College of Science, Engineering and Food Science - Doctoral Theses

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    Impact of food, environmental and pharmaceutical antimicrobials on the gut microbiome
    (University College Cork, 2024) Walsh, Lauren; Ross, R. Paul; Hill, Colin; Science Foundation Ireland
    This thesis is concerned with antimicrobials (both protein, peptide and chemical based) and their role in the gut microbiome from a functional and compositional perspective, as well as the isolation and development of new bacteriocins against pathogenic bacteria of interest. Pharmaceutical antimicrobials such as antibiotics, bacteriocins, phages and their endolysins are discussed in chapters 1, 3, 4 and 5. Chapter 1 describes antibiotic alternatives that could potentially be used to treat nosocomial methicillin resistant Staphylococcus aureus (MRSA) infection. Some alternative options include bacteriocins, phages and phage lysins. In Chapter 5, the antibiotics fidaxomicin and vancomycin were compared with the two bacteriocins, thuricin CD and nisin, as potential therapeutics to combat CDI and to assess their overall impact on the gut microbiome. Chapters 3 and 4 specifically discuss the isolation of novel bacteriocin producing bacteria. Chapter 3 describes the isolation of two bacteriocin producing strains termed AS1 and AS2. Chapter 4 outlines the isolation of Paenibacillus ottowii FAA_942_34, which demonstrated activity against IBD-associated bacteria. Environmental antimicrobials and food antimicrobials were examined in chapters 2, 6 and 7. Chapter 2 is a review focusing on the herbicide glyphosateTM, specifically focusing on the compositional and functional changes that glyphosate elicits in the gut microbiome. In chapter 6, glyphosate and four food preservatives were analysed for their effect on the gut microbiome. In Chapter 7, the heavy metal cadmium was used as a selective agent to identify transformants acquiring pJOS01. Following electroporation of pJOS01 into Staphylococcus aureus RN4220, a smaller 21 Kb plasmid termed pJOS02 was recovered in transformants. Formation of pJOS02 from pJOS01 is thought to result from the presence of inverted repeat regions at either end of pJOS02. Overall, the results of this thesis outline a variety of antimicrobials and their effect on the gut microbiome and their potential as therapeutics. This research builds on the growing amount of knowledge around the antimicrobials, the gut microbiome and the effect antimicrobials have on the composition and functionality of the gut microbiome.
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    Ordered macroporous metal oxides and carbonaceous composites for Li-ion and beyond Li-ion batteries
    (University College Cork, 2023) Carroll, Aoife; O'Dwyer, Colm; Irish Research Council
    This thesis provides an in-depth investigation of three-dimensional ordered macroporous materials, specifically inverse opal materials, for electrochemical energy storage systems, particularly rechargeable batteries. Exploring the potential of composite structures, this research focuses on TiO2/GeO2 nanocomposites and C/TiO2 inverse opal anodes in Li-ion batteries, and carbon inverse opal anodes in Na-ion and K-ion batteries. Employing comprehensive characterization techniques, this research studies intricate material properties and electrochemical responses inherent in these structures. The composite materials exhibit promising features such as enhanced electrolyte penetration, improved specific capacities and coulombic efficiency, and robust structural integrity during extended charge-discharge cycling. The study findings shed light on the unique advantages of inverse opal composites for application in next-generation battery technologies. Highly ordered, macroporous inverse opal structures were fabricated as TiO2/GeO2 nanocomposites with varying GeO2 content, showcasing coulombic efficiency and capacity retention. The overall capacity of these interconnected binder-free anodes was affected by the Ge content and its distribution at both slow and fast rates. Characterization techniques such as X-ray diffraction, high-resolution transmission electron microscopy (HRTEM), selected area electron diffraction, energy-dispersive X-ray spectroscopy, and electron energy loss spectroscopy were employed to analyse these anodes. The electrochemical response over 2000 cycles and at various rates elucidated the impact of the composite on key metric in battery cells. The results indicated that a composite of intercalation and alloying compounds yielded good specific capacity and excellent coulombic efficiency (>99%), even with low quantities of the GeO2. The cycling life reveals an increase in capacity with improved coulombic efficiency with suspicion that the GeO2 material becomes electrochemically active within the composite matrix, undergoing modifications during cycling. C/TiO2 composite were synthesized from sucrose as the carbon precursor to form interconnected, porous inverse opal structures. Material characterization revealed amorphous TiO2 and disordered carbon with a large pore size of ~400 nm. An atomic ratio of ~8:1 in favour of carbon yielded promising electrochemical responses with high specific capacity and capacity retention at 150 mA/g rate. Diffusion processes were shown to be the dominant contributor to current responses for all scan rates, with double-layer capacitance accounting for less than ~45 % even at the high scan rate of 1000 mV/s. When compared to individual carbon and TiO2 inverse opals the composite demonstrated improved coulombic efficiency and high-rate performance attributed to the synergistic benefits of combining these two intercalation materials. Carbon inverse opals were fabricated in a similar way from sucrose to study the effect of the macroporous structure on performance in sodium-ion and potassium-ion batteries. Composed of disordered carbon with short-range graphitic regions, the storage mechanism involved primarily diffusion processes at lower scan rate with capacitive behaviour governing the current response at faster scan rates. Structural integrity was maintained in all cells after 250 cycles showcasing impressive resistance to structural stresses. Comparing the inverse opal material to thin films of the same composition highlighted the improved capacity retention and cycling stability inherent to the three-dimensional ordered macroporous structure.
