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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Unravelling Phage-Host Attachment and Recognition Modalities (PHARM) in the dairy bacterium Streptococcus thermophilus
(University College Cork, 2026-06-12) Kampff, Zoe; Mahony, Jennifer; van Sinderen, Douwe; Research Ireland
Streptococcus thermophilus is one of the most economically important bacterial starter cultures employed in the global dairy industry and is used extensively in the manufacture of yoghurt and cheese. Despite its technological importance, bacteriophage infection remains a major cause of fermentation delays and/or failure, resulting in reduced and inconsistent product quality and significant economic losses. Successful phage infection is dependent upon interactions between phage-encoded receptor-binding proteins and specific bacterial receptors. In S. thermophilus, cell wall polysaccharides including rhamnose-glucose polysaccharides (RGPs) and exopolysaccharides (EPSs) are central to phage recognition and binding processes. The overall aim of this thesis was to investigate the diversity, biosynthesis and biological functions of these polysaccharides and determine how variation in their structures influences phage-host interactions.
Comparative genomic analysis demonstrated that genes associated with RGP biosynthesis are widespread throughout the Streptococcus genus. Hierarchical clustering analyses revealed extensive diversity within rgp loci and facilitated the identification of multiple distinct rgp genotypes among members of the salivarius group of streptococci. Additionally, the elucidation of the chemical structures of previously uncharacterised RGPs established direct links between the rgp genotype and the associated RGP structure, providing new insights into the evolution and diversification of streptococcal cell wall polysaccharides.
Functional genomic analyses of bacteriophage-insensitive mutants (BIMs) possessing mutations within the rgp locus of the S. thermophilus strain UCCSt50 provided important insights into the genetic basis of RGP side chain biosynthesis. Structural characterisation of the RGPs of specific BIMs, together with transcriptional analyses and heterologous complementation studies, enabled the construction of a preliminary model of RGP side chain assembly and provided experimental evidence supporting the functional assignment of several genes involved in RGP side chain biosynthesis. Furthermore, these studies demonstrated that structural variation within the RGP directly influences phage susceptibility. The RGP was identified as the receptor for phage P738 and distinct RGP-attracted phages were shown to possess distinct structural requirements for host binding.
Comparative genomic and structural analyses of the EPS biosynthetic loci further revealed extensive diversity among eps genotypes and enabled the assignment of experimentally resolved EPS structures to established genotype groups. Collectively, these findings establish direct relationships between polysaccharide genotype and biochemical structure for both RGP and EPS in S. thermophilus and provide a foundation for predicting polysaccharide structure from genome sequence information.
Overall, the work presented throughout this thesis demonstrates that cell wall polysaccharide diversity is a major determinant of phage-host interactions in S. thermophilus. More broadly, these findings position S. thermophilus as a valuable model through which fundamental aspects of streptococcal cell wall polysaccharide biology can be explored.
A retrospective study of outcome predictive models for anterior circulation stroke post-endovascular thrombectomy: Are CT-derived morphomics useful?
(S. Karger AG, 2026-06-13) Manole, Constantin; Shet, Sahil; O'Brien, Alan; Kakish, Eid; O'Regan, Patrick; Maher, Michael M.; Kelly, Roisin; Hegarty, Aidan; Fanning, Noel; Ryan, David J.
Introduction: In acute ischaemic stroke secondary to a large vessel occlusion, endovascular thrombectomy (EVT) is the standard of care. However, prediction of functional outcomes following EVT remains challenging. We sought to determine whether CT-derived morphomic data on body composition can improve outcome prediction following EVT. Methods: A retrospective analysis of anterior circulation stroke patients who underwent EVT between 2021 and 2023 at a single centre was conducted. Demographic, clinical, and morphomic data including neck muscle and fat area and density were collected. Multivariate logistic regression was used to develop pre-procedure and 24-h post-EVT models for predicting 90-day outcomes. A positive outcome was defined as a modified Rankin Scale (mRS) score of ≤2 at 90 days post-EVT. These models were subsequently tested on 2 separate validation cohorts. Results: High pre-procedure ASPECTS scores, lower baseline NIHSS scores, absence of post-procedure haemorrhage, younger age, and early neurological improvement were the strongest predictors of a positive outcome. None of the morphomic variables were significantly correlated with outcome. The 24-h model was highly accurate in predicting post-EVT outcomes in both validation cohorts. Conclusion: CT-derived morphomic variables did not significantly improve prediction of stroke outcomes post-EVT. Clinical and imaging variables (especially 24-h post-procedure data) showed high accuracy in predicting functional outcomes at 90 days.
