CORA
Cork Open Research Archive (CORA) is UCC’s Open Access institutional repository which enables UCC researchers to make their research outputs freely available and accessible.
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Implications of changes to primary production and management practices in pasture-based dairy systems, on the compositional and processing properties of milk and Cheddar cheese quality
(University College Cork, 2025-10-15) Page, Richard M.; O'Callaghan, Tom; O'Mahony, Seamus Anthony; Lamichhane, Prabin; Teagasc
This thesis considers the effects of some key primary production and management practices on the compositional, technological and ripening properties of Cheddar cheese. In Ireland’s predominantly pasture-based dairy system, about a third of all milk is used for cheese production. As dairy farming practices evolve (e.g., adoption of practices to enhance sustainability of primary milk production), the composition of milk can change, with implications for dairy products made therefrom. Developing a deeper understanding of how farm-level decisions influence cheese quality is therefore of scientific and commercial relevance.
The impacts of dairy production practices on the processing of milk into cheese were initially explored through a review of the literature. Various practices, both intrinsic and extrinsic to the dairy animal, were considered in-turn. Due consideration was also given to interactions taking place within the dairy food system, because primary production practices impact on each other, making it a highly complex system. Substantial evidence is available to suggest that some changes in production practices can be made without adverse impacts on cheese quality. The experimental chapters of this thesis then contribute to this evidence-base by examining pertinent research gaps, improving our understanding of the influence of milking frequency, pasture type, and cow breeding and genetics on cheese biochemistry.
Twice-a-day (TAD) milking is most commonly used within Irish pasture-based systems, and the impact of milking frequency on cheese production was explored by contrasting TAD with once-a-day (OAD) milking. Most notably, OAD milking yielded significantly more cheese from a given volume of milk compared to TAD, suggesting a possible increased economic value for OAD milk within cheese manufacturing. The OAD strategy also resulted in cheese that was significantly more yellow, a difference confirmed to be associated with significantly higher β-carotene content, β-carotene being both a pigment and pro-vitamin A. Consumers often favour more yellow dairy products, and increased β-carotene concentrations could provide nutritional benefits (supporting iron metabolism, skin and mucous membrane function, vision and the immune system).
Pasture-type was investigated through comparisons of milk and cheese derived from multispecies swards (MSS) and perennial ryegrass (PRG) diets. Milk compositions were found to be broadly similar, but MSS milks had significantly higher protein content. Significantly higher actual cheese yields (Ya) resulted from MSS grazing as compared to PRG, at 11.13 and 10.58%, respectively. For many investigated attributes, cheese obtained from the differing pasture diets were broadly comparable. These novel findings provide assurances that a biodiverse MSS strategy can be adopted while maintaining Cheddar cheese quality. The increased cheesemaking efficiency suggested through increased cheese yields could also offer an opportunity for manufacturers.
Investigations into crossbreeding compared differences arising when using Jersey-Holstein-Friesian (JFX) milk compared to Holstein-Friesian (HF) milk in the production of Cheddar cheese. The JFX milk had higher protein and fat content, but no statistically significant differences in set-to-cut time or cheese yield resulted. Cheese produced from both breeds was broadly comparable, but JFX derived cheese was significantly more yellow in colour. These intrinsic aspects of primary production were then explored further through investigations into genetic polymorphism of κ-CN, using milk collected according to the following treatment groups: HF with AA κ-CN (HF-AA), HF with AB κ-CN (HF-AB), and JFX with AB κ-CN (JFX-AB). On average, HF-AA milks had lower fat, protein and casein contents, smaller fat globule size, higher pH and larger casein micelle size compared to HF-AB and JFX-AB milks. The HF-AA treatment was associated with poorer rennet coagulation properties and lower cheese yields compared to HF-AB and JFX-AB. The highest cheese yields and fastest coagulation times were associated with the JFX-AB treatment. These findings suggest crossbreeding can be combined with the selection of appropriate genetic variants to achieve improved production trait outcomes.
Considered collectively, these findings advance our understanding of how decisions on the farm can influence the processing performance of milk obtained from Irish pasture-based systems, and the key quality attributes of cheese made therefrom. When milking frequency, grazing system and breeding selection strategies are applied appropriately on the farm, milk can be processed into Cheddar cheese without adverse impacts. Additionally, some areas have been highlighted where targeted use of these primary production strategies can enhance cheesemaking efficiency and product quality. The findings contained herein offer potential future benefits for stakeholders within Irish dairy food systems, in particular for processors and dairy consumers.
