College of Science, Engineering and Food Science - Doctoral Theses

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    The gut microbiome of the wild great tit (Parus major): drivers and fitness consequences
    (University College Cork, 2023) Somers, Shane Edmond; Quinn, John; Ross, R. Paul; Stanton, Catherine; Irish Research Council for Science, Engineering and Technology; European Research Council; Science Foundation Ireland
    The gut microbiome plays a vital role in its host’s ecology. Clinical studies have shown gut microbes increase host health and fitness by providing digestive and immune functions, as well as aiding development. Natural variation in the microbiome is widely believed to affect host fitness in the wild but we are lacking experimental studies to test this. The microbiome varies with both host and environmental factors but most studies to date have focussed on individual factors and not adequately addressed the multiple overlapping and hierarchical drivers of microbiome variation working at environmental, host and microbial scales. This thesis investigates the role of the gut microbiota in host fitness, and how this is affected by and varies across contexts. Additionally, we address sources of variation in the gut microbiota at a host and environmental level, accounting for host ecology and drivers at different scales. We find that the host’s weight is correlated with microbiome diversity during development but that the direction of this relationship is context dependent. This shows that the microbiome interacts with the environment to determine host fitness and is important because it helps explain the contradictory findings linking diversity to weight. We also show that the interaction between the host, its microbiome and environment change with developmental stage. Specifically, we found that the microbiome of developed individuals is remarkably resilient to environmental perturbation, while developing individuals are much more sensitive, with important implications for future experiments. We developed a novel method for experimentally perturbing the microbiome that will allow microbiome researchers to begin testing hypotheses linking the microbiome to host ecology and evolution in natural settings. Finally, we show that welfare measures, such as environmental enrichment may interact with the gut microbiota to impact on host health and behaviour. In summary, I show that variation in the microbiome is linked to host ecology and that this variation is linked to host fitness.
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    Studies in the synthesis and impurity profiling of pharmacologically active benzodifurans
    (University College Cork, 2022) O'Connor, Richard Eric; Keating, J J; Higher Education Authority
    Substituted 2,3-dihydrobenzofuran derivatives as well as their benzofuran and benzodifuranyl analogues are versatile heterocycles that are increasing in prominence as key building blocks in organic chemistry. In particular, benzodifuran-containing structures are gaining significant interest in medicinal chemistry as pharmacophores and in industrial chemistry as scaffolds for organic electroluminescent devices, organic field-effect transistors, solar cell sensitizers and semiconducting polymers. The synthesis of pharmacologically active benzodifurans are complex multi-step processes and each individual step has the potential for considerable side-product/impurity formation. This project focused on synthetic strategies to benzofuran and benzodifuran derivatives in addition to their hydrogenated and substituted analogues. The chosen synthetic routes to target molecules further focused on the propensity of synthetic steps to produce impurities, modifiable variables to modulate impurity formation and the impurity profile of each synthetic route explored. Organic process impurities identified were isolated and fully characterised where possible, in addition to intended products.
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    Monitoring and modelling the long-term performance of Dublin Port Tunnel
    (University College Cork, 2023) Wang, Chao; Li, Zili; Friedman, Miles; Science Foundation Ireland; Transport Infrastructure Ireland
    Dublin Port Tunnel, the biggest urban road tunnel in Ireland, functions as a critical part of an arterial road network between Dublin Port and the rest of Dublin city. Since its opening in 2006, the tunnel has been observed with progressively developing deteriorations; onsite observations and maintenance records have identified three main types, i.e., tunnel leakage, lining crack and concrete spalling, as the greatest engineering concerns to asset owners. The increasing structure deformation may disrupt tunnel operation, threaten tunnel serviceability, and/or even endanger tunnel integrity and safety in the long term. To better the understanding of the structural health condition of this critical underground infrastructure, this thesis specifically investigates the long-term ageing performance of a cross passage twin tunnel section of Dublin Port Tunnel subject to various deteriorations through an integrated assessment based on innovative field monitoring (i.e., wireless sensor network) and advanced numerical modelling (i.e., finite element modelling), where previous investigations mainly concentrated on the responses of a single tunnel section to short-term external disturbances (e.g., adjacent construction and surcharge). Characterisation of the selected deteriorated tunnel section on the basis of historical data, maintenance records, geotechnical and hydraulic reports is conducted first. Ground and tunnel parameters are obtained through applying theories and principles of soil and rock mechanics, followed by the determination of the current hydraulic permeability (conductivity) of the deteriorated section on the basis of monitored water flow. A modified analytical model for ground-lining relative permeability is proposed by assuming radial groundwater flow through all three ground layers and the hydraulic health status of the tunnel section is evaluated to be partially permeable. To quantitatively investigate the tunnel structural behaviour, an innovative wireless sensor network field monitoring system is adopted to monitor the long-term structural performance of the select cross-passage twin tunnel section, with the system’s reliability and robustness being tested inside an underground cave in the first place. The trial deployment of the wireless sensor network monitoring system inside the cave proves it functionally effective and environmentally adaptable in harsh underground conditions. In the case study of Dublin Port Tunnel, wireless field measurements of the cross-passage tunnel section show that its deformation is still increasing with time even after more than a decade’s operation. The mode and magnitude of the observed ongoing tunnel deformation are believed to be caused by three effects: twin tunnel interaction effect, cross passage effect and seasonal effect, and the mechanisms behind these observations are deemed to be related to both the surrounding ground and tunnel: ground hydro-geological degradation and tunnel hydro-mechanical deterioration. The seasonal temperature change contributes to the cyclic variation of the elastic and reversible deformation whilst tunnel deteriorations lead to the plastic and irreversible deformation. The field measurements are then compared against the numerical results from a series of soil-fluid coupled three-dimensional finite element analyses where the time-dependent ground and tunnel deteriorations are considered. The three-dimensional finite element (FE) analyses evaluate the individual effect of tunnel hydraulic and mechanical deterioration, ground permeability anisotropy, and ground creep. The numerical rate of tunnel deformation is compared against the field measurements to examine the numerical model. The FE results suggest that limestone rheology is the dominant factor contributing to the ongoing tunnel deformation, despite a slight difference between the deformation modes possibly due to the neglection of localised ground creep in the ground in between the twin tunnels. Parametrically, coupled deterioration leads to greater deformation than that individual deterioration does, and localised deterioration induces more accurate tunnel performance than that uniform deterioration does.
