University of Galway Research Repository

Recent Submissions

  • Publication
    A statistical mechanics investigation of sarcomere and titin organisation in cardiac myocytes and disease evolution
    (University Of Galway, 2024-07-18) Coleman, Ryan J.; McGarry, Patrick
    A fundamental examination of sarcomere function in cardiac myocytes serves as a focal point for this computational modelling exploration, where thermodynamic considerations of fundamental sub-cellular components guide predictions of sarcomere maturation. A steady-state framework predicting sarcomere organisation is developed in a three-state model of actin-myosin organisation of sarcomeres, stress fibres, and unbound cytoskeletal proteins, where global conservation of these cytoskeletal proteins is considered. Contributions of internal energies, strain energies and work associated with deformation, as well as entropic considerations, inform thermodynamically motivated sub-cellular formation of sarcomeres in myofibrils and stress fibre (SF) organisation. A non-local finite element model of the cell allows us to interpret sarcomere organisation within modelled cardiac myocytes, where we implement a statistical mechanics framework for cell homeostasis through a bespoke nested sampling methodology to generate a population of cells. We refer to this population as the homeostatic ensemble, where we maximise morphological entropy of cells subject to the constraint that the ensemble average free-energy is equal to the homeostatic free energy associated with a suspended cell. A modelling study investigates the response of human induced pluripotent stem cell (HiPSC) cardiac myocytes on confined aspect ratio micropatterned patches with substrates of equivalent stiffness to the native myocardium. Free energy considerations of cytoskeletal actin-myosin organisation, passive energies associated with deformation of the cell cytoplasm and membrane, and deformation of the attached substrate, inform homeostasis of modelled cardiac myocytes. Predicted patterns of sarcomere alignment and sarcomere density are shown to be in agreement with reported experimental data. This computational framework uncovers that Gibbs free energy decreases with increasing sarcomere density, which drives an increase in sarcomere length and the elongation of cells into high aspect-ratio spread-states. Constrained cell spreading on high aspect-ratio rectangular micropatterned patches is shown to facilitate strong sarcomere formation. In contrast, constrained spreading on square micropatterned patches results in low sarcomere formation. Titin is a protein which guides sarcomere formation in muscular cells. A wealth of experimental evidence supports the fact that titin plays a role in sarcomere formation and active contractility in cardiac myocytes. However, the underlying mechanisms are poorly understood, and no computational myofibril model to-date has incorporated a description of titin biomechanical behaviour. We develop a novel theoretical model to predict the force-deformation response of the sub structural immunoglobulin (Ig) domains of titin. Chemical potentials and consideration of thermodynamic equilibrium govern the folding and unfolding of Ig domains. Our model is shown to correctly predict complex patterns of active unfolding and extension in response to applied loading, providing accurate predictions of previously reported experimentally measured force-displacement data and Ig folding and unfolding data. Our model reveals that application of a mechanical load to an Ig chain results in an imbalance between chemical potentials of folded and unfolded Ig domains, inducing transient unfolding of Ig domains in order to restore thermodynamic equilibrium. This novel titin model provides a deeper understanding of the underlying thermodynamic principles governing the folding and unfolding of Ig domains, and can be directly incorporated into a dynamic model of sarcomerogenesis in cardiac myocytes. In the field of tissue culture engineering, cyclic loading regimes are often applied to HiPSC cardiac myocytes, as it is experimentally observed to induce sarcomerogenesis. To investigate this phenomenon, our thermodynamically motivated framework for sarcomere organisation under steady-state conditions is extended to a transient framework, predicting actin-myosin organisation in response to dynamic loading. The biomechanical contributions of titin is included within the implemented energetic contributions of sarcomeres, using our developed framework for Ig domain unfolding. Our model predicts that biaxial cyclic deformation of cells results in increased sarcomere concentration, with a corresponding decrease in SFs. Our model predicts that if the maximum cyclic strain magnitude is increased (ranging from 5% up to 20%), the formation of sarcomeres is increased, with an associated increase in cell contractility. These model predictions are in strong agreement with previously reported experimental measurements of sarcomere formation and cell contractility as a function of applied cyclic strain magnitude. Our model uncovers the thermodynamic drivers of sarcomere formation, based on changes in chemical potential of sarcomeres, SFs, and unbound proteins during dynamic loading. Our model also elucidates the thermodynamic mechanism by which unfolding and folding of Ig domains in titin affects sarcomere formation. In the final