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Leaf traits: A bridge between modern and fossil plant extinctions
No full textGlobally, 45% of flowering plant species are estimated to be threatened with extinction. Many factors are responsible for this figure, including climate change, that are pushing plant species towards their survival limits and increasing the likelihood of a sixth mass extinction event. Five mass extinction events have been identified in the fossil record that resulted in the collapse and reordering of entire ecosystems. However, it is thought that plants do not experience mass extinction on the same scale as animals due to the lack of observed extinctions across mass extinction boundaries. Plant extinction, both modern and in the fossil record, will be explored by studying leaf traits, which include the macromorphological, stomatal and chemical characteristics of a plant’s leaf. Although there is no consistent response, some fossil plant groups show shifts in leaf traits associated with plant survival across mass extinction events in the fossil record. However, only a tiny percentage of the diversity of plants has been preserved in the fossil record and understanding the taphonomic influences that filter which leaves become preserved in the fossil record is essential to interpreting the plant fossil record. The leaf traits of two modern floras, the Irish angiosperm flora and the Brazilian Fabaceae, were measured using herbarium specimens to assess the relationship between their leaf traits and extinction risk. Extinction risk was based on the IUCN Red List. Five species were analysed in a mesocosm study to assess the effect of the leaf chemical profile on decomposition across plant functional groups. The leaf traits of the Spitsbergen Cenozoic fossil flora were measured, along with a quantitative analysis of leaf traits observed in the fossil record literature, to examine the response of leaf traits in the fossil record. Results from the Irish angiosperm flora and the Brazilian Fabaceae showed no correlation between the leaf traits studied and extinction risk. Analysis of the chemical profile of different functional groups indicated that woody angiosperms and gymnosperms contain chemical compounds more resistant to decay than herbaceous angiosperms. This result was largely consistent when analysed across decomposition time and environment. The leaf traits preserved in the Spitsbergen Cenozoic fossil flora suggested a strong influence of life form on the leaf traits preserved. The new trait ‘Taphonomic Completeness Score’ indicated a poorer quality of fossil preservation for the herbaceous angiosperms compared to the woody angiosperms and gymnosperms. The quantitative analysis of leaf traits in the fossil record literature showed a lack of response of leaf size across mass extinction boundaries. The lack of a relationship between leaf traits and extinction risk in the modern floras suggests that climate change is not the primary driver of modern plant extinction. Likely, climate change acts in synergy with other drivers of extinction to push plants closer to the brink of extinction. Through preservation experiments and studies of the fossil record, it appears that herbaceous species possess a set of leaf traits, morphological and chemical, that make them less likely to be preserved in the fossil record. This bias against herbaceous species in the fossil record is important to interpretations of the fossil record as a high proportion of living herbaceous species are threatened with extinction. If this trend continued throughout Earth's history, the impact of mass extinctions on n herbaceous species
may be underestimated
Advancing payment channel networks for next generation monetary system infrastructures
No full textIn the aftermath of the 2008 global economic downturn, the emergence of Bitcoin as a disruptive force in the financial sector posed a significant challenge to traditional centralised financial systems. Nonetheless, both conventional and decentralised financial systems harbour inherent limitations that necessitate attention in preparation for the future. The clash between centralised governing bodies and decentralised payment systems spurred the emergence of a new concept known as Central Bank Digital Currency (CBDC), envisioned as a prospective future standard. While the current focus has predominantly dwelled on the adverse repercussions of CBDC's digitisation on existing financial systems, the impact on individuals' financial autonomy and adaptability to evolving monetary requirements constitute a crucial focal point for designing a futuristic monetary framework. This thesis identifies payment channel networks (PCNs) as a potential candidate as an infrastructure for a next-generation monetary system and lays the groundwork for its development. We commence by identifying issues with the current monetary landscape and the future monetary requirements based on the influence of technological advancements in various domains. In addressing these challenges, PCN possesses inherent scalability and security, with areas that require refinement. The thesis proposes enhancements to PCNs in two directions: facilitating payment intermediaries and enhancing user experience, where we develop innovative methods to make intermediaries more profitable and subsidised while