PhD Theses, ATU Galway-Mayo
https://research.thea.ie/handle/20.500.12065/3195
2024-03-29T01:34:23ZThe Irish War of Independence (1919–1921) in County Galway: Local Histories, Memories & Post-Conflict Heritage Initiatives
https://research.thea.ie/handle/20.500.12065/4374
The Irish War of Independence (1919–1921) in County Galway: Local Histories, Memories & Post-Conflict Heritage Initiatives
Kavanagh, Eilish
The Government of Ireland's Decade of Centenaries programme has aroused much interest of late in the revolutionary events that preceded the creation of the Irish Free State in 1922. This thesis explores local histories, memories and heritages of the Irish War of Independence (or Anglo-Irish War) in County Galway. In the process of compiling local histories, information is furnished about the people and places affected by the conflict. Lasting from 21 January 1919–11 July 1921, this was a guerrilla war fought by the Irish Republican Army (IRA) against the forces of the British Government. By utilising a broad range of sources, including witness statements, pension files, newspapers and literature, this study investigates key events,
such as the Ballyturin and Merlin Park ambushes, the killing of combatants and the impact of reprisals on civilians. New insights are provided about the controversial deaths of individuals such as Louis D’Arcy, Fr Michael Griffin, brothers Pat and Harry Loughnane, Eileen Quinn, and Michael Walsh. These deaths commanded considerable national and international attention. The thesis proceeds by asking how, why and in what ways has memory of the conflict transmitted in County Galway by means of anniversary commemorations and built/cultural heritages? Initially, the focus centres on recovering the lost memories of the women of the revolutionary period, whose contributions and experiences were ignored and forgotten for many years. This section also shows how traumatic legacies of the conflict prompted a series of intergenerational remembrances. Over the course of century, these included the anniversary commemorations of Michael Walsh, the Loughnane brothers, Fr Griffin, and Eileen Quinn. Whilst a more cautious approach to memorialisation unfolded during the Northern Ireland Troubles, opportunities for remembrance still presented in County Galway, albeit through the death of a veteran or a close relative. From the late 1990s onward, the success of the Peace Process led to a revival of interest in the revolutionary period. Notable here was the reinterment of Galway-born Volunteer Thomas Whelan and nine others, including Kevin Barry, who were exhumed from graves in Mountjoy Prison and given a full state funeral in Glasnevin Cemetery in 2001. Buoyed on by the centenary anniversary of the Easter Rising in 2016, there was major public interest in the centenary of the War of Independence in 2019–2021. Whilst restrictions imposed in response to the outbreak
of the Covid-19 pandemic led to the cancellation of many public events, local communities were still able to mark the centenary through online platforms.
This thesis ends by outlining post-conflict heritage initiatives that have been developed by the ATU Heritage Research Group, in partnership with Galway County Council. The first of these is the Galway County War of Independence Heritage Inventory, which includes listings for historic sites, artefacts and manuscripts, memorials, and memorabilia. A second legacy initiative is The Loughnane Brothers Heritage Trail: Explore Historic Sites & Memorials of Ireland’s War of Independence. This will be disseminated to the public in two formats in December 2022, namely an ArcGIS ESRI StoryMap and a 79-page bilingual guide book. Both versions furnish details about eleven sites related to the capture, killing and memorialisation of Pat and Harry Loughnane. By striving to illuminate connections between the past and present, it is hoped to leave behind a worthwhile cultural legacy for current and future generations
2022-01-01T00:00:00ZAddressing cohort uncertainty through advanced length frequency and stage-based assessment models with application to anglerfish
https://research.thea.ie/handle/20.500.12065/4357
Addressing cohort uncertainty through advanced length frequency and stage-based assessment models with application to anglerfish
Batts, Luke; Gerritsen, Dr Hans; Brophy, Dr Deirdre
Fisheries stock assessments are important tools for successful management of fisheries. Reliability of a stock assessment model is often determined by the data available and accounting for key uncertainties in the data is an important aspect of stock assessments and management. Central to many assessment
models is the tracking of cohorts through the population, but uncertainty in the identification of cohorts, in the form of uncertainty in age-estimation and fish growth, can impact model performance. Overall, the aim of this thesis was to develop methods to address this cohort uncertainty, as well as assess
the impact of biased age-composition data on the fisheries advice process. I focus on anglerfish as the main case study species, as their assessment and management is affected by the challenges touched upon earlier. To provide context, Chapter 1 gives an overview of stock assessment and management, focussing on the challenges of uncertainty in age-estimation and growth, as well as the approaches used to account for them. Anglerfish fisheries are also summarised and issues affecting their assessment and management discussed. Chapter 2 addresses the topic of cohort uncertainty by developing a new
method of length frequency analysis. The model is a maximum likelihood-based procedure that uses Gaussian mixture models and the Expectation Maximisation algorithm to estimate von Bertalanffy growth parameters from length frequency data from fisheries surveys. The model was applied to length data from the white-bellied anglerfish stock in the Celtic Sea and Bay of Biscay. The basic model estimated a single set of growth parameters, whereas the hierarchical extension to the model was able to model some of the natural variability in fish growth between cohorts or years with bivariate random effects on key parameters. Chapter 3 approaches the issue of cohort uncertainty from a different perspective,