Psychosocial impact of sarcoma
(University College Cork, 2026-04-28) Beghean, Rahela; O'Keeffe, Fiadhnait; Larkin, Fionnuala; O'Driscoll, Louise
Background: Sarcoma is a rare and heterogeneous cancer that can involve complex treatment, visible bodily change, functional disruption, uncertainty, and limited diagnosis-specific support. This thesis examined the psychosocial impact of sarcoma in adults, with a focus on adaptation and predictors of distress and wellbeing.
Methods: Two linked studies were conducted. Study 1 was a qualitative meta-synthesis of 40 studies exploring adults’ experiences of sarcoma. Study 2 was a cross-sectional survey of 164 adults with sarcoma examining psychosocial predictors of anxiety and depressive symptoms.
Results: Study 1 identified sarcoma as a cumulative psychosocial disruption across the illness trajectory, from diagnosis and treatment to recovery and survivorship. Five themes were identified, showing how adults with sarcoma may experience diagnostic uncertainty, treatment-related threat, altered body image, functional loss, identity disruption, fear of recurrence, social disconnection, and unmet information and rehabilitation needs. Adaptation was understood as ongoing and non-linear, shaped by coping, meaning-making, family and peer support, continuity of care, rehabilitation, and access to sarcoma-informed professionals. Study 2 found high levels of distress, with 66.5% of participants reporting clinically significant anxiety and 46.3% reporting clinically significant depressive symptoms. Lower self-compassion and greater pain interference predicted both anxiety and depression, while body image distress additionally predicted depression. Perceived social support was high but did not independently predict distress.
Conclusion: Psychosocial distress in sarcoma is substantial, embodied, and shaped by individual and contextual factors. Findings support sarcoma-informed psychosocial assessment, integrated rehabilitation, and targeted interventions addressing pain-related disruption, body image distress, self-compassion, uncertainty, and adaptation.
Pornography use and its association with risk taking sexual behaviours among Irish adolescents
(Elsevier B.V., 2026-08-07) Murphy, Nicola M.; Neville, Breeda; Major, Emmet S.; Barrett, Peter M.
Objectives Online pornography is increasingly accessible to European teenagers due to the proliferation of mobile phone ownership. This raises concerns regarding the influence that pornography may have on adolescent sexual health behaviours. This study examines the association between pornography use and potential risk-taking sexual behaviour among adolescents in the West of Ireland. Study design This is a cross-sectional study design, comprising secondary data analysis of the third Planet Youth Survey in the West of Ireland carried out in November 2022 and based on the international Planet Youth Survey. Methods A cross sectional analysis was conducted using anonymised data from the third wave of the Planet Youth Survey (November 2022), involving 5277 adolescents aged 13-17 from all post-primary schools and Youthreach centres in Galway, Mayo and Roscommon in Ireland. Exposure variables included recent pornography use, use of pornography as a sexual health information source, and reported pressure to view pornography. Outcome variables included engaging in condomless sex, sexual activity under the influence of alcohol or drugs (in the previous year) and very early initiation of sexual activity (<15 years). Data were analysed using multivariable-adjusted logistic regression. Results Thirty-seven percent of respondents reported using pornography in the previous year, with a higher prevalence (51%) among males. Pornography use was significantly associated with engaging in condomless sex (aOR 3.38, 95% C.I. 2.60-4.43), sexual activity under the influence of alcohol/drugs (aOR 3.60, 95% C.I. 2.97-4.37) and very early sexual initiation (aOR 2.79, 95% C.I. 2.00-3.91). Higher levels of parental monitoring consistently conferred a protective effect across all three outcomes. Conclusions Pornography use is prevalent among adolescents in Ireland and is associated with risk-taking sexual behaviours. While causality cannot be inferred, these findings support the prioritisation of integrated, evidence-based sexual health strategies incorporating parental engagement, comprehensive school-based sexuality education and broader public health interventions to address risk-taking sexual behaviours among adolescents.