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    Multifaceted computational modelling in pharmaceutical research and development
    (University College Cork, 2023) Vinay Kumar Reddy, Cheemarla; Tiana, Davide; Lawrence, Simon; Swiss Forum for International Agricultural Research; National Institute of Neurological Disorders and Stroke
    Drug development is a multi-step process and takes around 12 to 15 years for a new drug to get approved. In the current scenario, to accelerate the drug development process and to reduce the time frame, most pharmaceutical companies have in-house developed workflows comprised of a hybrid use of computational and experimental approaches. This thesis was focused on employing state-of-the-art molecular modelling methods in three significant areas of pharmaceutical research and development. This thesis comprises an introductory part (chapter 1) and a productive part (chapter 3 to chapter 5). The first chapter of this thesis is the literature review, outlining the foundational studies and research framework used in chapters 3 to 5. The second chapter describes the thesis structure and objectives of the other three chapters. The third chapter explores the hit identification process, utilising docking to screen a small database of phytopharmaceuticals against sclerostin protein followed by an investigation of the stability of the protein-ligand complexes through standard molecular dynamics and funnel meta dynamics. The fourth chapter involves the modelling of adsorption and diffusion of doxorubicin, paclitaxel, carboplatin, and gemcitabine anticancer drugs and also drug combinations such as doxorubicin with carboplatin, paclitaxel with gemcitabine and carboplatin employing NUIG-4 metal-organic framework as drug delivery agents. In this chapter, the comprehensive understanding of molecular interactions governing drug adsorption and diffusion was studied using Grand Canonical Monte Carlo (GCMC) and Molecular Dynamics (MD) simulations. The fifth chapter focuses on investigating the mechanism of chiral Bronsted acid catalysed asymmetric synthesis of homoallyl alcohols from ortho vinyl benzaldehydes and allyl boron pinacol ester using density functional theory methods (DFT), QTAIM, and NCI analysis. Furthermore, a comparative analysis of transition structures of Ortho vinyl and ortho alkynyl benzaldehyde substrates was studied.
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    The role of dietary fibre and plant-based foods in the diets of teenagers (13-18y) in Ireland
    (University College Cork, 2024) McGowan, Clíodhna; Walton, Janette; Kehoe, Laura; Flynn, Albert; Cashman, Kevin; Coffey, Aidan; Department of Agriculture, Food and the Marine, Ireland
    Background: Adequate nutrition during the teenage years is essential to support optimal growth and lay the foundations for long term health. This life stage is also characterised by social development, increasing autonomy and independence and is a critical stage for the optimisation of health and health-related behaviours as habits developed during this time often continue into adulthood. Dietary fibre is a nutrient of interest in public health due to its essential role in normal laxation and association with reduced incidence of non-communicable diseases. Plant-based foods such as ‘fruit & vegetables’ and ‘cereals, grains & potatoes’ are key sources of dietary fibre in the diet, and feature prominently in all food based dietary guidelines (FBDG) due to their nutrient density and association with a number of health benefits. Data from the National Teens’ Food Survey (NTFS) (2005-06) (a nationally representative survey of teenagers in Ireland) reported an intake of dietary fibre below recommendations, and a poor compliance with the Irish FBDG for ‘fruit & vegetables’ and ‘cereals, grains & potatoes’. There have been many changes in the environmental, social and cultural contexts which influence teenagers lifestyles including dietary choices since the NTFS, along with updated international recommendations for dietary fibre intake for teenagers and updated Irish FBDG. New detailed dietary data for teenagers has become available from the nationally representative National Teens’ Food Survey II (NTFS II) (2019-20). Aim: The overall aim of this PhD thesis was to use data from the NTFS II (2019-20) to examine intakes of dietary fibre and the role of plant-based foods such as ‘fruit & vegetables’ and ‘cereals, grains & potatoes’ in the diets of teenagers (13-18y) in Ireland. An additional aim of this thesis was to examine changes over time compared to the previous NTFS (2005-06). Methods: The analyses for this thesis were based on data from the NTFS II (13-18 years, n 428) and the NTFS (13-17 years, n 441). Dietary intake data