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    A cross-disciplinary analysis of the materials used in the making of Irish works of art
    (University College Cork, 2023) Biolcati, Veronica; Iacopino, Daniela; Ó Macháin, Pádraig; Irish Research Council
    Nowadays, the fields of cultural heritage preservation and heritage science are experiencing a growing demand for non-invasive analytical methodologies. These approaches aim to minimize direct interaction with artefacts in order to minimize any potential damage. In fact, non-invasive analytical techniques, by virtue of their non-destructive nature, do not induce modifications in the physical or chemical constitution of the art objects, and they often obviate the need for sampling. Since decades, X-ray fluorescence spectroscopy (XRF) is routinely used as preliminary step in most analytical surveys of artworks. This publication-based thesis, under the auspices of the Inks & Skins project, presents three case studies which used XRF for the elemental characterization of the materials under analysis. XRF plaid a key role in all investigations, as it informed about material availability, artistic techniques, and manufacturing technologies among others. Following the introduction on the principle of XRF and a brief overview on inks and metals, chapter two presents the multi-analytical investigation of the Irish Gaelic manuscript on animal skin, the Book of Uí Mhaine. The presented publication was the culmination of an interdisciplinary analysis of the composing material and manufacturing techniques of the largest Gaelic Books surviving from the medieval vernacular period. XRF elucidated the elemental composition of inks, pigments, and parchment support. The extensive data collected in this study served as comparative tool for the undergoing research on the materials and techniques used in other (27 at the time of this thesis) medieval Irish manuscripts from different traditions. Chapter three presents the publication raising from the study of inks used to write nineteen satiric poems in Harward’s Almanac, a 17th century Dublin book. In this specific case XRF aided to establishing the original order in which the verses were written. Again, this work would have not been possible without a transdisciplinary approach which included paleography, codicology, material science, and statistical analysis. The fourth chapter offers a detailed description of an XRF-based analysis of three gold and silver medieval Irish chalices. This technical study was performed in order to put into historical contest a gilded silver chalice recently sold on auction as to be of medieval and Irish origin. This was done by comparing its materiality with two other late medieval silver-gilt chalices. The study helped to reveal their manufacturing technique, the nature of the decorating enamels and glass, and their story they went through. This work could have not been possible without the essential work and research of art historians. Finally, to highlight the enormous potential of XRF technique, all the analysis were performed on-site at partner institutions, libraries, and museums.
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    Molecular characterisation of a conjugative Bifidobacterium megaplasmid
    (University College Cork, 2023) Dineen, Rebecca L.; van Sinderen, Douwe; O'Connell Motherway, Mary; Science Foundation Ireland
    Bifidobacterium species are highly abundant autochthonous bacteria of the human gut microbiota, particularly during host infancy. Various members of the Bifidobacterium genus have been associated with a plethora of health-promoting attributes, among which maintaining gut homeostasis, limiting pathogenic bacterial invasion as well as their purported ability to modulate host immune responses are notable examples. Due to their positive association with human health, this genus has received substantial scientific attention and commercial interest. Plasmids were once considered an atypical feature of Bifidobacterium and those identified within this genus were primarily small cryptic plasmids which were presumed to replicate by a so-called rolling circle mechanism. However, the recent availability of long-read single-molecule sequencing technologies precipitated the resolution of the first reported bifidobacterial megaplasmid isolated from the common and abundant inhabitant of the human gut, Bifidobacterium breve JCM7017. The discovery of this >190 kb conjugative megaplasmid, denoted pMP7017, and the subsequent identification of pMP7017 homologs in several B. longum subsp. longum strains, highlights the prevalence of this megaplasmid family within this genus, representing an unexplored feature. Conjugative plasmids such as pMP7017 play a central role in bacterial evolution and have the potential to significantly influence the activity of the microbiome community and, by extension, impact human health and physiology. The research described in this thesis covers the replication functions of megaplasmid pMP7017 and exploits these functions for the development of important molecular tools that facilitate the genetic engineering of these genetically recalcitrant bacteria. As pMP7017 represents the first and, thus far, only experimentally validated conjugative plasmid of bifidobacterial origin, research performed within the context of this thesis also concerned examination of the conjugative functions of this megaplasmid. While the molecular characterisation of pMP7017 represents an opportunity for the development of much needed molecular tools and provides a starting point in the understanding of bifidobacterial DNA transfer systems, an integrated approach of comparative analyses and metagenomic data mining has generated highly relevant and insightful information concerning the biology and distribution of pMP7017 and related megaplasmids.