technical chapter of this thesis, we develop transient models of immune cell behaviour and virus replication following SARS-CoV-2 infection. We then extend our nested sampling statistical mechanics methodologies to investigate the dynamics of viral spread in a population with heterogeneous immunity, by developing a modified heterogeneous SEIR framework based on our dynamic immune cell model. We develop an immunological model to simulate a multi-layered response to viral infection. A series of kinetic equations is developed to describe the increase in viral titre following initial infection of respiratory tract cells. This induces an innate and targeted immune response, including the generation of IgA and IgG antibodies, in addition to T cells. Model outputs include: (i) duration of pre-symptomatic infectiousness; (ii) evolving viral load; (iii) duration of infectiousness; (iv) number of infected cells; (v) time-dependent concentration of antibodies and memory B cells; (v) time-dependent concentration of T cells and memory T cells. The distribution of heterogeneous immune responses in a population is simulated by incorporating the following considerations: (i) age dependent strength of innate immunity; (ii) heterogeneous distribution of memory B cells and memory T cells due to prior infection. The computed distribution heterogeneous immunity is input into a modified SEIR framework, whereby the computed viral load determines the level of infectiousness, while the computed number of infected cells determines if transmission is classified as symptomatic or asymptomatic. Our immunological model is also use to determine the following key features of the SARS-CoV-2 pandemic: (i) increased viral load due to enhanced cell invasion of alpha- and delta-variants; (ii) efficacy of vaccines as a function of the rate of cell invasion by a variant. This novel framework is used to simulate the spread of SARS-CoV-2 in several European countries. A nested sampling approach is implemented to determine the mean and standard deviation of model parameters, based on reported age-stratified hospitalisations and fatalities. Computed partition functions reveal strong evidence for our novel heterogeneous immunity model compared to a standard homogeneous SEIR model.
  • Publication
    Practiced language policy in family language policy research
    (Palgrave Macmillan Cham, 2024-06-16) Smith-Christmas, Cassie
    This chapter examines the concept of ‘practiced language policy’ in the context of the sociolinguistic subfield of ‘Family Language Policy’ (FLP). This chapter centres on four main aspects of practiced language policy vis-à-vis FLP: first, how caregivers construct FLPs through language practices; how children re-negotiate FLPs through their own language practices; how language practices between siblings specifically contribute to re-shaping FLPs; and finally, the creative and affective re-negotiations of certain linguistic norms through language practices over time. This chapter illustrates how ‘practiced language policy’ is a valuable way to conceptualise the co-agentive and dynamic nature of FLP, namely, how caregivers and children take turns in filling the opposing roles of what (Spolsky, Language Policy 18:323–338, 2019), p. 335) terms ‘advocates without power and managers with authority.’
  • Publication
    Sun-related knowledge and practices in Irish construction and agricultural workers
    (Oxford University Press, 2024-07-11) Hogan, Victoria; Hogan, Michael; Kirwan, O.; Langan Walsh, C.; McLaughlin, C.; Moynihan, Á.; Connolly, A.; Walsh, J.; Coggins, Marie
    Background Agricultural and construction workers spend much of their work time outdoors and have higher risks of developing skin cancer when compared to indoor workers. However, there is limited research on ultraviolet radiation (UVR) exposure knowledge, sun safety practices and constraints within these occupational groups in Ireland. Aims This study aimed to examine self-reported time spent outdoors in a sample of Irish agricultural and construction workers; to describe and compare UVR exposure knowledge, safety practices and perceived constraints in both occupational groups, and to assess the association of demographic, personal and occupational factors with sun-related knowledge, practices and perceived constraints. Methods Agricultural workers (n = 154) and construction workers (n = 467) completed a questionnaire, which measured solar UVR exposure knowledge, safety practices, and perceived constraints to sun personal protective equipment and sunscreen use in addition to demographic, personal, and workplace characteristics. Mann–Whitney and Kruskal–Wallis tests were used to examine differences in knowledge, practices and perceived constraints by these characteristics. Results Both groups spend a significant proportion of their working week outdoors (25 hours per week on average). Although participation in sun safety training was high for both groups, UVR exposure knowledge and sunscreen use were low, and annual rates of reported sunburn were high. Knowledge, practices and perceived constraints also differed significantly according to demographic, personal, occupational and workplace characteristics. Conclusions In addition to training by employers and advisory groups, interventions are required to address perceived barriers that impede the uptake and usage of control measures that can lower risk.