implementing and and testing the performance of stage-based stock assessment models. Stage-based assessment models have less data requirements and simpler population dynamics than more complex assessment models, so are likely to be more robust to cohort uncertainty in the data. The stage-based
assessment models implemented were: Catch-Survey Analysis (CSA), and a model first described in a theoretical paper by Schnute (1987). The performance of these two theoretically different stage-based assessment models was assessed with a simulation-testing framework and on a real anglerfish stock. The findings showed both models are useful stock assessment models, with CSA more robust but less precise than the Schnute model. The Schnute model was more precise than CSA but required growth and mean fish weight data unaffected by selectivity. As part of the work conducted for Chapter 3, the R package ‘sbar’ was developed. This is a fully documented R package that contains the functions to
run the stage-based assessment models. Chapter 4 outlines the key assumptions and data requirements of the models, as well as demonstrating use with data from a real anglerfish stock. Versions of the Schnute model not described or tested in Chapter 3 were also detailed here. A goal of this chapter was to
allow new users to begin running stage-based assessment models with relevant background information provided. Chapter 5 addresses the impact of using age-composition data generated with a biased growth function in stock assessment and management over time. A management strategy evaluation framework was used, with both stage-based and age-based management procedures tested. A method for
estimating CSA reference points was also developed. Both management procedures were affected by the biased sampling data, but in different ways. Performance statistics indicated that it is important to consider the uncertainty and potential bias in growth estimates when generating age-composition data.
Overall, the research presented in this thesis has developed and implemented techniques that aim to further advance the field of fisheries stock assessment and management when cohorts are uncertain. The thesis focussed on anglerfish for the majority of case studies due to the fisheries’ reported issues, however the methods implemented here are useful in a wider context and there are many species to which the techniques could be applied.
2022-02-01T00:00:00ZUnlocking the archive: using the biochemical and isotopic composition of fish scales to understand the marine phase of Atlantic salmon
https://research.thea.ie/handle/20.500.12065/4356
Unlocking the archive: using the biochemical and isotopic composition of fish scales to understand the marine phase of Atlantic salmon
O'Toole, Christina
The Atlantic salmon is a species of great importance culturally, economically and ecologically. Recent declines suffered by many populations have been linked to marine mortality, therefore a better understanding of the marine phase is needed to inform management decisions, slow population declines, and protect this iconic species. The overall aim of this research was to develop, validate and apply methods that unlock the information contained in Atlantic salmon scales to enhance our knowledge of the marine phase. Fish scales incorporate biochemical and isotopic signatures as they grow, acting as a chronological record of the fish’s life history. Large, multi-decadal archives of Atlantic salmon scales are held by many organisations, containing vast amounts of data to be explored. Stable isotopes of scales can be used to examine the diet, origin, and trophic level of prey of a fish, but inorganic carbonates on the scale surface can confound results. The carbon isotopic ratio (δ13C) of acid-treated and untreated scales from 208 Atlantic salmon was analysed. Acid-treatment had a negligible effect on (δ13C) and therefore does not need to be performed prior to stable isotope analysis (SIA) of Atlantic salmon scales, saving scale material, time and money. A recent isotope-based geolocation tool suggests that the marine feeding location of salmon can be determined by correlating a time series of scale δ13C with sea surface temperature (SST). To validate the method, SIA of archived scales from 100 fish (10 years of a 50-year period) caught at their feeding grounds west of Greenland was completed. The highest area of correlation between scale δ13C and SST, the Labrador Sea, accurately represented the foraging location of the fish. This validation allows the results of the geolocation tool to be interpreted with increased confidence. Cortisol, the most commonly measured stress hormone in fish, was recently extracted from fish scales as a measure of chronic stress. In this thesis, the method was adapted for use on Atlantic salmon scales and used to extract cortisol from the scales of 156 experimentally reared post-smolts that were exposed to 3 temperatures (6, 10.5 and 15°C) and varying starvation stressors. Cortisol increased significantly in fish kept at 15°C. Fluctuations occurred in fish at 6°C and in starved fish at 10.5°C, but a larger sample size is needed to determine the significance of these results. This research determined that scale cortisol is a suitable biomarker for temperature stress in Atlantic salmon and, due to optimisation to require lower weights of scale material, may open this method up to a wider range of species and life stages. Using the method, the stability of cortisol was confirmed in archived scales, then cortisol was extracted from 120 archived scale samples (6 years over a 29-year period). No interannual trends were detected, and individual variability appeared to drive the
differences in cortisol. Combining cortisol data with other analyses could help understand the factors affecting scale cortisol in Atlantic salmon. This research illustrated the value of scales for examining the marine phase of Atlantic salmon, which may be key to preventing further declines. The methods developed and validated in this thesis can be used to determine marine feeding location and to examine the response of salmon to stressors experienced during their life cycle.