boosting user confidence and convenience. This involves creating novel fee mechanisms and node subsidisation to benefit intermediaries, as well as designing stablecoins and card payment systems to improve the end-user experience. The efficiency and security of these methods are theoretically and empirically demonstrated with extensive simulations. These strategies elevate the potential of PCNs to serve as a comprehensive monetary infrastructure, effectively mitigating existing shortcomings. We also manifest how PCNs align with future monetary requirements in various contexts, such as micropayments, machine-to-machine (M2M) payments, the Metaverse, and mass customisation, especially in application areas such as future supply chains. Finally, we conceptualise a PCN-based monetary system that is not only resilient and future-ready but also deeply people-centric in its design, providing cash-like functionality. With its robust and stable currency, this monetary system is designed to put the user at the forefront, aiming to advance the financial landscape and establish the foundation for a better future.Science Foundation Ireland, VistaMilk, and the Insight Centre for Data Analytic
(In)access and distance: A survivor/victim-centred analysis of transitional justice in Liberia
No full textFocusing on the case study of Liberia, the thesis examines the dynamics of access to transitional justice using a survivor/victim-centred analysis. This research is the first comprehensive qualitative assessment of transitional justice in Liberia in the aftermath of the Truth and Reconciliation Commission’s mandate. The thesis provides a groundbreaking analysis by tracking the implementation of the National Palava Hut Programme through direct observation, with emphasis on the perspectives of participants. The study is based on extensive qualitative data collected through fieldwork in Liberia, including interviews, focus group discussions, and empirical research on transitional justice and peacebuilding processes. Through thematic analysis of the interconnected themes of space and familiarity, the thesis uncovers three layers of distance—physical, conceptual, and vernacular—that hinder people's access to transitional justice. The study reveals that even when transitional justice mechanisms are based on familiar justice processes, still, they may generate accessibility barriers. The thesis also clarifies that access does not guarantee a survivor/victim-centred approach to transitional justice. Accordingly, the research suggests restructuring transitional justice beyond levels and mechanisms, emphasising spatial, relational, and vernacular factors to improve access. Liberia is currently at a critical juncture. As the country recommits to transitional justice, practitioners should embrace a hybrid approach in designing future programmes. The study highlights the importance of focusing on survivors/victims’ post-conflict needs and conceptualisations of justice based on accessible vernacular.This work was supported by the Hardiman Research Scholarship; the University of Galway, College of Business, Public Policy, and Law Postgraduate Research Fund; and the Irish Centre for Human Rights PhD Field Research Travel Funding
Agricultural by-products as part of an aquaculture-based circular economy: Nutrition, sustainability and economics
No full textAquaculture faces sustainability concerns with respect to the sourcing of protein meals such as fish meal and soybean meal for aquafeeds. Processed animal proteins are a protein rich waste stream from the agriculture industry which could act as sustainable alternatives to conventional aquafeed ingredients. This thesis examines the regulations surrounding processed animal proteins as well as the nutritional, sustainability and economic benefits of implementing this circular economy. The shelf-life stability of these feather and poultry meal products was assessed while feeding trials on two globally important aquaculture species were conducted using these products. The trials examined growth performance, feed utilisation as well as several health indicators. Results found that both feather meal and poultry meal are promising protein replacers in aquafeeds and in many cases have advantages over conventional soy protein concentrate. In addition to this, the cost of these feed ingredients is comparably low which allows for uptake in both low- and high-income regions. This thesis has concluded that as part of an effort to increase global food security, the utilisation of processed animal proteins through a ‘waste to wealth’ approach will be crucial in maintaining aquaculture output.Irish Research Council and JG Pear
Synthesis, characterization, and photocatalytic evaluation of foreign metal ions incorporated iron oxide/oxyhydroxide