  • Publication
    Retrofitting homes: Evaluating the householder's retrofit journey, existing retrofit services, and future directions for success in Ireland's retrofit industry
    (University of Galway, 2024-07-16) McGinley, Orlaith; Goggins, Jamie; Moran, Paul; Haines, Victoria
    Ireland's Climate Action Plan (2019) set ambitious targets for existing dwelling retrofits, including retrofitting 500,000 existing dwellings to a B2-Building Energy Rating (BER) or better by 2030, at an average rate of 50,000 dwellings per annum. Various policies have been established for the achievement of these targets, including establishing One-Stop-Shop (OSS) retrofit delivery models, which aim to remove retrofit barriers by offering full-service retrofitting for homeowners. The success of policies established for the achievement of Ireland's retrofit targets depends on many householders deciding to retrofit, and the alleviation of persistent demand and supply-side barriers. This research evaluated existing OSS services and other retrofit services in Ireland, from the perspectives of householders who have completed or partially completed their retrofit journey using these services, and retrofit industry stakeholders involved in, or with expert insights into, Ireland's retrofit industry. The research evaluated the householder retrofit journey in detail, including the drivers which motivated householders to progress through each stage of their retrofit journey, the barriers that prevented them from doing so, and householders' experiences of engaging with OSS and other retrofit services in Ireland. In addition, the research examined the key challenges facing the supply side in enabling widescale retrofit uptake in Ireland. To do so, in-depth interviews were conducted with 17 householders, as well as semi-structured interviews with 25 industry stakeholders. The performance of implemented retrofits, including the multiple benefits received through the works, was also examined through a pre- and post-retrofit dwelling monitoring study of five case study dwellings in the west of Ireland. The research confirmed the importance of understanding the complexity of the retrofit journey, and establishing policies which address barriers at particular retrofit journey stages to increase their effectiveness. Various areas of improvement for both OSS and other retrofit services in Ireland were revealed, including changes to the policy landscape. The research also revealed that householders receive multiple economic, social and environmental benefits through retrofitting, but place most value on the social benefits, and highlighted the unintended consequences that can occur due to poor quality works and householders' practices within the home. Industry challenges, particularly relating to upscaling and upskilling the industry, were highlighted as critical challenges to address. Potential ways to address these challenges were highlighted. This research, therefore, presents in-depth insights that can contribute to the design of retrofit policy, and serve to inform how OSS and other retrofit services in Ireland can be improved to drive extensive retrofitting in Ireland. Recommendations for policy, industry and further research are presented.
  • Publication
    The developmental potential of stem cells in Hydractinia symbiolongicarpus
    (University of Galway, 2024-07-15) Varley, Áine; Frank, Uri
    Hydractinia is a sessile, colonial invertebrate and a member of the phylum Cnidaria. They possess a remarkable population of adult stem cells known as i-cells which are the source of Hydractinias impressive regenerative ability. Previous work had identified the presence of i-cells during embryogenesis and metamorphosis. I was able to show the first appearance of putative i-cell progenitors in early embryogenesis in Hydractinia. i-cell progenitors first appeared at the 32/64-cell stage, often with many individual cells at once expressing Piwi1 (which is an i-cell marker). The true developmental potential of these putative i-cell progenitors remains to be studied. Past studies have shown that a population of i-cells can give rise to all somatic cell lineages as well as germ cells in Hydractinia. However, whether this population consisted of distinct, lineage-committed i-cells or pluripotent cells has not yet been confirmed. This work determines the developmental potential of a single i-cell in Hydractinia. Making use of Hydractinia’s remarkable growth, plasticity, I established a method for transferring a single i-cell from a double transgenic Piwi1::GFP Beta-Tubulin::mScarlet reporter colony into a wild type animal via stolonal contact. This method allowed tracing all progeny of a single grafted icell in the host tissue in vivo. I observed that wild type Hydractinia tissue possessing an initial single transgenic donor i-cell developed into a chimeric animal with a mixture of cells derived from the transgenic donor and the wild type recipient. Donor-derived cells, representing all major somatic lineages and germ cells were scattered in the recipient’s tissues in both feeding and sexual polyps, and in the stolonal compartment. This study shows that Hydractinia possesses pluripotent i-cells. Additionally, somatic cell types in Hydractinia did not exhibit any stem cell like qualities such as continuous proliferation and passive displacement.