortical astrocyte cultures. Moreover, we demonstrate that early-life stress induces changes to the monoaminergic and immune systems as well as altered neuroendocrine response to stressors later in life. In addition, we found that early-life stress alters the gut microbiota in adulthood. These data demonstrate that n-3 PUFAs can attenuate CORT-induced cellular changes, but not those caused by LPS, within the cerebral cortex. Similarly, phospholipids were unable to reverse LPS-induced inflammation in cultured astrocytes. In addition, this thesis proposes that n-3 PUFAs may prevent the development or lessen the symptoms of mental illnesses, ameliorating anxiety- and depressive-like symptoms as well as cognitive effects, particularly when administered during neurodevelopment. Such effects may be mediated by GR activation as well as by modification of the gut microbiota composition. Taken together, our findings suggest that n-3 PUFAs have therapeutic potential for stress-related disorders and we provide evidence for the mechanisms by which they may exert these effects. These findings contribute to an exciting and growing body of research suggesting that nutritional interventions may have an important role to play in the treatment of stress-related psychiatric conditions.