2022-04-01T00:00:00ZVirulence factors associated with amoebic gill disease from Neoparamoeba perurans
https://research.thea.ie/handle/20.500.12065/3658
Virulence factors associated with amoebic gill disease from Neoparamoeba perurans
Ni Dhufaigh, Kerrie
Determining the virulence factors associated with pathogenic organisms is imperative in comprehending disease pathogenesis and ultimately paves the way for methods of treatment and disease management. Neoparamoeba perurans is an ectoparasitic amoeba responsible for the hyperplastic gill infection of marine cultured finfish referred to as amoebic gill disease (AGD). Neoparamoeba perurans is suspected to have a repertoire of putative virulence factors that enable the attachment and colonisation of the host, as well as resistance to host immune response. The primary aim of this study was to identify the virulence factors of N. perurans (both amoebic and bacterial) using a proteomic approach, and to increase understanding of the parasite’s mechanisms as an infectious agent in AGD of farmed fish. This thesis is divided into five chapters comprising: an introduction to AGD, N. perurans and virulence factors, three experimental chapters written as manuscripts for publication and finally, a general discussion that reviews the findings and future outcomes of this research. The first experimental chapter (chapter two) confirmed the reported loss of N. perurans virulence in long-term culture, as determined by an in vivo challenge trial. This work validated AGD infection in the virulent cohort and validated the lack of AGD infection in the attenuated cohort by gill scoring, histopathology, and qPCR of gill tissue. The microbiome of the virulent-1 and attenuated N. perurans were characterised by 16S rRNA Illumina MiSeq sequencing for informing the bacterial database protein search. Two-dimensional gel electrophoresis (2D gel) and LC-MS/MS analysis revealed that hydrophilic virulence proteins are differentially expressed between a virulent-1, virulent-2 and attenuated culture. Differentially expressed proteins were actin-associated proteins, lipoxygenase, an ABC membrane transporter and profilin. Overall, these proteins suggest that the virulent-2 culture of N. perurans maintains elevated levels of proteins involved in cytoskeletal, oxidative and immunomodulatory roles. The second experimental chapter (chapter three) assessed the extracellular secretions, or exoproteome, of a virulent-3 and attenuated parasite for virulence factors. Using label–free LC-MS/MS, proteins that were differentially expressed were found to be elevated in the attenuated parasite. Additionally, the extracellular secretions of the attenuated parasite had a greater cytotoxic effect on the salmonid RTgill W1 cell line compared with that of the virulent-3 isolate. This effect was believed to be associated with the increased growth of bacteria in the attenuated culture of N. perurans. Antibiotics were employed to reduce the presence of bacteria in the culture, which lessened the cytotoxicity observed in RTgill W1. Neoparamoeba perurans specific proteins were found in both exoproteomes that have serine protease activity which may facilitate AGD infection, but are not the main drivers of cytotoxicity. Additionally unknown and hypothetical proteins of N. perurans were identified that warrant further investigation. The third experimental chapter (chapter four) investigated the cell-surface and membrane proteome of a virulent-3 and attenuated N. perurans. Proteins involved in potential cell-mediated adhesion roles such as GAPDH and GTPase signalling proteins were found and may represent putative targets of treatment. Overall, the proteins identified reveal moonlighting roles for common proteins such as proteins involved in glycolysis that may aid host ligand attachment.
The outcome of this work is expected to facilitate progress in the design of N. perurans targeted therapies for the treatment of AGD in farmed fish. Developing treatments that target and disrupt N. perurans will improve gill health in salmonids and will promote aquaculture sustainability and productivity.
2020-10-01T00:00:00Z