Synthesis and optimisation of Aurivillius phase thin films for next generation data storage
(University College Cork, 2025-12-11) Dutta, Debismita; Keeney, Lynette; Nolan, Michael; Science Foundation Ireland
Aurivillius phase oxides are well-established room-temperature ferroelectrics, whose high Curie temperatures and intrinsic fatigue resistance make them attractive candidates for emerging energy-efficient non-volatile memory and neuromorphic device concepts. However their integration in vertically oriented device architectures is limited by three interconnected challenges: (i) their spontaneous polarisation is predominantly in-plane, which is misaligned with the out-of-plane electric fields used in standard capacitor geometries; (ii) there is no predictive framework linking complex three-dimensional defect motifs to measurable X-ray diffraction (XRD) signatures; and (iii) crystal twinning frequently emerges during thin-film growth, reducing domain coherence and hindering reliable switching.
This thesis addresses these challenges through controlled thin-film synthesis, advanced structural characterisation, and analytical model development. Supersaturation, tuned through the precursor delivery kinetics and oxygen partial pressure of Direct Liquid Injection Chemical Vapour Deposition (DLI-CVD), serves as the unifying experimental variable across the three chapters, governing whether Bi₄Ti₃O₁₂ thin films grow via two-dimensional nucleation, dislocation-mediated spiral formation, or diffusion-limited single-variant epitaxy. This work identifies for the first time that films exhibiting spiral morphologies displayed a measurably enhanced vertical polarisation, with the required switching voltage reduced from ±20 V to ±5 V. Correlative piezoresponse force microscopy, density functional theory, and electron microscopy reveal a previously unrecognised mechanism by which inclined out-of-phase boundary defects generated by spiral growth alter local symmetry and strain environments, thereby stabilising an out-of-plane polarisation in a material class normally constrained to in-plane orientation. To interpret the diffraction signatures of these non-planar defects, a new three-dimensional XRD model was developed. This framework extends the structure-factor formalism to incorporate both vertical registry offsets and angular boundary inclinations, enabling accurate simulation of the asymmetric peak splitting observed experimentally. The model provides a non-destructive estimation of defect density and orientation, establishing a predictive link between defect topology and reciprocal-space features.
Finally, the thesis demonstrates a previously unreported route to supressing crystal twinning. By regulating supersaturation during metal–organic chemical vapour deposition, the twinning typically observed in Aurivillius films on epitaxially matched substrates can be effectively eliminated. Lower supersaturation enhances adatom mobility and promotes single-variant epitaxy, yielding films with improved structural coherence and spatially uniform ferroelectric switching. This approach provides an accessible, growth-parameter-based route to producing twin-free layered ferroelectrics without substrate modification or post-processing. Collectively, these findings provide new insight into the layered crystallography of Aurivillius phases and the growth mechanisms that modify their ferroelectric response. The thesis delivers three distinct advances: (i) a previously unrecognised mechanism by which spiral growth enhances out-of-plane polarisation; (ii) a new three-dimensional XRD framework that predicts diffraction signatures arising from complex defect geometries; and (iii) a previously unreported supersaturation-controlled route for eliminating twin variants in layered ferroelectric thin films. Together, these advances contribute a materials-centric foundation for integrating layered ferroelectrics into vertically oriented memory and neuromorphic device platforms, where controlled polarisation, structural coherence, and engineered defect landscapes are essential for meeting key requirements for reliable operation at technologically relevant scales.
Detection & avoidance of adverse medication outcomes in older adults living with multimorbidity and polypharmacy
(University College Cork, 2026-03-31) Daunt, Ruth; O'Mahony, Denis; Curtin, Denis
Advances in pharmacotherapy has transformed modern healthcare, contributing to increased longevity globally. This growing population of older adults, many of whom live with multimorbidity and polypharmacy, is at risk of adverse medication outcomes. Two under-investigated components of adverse medication outcomes include prescribing cascades and the impact of medication on quality of life.
This doctoral thesis, comprising eight chapters, was designed to address these two important and interrelated aspects of adverse medication outcomes. The first chapter provides an introduction, divided into three sections, (i) medications, (ii) prescribing cascades, and (iii) patient-reported outcomes and medication-related burden. The second chapter presents a prospective prevalence study of prescribing cascades in hospitalised older adults with multimorbidity and polypharmacy. The third explores factors influencing hospital physicians’ recognition of prescribing cascades. The fourth chapter develops a modified, short-form of the original MRB-QoL (mMRB-QoL) for older adults with multimorbidity and polypharmacy. Chapter five considers the relevance of the research and outlines potential directions for future research. Chapter six contains peer-reviewed articles that were published during the writing of this thesis. References and appendices are presented in chapters seven and eight, respectively.