was collected at brand level using a 4-day weighed food record (NTFS II) and a 7-day semi-weighed food record (NTFS). Energy and nutrient intakes were estimated using Nutritics© (NTFS II) and WISP© (NTFS) based on food composition data from McCance & Widdowson’s ‘The Composition of Foods’ 5th, 6th and 7th editions (plus all nine supplemental volumes). During both surveys, modifications were made to the food composition database to include recipes of composite dishes, fortified foods, generic Irish foods and new foods on the market. Usual intakes of energy and dietary fibre were estimated using the National Cancer Institute (NCI) method using SAS Enterprise Guide©. Dietary fibre intakes were compared to the adequate intake (AI) for normal laxation, proposed by EFSA for this age group (13-14y: 19g/d, 15-17y: 21g/d, 18y: 25g/d). All further analyses were conducted using SPSS© Version 29.0. The percent contribution of food groups to the mean daily intake (MDI) of dietary fibre were calculated by the mean proportion method. Differences in the intake of dietary fibre between sexes (boy, girl), age groups (13-14y, 15-18y) and surveys (NTFS II, NTFS) were calculated using independent sample t-tests. Dietary determinants of dietary fibre intake were investigated by splitting the population into low, medium and high dietary fibre intake groups and examining the key food groups which contributed to the difference in dietary fibre intake between the high and low intake groups and associated patterns of consumption of these food groups. Differences in the MDI of dietary fibre between the low, medium and high intake groups were assessed using ANOVA and Tuckey’s post-hoc analysis. The difference in the percentage of consumers of each food group identified as determinants of dietary fibre intake between dietary fibre intake groups (low, high) were assessed using the Chi-Square test for independence. The differences in consumption patterns between the low and high dietary fibre intake groups were assessed in consumers only using the Mann Whitney U test. To examine the role of ‘fruit & vegetables’ and ‘cereals, grains & potatoes’ in the diets of teenagers in Ireland, the MDI of each food group and subgroup was estimated by summing the weight of each food group consumed for each participant and dividing the total by the number of recording days (NTFS II: 4, NTFS: 7). The percent contribution of ‘fruit & vegetables’ and ‘cereals, grains & potatoes’ to energy, macro- and micro-nutrient intakes were calculated by the mean proportion method. Differences in the intake of ‘fruit & vegetables’ and ‘cereals, grains & potatoes’ between sexes (boy, girl), age groups (13-14y, 15-18y) and surveys (NTFS II, NTFS) were calculated using independent sample t-tests. Analyses to estimate intakes of fruit & vegetables included intake of fruit and/or vegetables from composite dishes and the calculation of inedible or unconsumed portions. To assess compliance with Irish FBDG, intakes of ‘fruit & vegetables’ and ‘cereals, grains & potatoes’ were converted to servings using the Irish FBDG recommendations and standard food portion sizes. Results: Teenagers in Ireland had a usual intake of dietary fibre of 16.9g/d, which was below the AI proposed by EFSA across all age groups examined (13-14y, 15-17y, 18y). Teenage boys had higher usual intakes of dietary fibre compared to girls, however, girls had higher energy adjusted intakes, indicating girls consume a more fibre dense diet. Older teenagers (18y) had higher absolute and energy adjusted intakes of dietary fibre than younger teenagers (13-14y, 15-17y), indicating that older teenagers consumed a more fibre dense diet. The key sources of dietary fibre were identified as ‘bread & rolls’ (19%) (‘white bread & rolls’, 10%), ‘grains, rice, pasta & savouries’ (14%), ‘potato & potato products’ (13%) (‘chipped, fried & roasted potatoes’, 8%), ‘breakfast cereals’ (12%) (RTEBC, 11%), ‘meat & meat products including dishes’ (9%), ‘vegetables & vegetable dishes’ (9%) and ‘fruit & fruit juices’ (7%). Intakes of dietary fibre have increased in teenagers in Ireland since the NTFS (2005-06) (16.9g/d vs 15.5g/d), albeit remain below the EFSA AI for all age groups examined. The increased intakes are due to a higher intake of dietary fibre from ‘grains, rice, pasta & savouries’ and ‘breakfast cereals’ in teenagers in the NTFS II compared to the NTFS. To identify the dietary determinants of dietary fibre intake, teenagers were split into low, medium and high dietary fibre intake groups based on their MDI of dietary fibre. Those in the high intake group had over double the intake of dietary fibre compared to those in the low intake group (24g/d vs 11g/d). The main food groups that contributed to the difference in dietary