An assessment of the vulnerability of the coastline of County Cork using a geoinformatics driven approach
(University College Cork, 2026-04-16) Chalençon, Emma; Cawkwell, Fiona; Murphy, Jimmy; Department of the Environment, Climate and Communications
Coastal regions are increasingly exposed to climate change, sea-level rise, and intensifying human pressures, creating an urgent need for robust and decision-relevant assessments of vulnerability. However, existing approaches are often constrained by fragmented evidence bases and conceptual limitations. A review of the international literature highlights several critical gaps: the scarcity of consistent long-term shoreline change data in many regions, the predominance of Coastal Vulnerability Indices (CVIs) that focus narrowly on physical hazards and geomorphology, limited integration of social, economic, and environmental systems, and a lack of empirical validation linking index-based assessments to observed coastal behaviour. These shortcomings hinder the development of comprehensive, policy-relevant vulnerability assessments.
This thesis addresses these gaps through a geoinformatics-driven framework for assessing coastal vulnerability along the coastline of County Cork, Ireland. The approach integrates multi-decadal shoreline change analysis, sustainability-oriented vulnerability modelling, and field-based monitoring across multiple spatial and temporal scales.
To address the lack of baseline physical data, long-term shoreline change rates were derived from historical aerial photography using an automated vegetation-line extraction method designed for spectrally limited Red-Green-Blue imagery. The workflow employs colour vegetation indices, particularly the Normalised Green-Blue Difference Index (NGBDI), combined with iterative threshold optimisation and LiDAR-based constraints to produce spatially consistent shoreline positions with quantified uncertainties of approximately 0.6-1.2 m. This enables robust multi-decadal change rates and provides a scalable alternative to manual digitisation for data-limited coastlines.
Recognising the limitations of conventional CVIs, a Sustainable Coastal Vulnerability Index (SCVI) was developed to capture the multidimensional nature of vulnerability. Grounded in systems thinking and sustainability principles, the SCVI integrates five interrelated dimensions, coastal hazards, physical, socio-cultural, economic, and environmental susceptibility, representing both exposure and the capacity of coupled human-environment systems to respond to change. The index was implemented for the County Cork coastline within a Geographic Information System using 23 spatial indicators mapped at 50m resolution. Indicator weights were derived using the Analytic Hierarchy Process, and a multi-stage sensitivity analysis assessed the robustness of results to methodological choices. The analysis revealed pronounced spatial heterogeneity, with vulnerability hotspots emerging where hazardous processes, susceptible landforms, concentrated assets, and high-value ecosystems coincide, demonstrating that vulnerability is shaped by the interaction of human and environmental systems, not solely by physical hazard intensity.
To ground modelled vulnerability and remotely sensed proxies in empirical observations, a monitoring programme was established at five representative sandy beaches, Pilmore, Garretstown, Garrylucas, Inchydoney, and Owenahincha. Repeated Uncrewed Aerial Vehicle (UAV) surveys, Real-Time Kinematic Global Navigation Satellite System (RTK-GNSS) profiles, and targeted post-storm campaigns generated high-resolution digital surface models and elevation-change analyses, revealing spatially compartmentalised and temporally variable morphodynamic responses driven primarily by sediment redistribution rather than uniform shoreline retreat. Comparisons between multi-decadal vegetation-line trends, short-term morphological change, and index-based vulnerability illustrate how interpretations of coastal change depend strongly on the proxy, scale, and observation period considered.
Collectively, this thesis demonstrates that coastal vulnerability cannot be adequately characterised through single indicators, scales, or disciplinary perspectives. By integrating historical imagery analysis, sustainability-framed spatial modelling, and field-based monitoring, it delivers a transparent and transferable framework for evidence-based coastal management. The geoinformatics-driven approach provides tools to screen, prioritise, and communicate vulnerability at regional scale while explicitly acknowledging uncertainty, scale dependency, and the limitations of proxy-based assessments. The resulting datasets, methodologies, and decision-support products support climate adaptation planning for County Cork and offer a model applicable to other data-limited coastal regions.