Tissue identification for surgical guidance using biophotonics
(University College Cork, 2026-05-06) Ghauri, M. Daniyal; Andersson-Engels, Stefan; Konugolu, Sanathana; Burke, Ray; H2020 Marie Skłodowska-Curie Actions; Research Ireland
Optical spectroscopic techniques provide powerful non-invasive means for probing biological tissues to reveal their structural, functional and molecular characteristics. Their utilization spans diagnostic, therapeutic and monitoring regimes. Advancing these capabilities, this work establishes a unified framework for optical tissue identification and surgical guidance by integrating diagnostics, analytical modeling, phantom development and minimally invasive biomarker assessment.
The work begins with continuous wave (CW) diffuse reflectance spectroscopy applied for early detection of malignancy in the oral cavity. This study demonstrates that spectral signature can sensitively capture biochemical changes to differentiate diseased tissues from healthy. Motivated by the clinical promise of CW methods but recognizing limitations in quantitative and depth resolved characterization, an analytical hybrid model combining continuous wave and photon time of flight (pToF) spectroscopy was subsequently developed. It offers simplicity and portability of CW systems with depth sensitivity of time-resolved measurements to overcome the bulky hardware and long acquisition times typically required for broadband pToF systems. The resulting optical parameters enable real time interpretation of key physiological markers such as blood content and oxygenation, supporting informed diagnostic decision making. To support therapeutic applications, a hybrid solid–liquid anthropomorphic phantom was developed to replicate optical and anatomical features simultaneously. This complex model addresses the long-standing need for anatomically accurate optical phantom models for optimizing interstitial photodynamic therapy dosimetry. Extending optical assessment beyond direct tissue interrogation, Raman spectroscopic analysis of blood plasma was explored as a minimally invasive means to detect systemic biochemical alterations associated with localized tissue disease. Correlations between plasma derived spectral signatures and paired tissue biopsies demonstrate feasibility of optical blood based biomarkers for monitoring and patient stratification without the need for repeated tissue sampling.
Collectively, these explorations establish a comprehensive framework for optical tissue characterization that spans clinical deployment, analytical modeling, phantom validation and minimally invasive diagnostics. This work contributes to the advancement of precision healthcare, while paving the way for future interdisciplinary developments in biophotonics.
Optimising transfection methods for genome editing using iPSCs and CRISPR/Cas9
(University College Cork, 2026-02-28) Beltran, Jhoan Sebastian; Matsa, Elena; Lee, Ciaran
The emergence of induced pluripotent stem cells (iPSCs), together with major advances in genome editing technologies, has significantly expanded the potential of cell-based therapies in regenerative medicine and immunotherapy. Since their first description by Shinya Yamanaka and Kazutoshi Takahashi in 2006, iPSCs have been widely explored as a promising platform for the treatment of a broad range of diseases, including Parkinson’s disease, Alzheimer’s disease, and organ failure. Their capacity for unlimited self-renewal and differentiation into virtually any somatic cell type make them an attractive and versatile cell source for therapeutic applications.
Despite these advances, significant clinical challenges remain. One of the principal barriers to the clinical translation of iPSC-derived therapies is the potential immune rejection associated with allogeneic cell products. Consequently, multiple strategies have been proposed to mitigate immune recognition and improve the compatibility of transplanted cells.
This project aimed to contribute towards the development of hypoimmune iPSC lines by targeted knock-out of human leukocyte antigen (HLA) class I and class II molecules. To achieve this, the study evaluated alternative approaches for the delivery of genome editing cargo into iPSCs, assessing their potential as less invasive alternatives to electroporation. Transfection efficiencies obtained through cell-penetrating peptide (CPP)-mediated delivery and Lipofectamine-based methods reached approximately 40–50%%, with CPPs allowing higher viability and preservation of cellular morphology. In contrast, photoporation yielded lower transfection efficiencies, averaging around 22%. Overall, these findings suggest that CPPs may provide improved balance between cargo uptake and viability for iPSCs and will support future efforts to generate hypoimmune cell lines research and therapeutic applications.