fibre intake between the high and the low intake groups were ‘high fibre RTEBC’ (17%), ‘wholemeal & brown bread & rolls’ (11%), ‘vegetables & vegetable dishes’ (14%), ‘grains, rice, pasta & savouries’ (10%) and ‘fruit’ (10%). For ‘high fibre RTEBC’ there were more consumers in the high intake group compared to the low intake group (53% vs 33%) and those in the high intake group consumed it more often over the 4 days (2.8 vs 2.0 times) and consumed more at each eating occasion (72g vs 47g). For ‘wholemeal & brown bread & rolls’ there were more consumers in the high intake group compared to the low intake group (63% vs 24%). For ‘grains, rice, pasta & savouries’ there was no difference in the number of consumers between the groups but those in the high intake group consumed it more often over the 4 days (3.2 vs 2.4 times). For ‘vegetables & vegetable dishes’ and ‘fruit’, both food groups were more likely to be consumed by teenagers in the high intake group compared to the low intake group (vegetables & vegetable dishes: 90% vs 75%, fruit: 89% vs 57%) and be consumed more frequently during the recording period (vegetables & vegetable dishes: 6.9 vs 3.4 times, fruit: 5.5 vs 2.4 times). ‘Fruit & vegetables’ were consumed by all teenagers in the NTFS II with an MDI of 218g/d (‘fruit & fruit juices’: 122g/d and ‘vegetables’: 96g/d). Teenagers in the NTFS II had lower intakes of fruit & vegetables compared to teenagers in the NTFS (NTFS II: 218g/d, NTFS: 240g/d). The MDI of 218g/d equated to approx. 2.7 servings of ‘fruit & vegetables’ per day. This is below the Irish FBDG recommendation of 5-7 servings/day, with the majority of teenagers (92%) not meeting the recommended 5-7 servings per day and 22% of teenagers consuming less than one serving (80g) of ‘fruit & vegetables’ per day. For ‘vegetables’, 50% of intakes were from ‘vegetables in composite dishes’, which highlights the important contribution of composite dishes to vegetable intakes in teenagers, and the importance of including fruit and vegetables in composite dishes in estimates of fruit and vegetable intake (particularly for vegetables). ‘Fruit & vegetables’ contributed a small proportion of energy (5%) in the diets of teenagers in Ireland and made important contributions to the intake of dietary fibre (16%) and several micronutrients which have been identified as low in this population, including vitamin C (42%), vitamin A (24%), potassium (14%), folate (DFE) (14%) and vitamin B6 (11%). ‘Fruit & vegetables’ also contributed to the intake of total sugars (20%), due to the natural sugars present in ‘fruit & fruit juices’ and a negligible amount to free sugars (2%) due to ‘fruit juices & smoothies’. ‘Cereals, grains & potatoes’ were consumed by all teenagers in the NTFS II with an MDI of 345g/d (‘grains, rice, pasta & savouries’:128g/d, ‘total bread’: 85g/d, ‘potato & potato products’:84g/d and ‘breakfast cereals’: 48g/d). The overall food group contributed 4.8 servings for boys and 3.8 servings for girls with 1.6 and 1.1 servings, respectively, from ‘wholemeal & brown breads, cereals, pasta and rice and unprocessed potatoes’. This is well below the recommended intake of 4-7 and 3-4 servings per day for boys and girls respectively of ‘wholemeal & brown breads, cereals, pasta and rice and unprocessed potatoes’ in the Irish FBDG. ‘Cereals, grains & potatoes’ contributed significantly to intakes of energy (39%), carbohydrate (55%), protein (30%) and dietary fibre (60%) and made important contributions to a number of micronutrients including B vitamins (15-50%), vitamin D (25%), vitamin C (21%), vitamin E (22%), calcium (35%), potassium (33%) and iron (22%) in the diets of teenagers in Ireland. ‘Cereals, grains & potatoes’ also contributed to intakes of saturated fat, sodium and free sugars, primarily due to specific subgroups including ‘pizza’, ‘savoury dishes & products’ and ‘chipped, fried & roasted potatoes’, ‘bread’ and ‘breakfast cereals’. Teenagers in the NTFS II had lower overall intakes of ‘cereals, grains & potatoes’ compared to teenagers in the previous NTFS (NTFS II: 345g/d, NTFS: 364g/d) with lower intakes of ‘potatoes & potato products’ and ‘low fibre RTEBC’ and higher intakes of ‘grains, rice, pasta & savouries’. Conclusion: In conclusion, the findings from this thesis indicate that overall, teenagers in Ireland are not meeting dietary guidelines for dietary fibre, fruit & vegetables and cereals, grains & potatoes. However, a positive finding was that there is a proportion of the teenage population that had intakes of dietary fibre that reached the AI proposed by EFSA based on existing dietary patterns, providing an evidence base to develop dietary strategies to improve dietary fibre intake in this population group. Based on this evidence, these strategies should focus on increasing intake of ‘fruit & vegetables’ and promoting a swap from refined grains to wholemeal & brown breads, cereals, pasta and rice and unprocessed potatoes which would improve intakes of dietary fibre in teenagers in Ireland and also support FBDG for ‘fruit & vegetables’ and ‘cereals, grains & potatoes’, which have a much wider nutritional role in the diet as evidenced in this thesis. Findings from this thesis may provide evidence to public health campaigns to improve dietary fibre intakes and promote the consumption of plant-based foods to increase compliance with the Irish FBDG in teenagers in Ireland. The findings from this thesis may also provide information to policy makers across various sectors of Irish society including education and health to gain a more comprehensive understanding of the plant-based foods influencing intakes of dietary fibre in teenagers in Ireland.
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    Studies in synthesis using CO2 and H2 gases
    (University College Cork, 2023) Lowry, Amy; Mcglacken, Gerard P.; Byrne, Peter; Irish Research Council; Higher Education Authority
    This thesis is split into two parts based on two different areas of research. Part 1 Part 1 is sub-divided into four chapters. Chapter 1 involves a review of the existing research conducted in this area. Chapter 2 provides details on the research carried out in this project on the development of a Wittig CO2 utilisation methodology for the synthesis of α,β unsaturated carboxylic acids. Chapter 3 involves discussion on the development of protocols for purification of the α,β-unsaturated carboxylic acids synthesised. The Conclusions and Future Work section relating to this area of research is found at the end of Chapter 3. Chapter 4 outlines the experimental work for Part 1. CO2 utilisation continues to capture the attention of chemists due to the ever-increasing levels of CO2 and the negative effects of global warming. CO2 is an inexpensive and environmentally friendly C1 building block, which can be used in the synthesis of value-added chemicals. Many medicinally important compounds and natural products contain the elements of CO2 within their structure, including carboxylic acids, enoates, and carbamates. In particular, α,β unsaturated carboxyl compounds are typically accessed by metal-catalysed transformations or condensation reactions, which often require hydrolysis of the ester product to furnish the corresponding acid. In this project, a telescoped process was developed, that not only achieves CO2 activation, but exploits a novel application of the Wittig reaction, enabling direct installation of the carboxyl group by two successive carbon-carbon bond forming events. Reaction optimisation and purification studies were carried out and 34 α,β-unsaturated carboxylic acids were synthesised using the method, containing a wide range of functional groups, as well as a number of pharmaceutical precursors, in moderate to excellent yields. As part of this work, a novel method for purification of α,β-unsaturated carboxylic acids was developed. Part 2 Part 2 is sub-divided into three chapters. Chapter 5 involves a discussion on the background of the project and a review of the existing research conducted in the area. Chapter 6 involves a discussion of the research carried out in this project on the dearomatisation of benzofuroquinolines by a Pd-catalysed hydrogenation reaction. The Conclusions and Future Work section relating to this part of the thesis is found at the end of Chapter 6. Chapter 7 outlines the experimental work for Part 2. Within the McGlacken group, development of C-H activation methodologies has been a large area of research, and, in particular, benzofuroquinolines have been synthesised via direct intramolecular arylation of 4-phenoxyquinolines. The quinoline nucleus is one of the most frequently occurring ring systems in approved drugs, and hydrogenation of the quinoline nucleus and the selectivity thereof, has been reported in the literature. In addition, increasing interest in the concept of ‘escaping flatland’, whereby the saturation of compounds is increased, allowing for the exploration of more architecturally complex molecules that will potentially give rise to enhanced biological activities. In this part of the thesis, a range of differently substituted benzofuroquinolines were hydrogenated to generate 18 selectively dearomatised benzofuroquinolines. Investigations were carried out into different reaction conditions tolerated by the reaction, and the fate of halogen substituents in the reaction. In addition, a double reduction product side-product was identified and characterised, opening up the methodology to the formation of a new class of novel compounds.