No full textAmong the plethora of organic pollutants, pharmaceuticals (antibiotics) and textile dyes are the two biggest categories of underground and surface water pollutants today due to the large overproduction and incorrect disposal. Apart from having poor degradability, dyes are mostly carcinogenic for humans and animals, while consumption of antibiotic-polluted water, even in small concentrations, can cause antibiotic resistance over time. Photodegradation uses inexhaustible and safe energy of the sun to remove these contaminants by creating smaller and non-toxic products. Iron oxide and iron oxyhydroxide materials have received a lot of attention due to their high abundance, low cost, low toxicity, and magnetic properties. Hydrothermal synthesis is one of the most common methods for the preparation of these materials as it is the most powerful one when it comes to changing synthesis conditions to modify samples’ morphologies. The addition of dopants and the use of heterostructures can affect the properties and applications of the materials. Here, iron oxide and iron oxyhydroxide materials are synthesized using hydrothermal method and temperature, synthesis time, and doping concentrations are being varied to determine the effects on size, morphologies, and applicability of these materials. The dopants used are Cu2+, Ni2+, Sn2+, and Sn4+. The samples are characterized by a variety of techniques and Cu-doped samples are further explored for the photodegradation of methylene blue and tetracycline with the use of laboratory-built photoreactor. It was found that Cu α-FeOOH/α-Fe2O3 heterostructures form at 140 °C synthesis temperature, and they exhibit superior photocatalytic activity, degrading 90% of methylene blue in 5 h and 65% of tetracycline in 6 h
Investigating the role of shear stress and mucus in intestinal epithelium homeostasis using computational and organoid-based microphysiological systems
No full textThe intestinal epithelium is organized into crypt-villus structures, which support compartmentalized functions such as nutrient absorption and barrier integrity through tightly regulated processes of proliferation, migration, differentiation, and extrusion. The tissue is subjected to mechanical inputs, including shear stress and substrate stiffness, yet the influence of these on epithelial homeostasis and force distribution along the crypt-villus axis remains poorly understood. While in vivo studies offer insights, the complexity of the intestinal environment necessitates robust in vitro models to probe these interactions under controlled conditions. To address this, we developed an in-silico model to simulate the shear stress distribution along the epithelium and the mechanical role of mucus in protecting the epithelium. Our results indicated an increasing shear stress profile from crypt to villus. Building on this, we engineered a perfusable epithelium-on-a-chip platform featuring stiffness-tuned polyacrylamide gels and open-lumen organoid monolayers. The system recapitulates the crypt-villus architecture, permits direct access to the apical surface, and enables precise shear stress modulation. Our experiments demonstrated that shear stress selectively enhances crypt density and extrusion rates while maintaining traction forces and division rates, approaching a homeostatic cell turnover balance. Beyond its immediate findings, this platform offers a versatile tool for exploring epithelial biology, enabling the study of microbial interactions, drug delivery, and disease pathology in physiologically relevant conditions. By bridging the gap between static in vitro systems and the complexity of in vivo tissues, this work provides a foundation for future advances in modelling intestinal systems with precise environmental control
Dissecting ATR function using naturally occurring human mutations
No full textDNA in cells is subject to various exogenous and endogenous damaging agents, each capable of introducing harmful mutations to the DNA sequence. To counteract DNA damage, cells have evolved multiple signalling pathways aimed at preserving genomic stability. The ATR kinase plays a crucial role both in the DNA damage response (DDR) and in DNA replication stress response (RSR). Its critical role in regulating DNA replication explains why ATR is essential for cellular viability. Furthermore, mutations in ATR have been implicated in several human diseases, including Seckel Syndrome (SS) and cancer.
Recent advancements in cryo-electron microscopy have enabled detailed structural studies of the ATR protein complex. Comparative analysis with its yeast homolog, Mec1, which has higher resolution structures, has further elucidation ATR activation. Our analysis of the ATR primary sequence and molecular dynamic simulations of the ATR complex have provided further insights into ATR structure and function.
In particular, we have focussed upon the effects of two non-Seckel ATR mutations on ATR structure and function. Specifically, our analysis of the ‘Indiana’ mutation (ATR-Q2144R), a cancer-predisposing variant, suggests that this mutation results in abrogation of kinase activity via allosteric inhibition. Additionally, we have investigated the ‘Cleveland’ mutations (ATR-D47V), a mutation within the linker connecting HEAT repeats 1 and 2, and shown this mutation impairs ATR’s interaction with its partner protein, ATRIP, thereby diminishing ATR signalling.
Our findings underscore the significant impact of emerging non-Seckel missense mutations in ATR, that impair its function. Furthermore, this study highlights the advantages of integrating in silico modelling with in vivo and in vitro biochemical approaches to advance our understanding of ATR function and its role in maintaining genome integrity.Science foundation Ireland & Irish research Council (Research Ireland
Investigation of algal-derived polysaccharides against ramularia leaf spot (rls) in barley
No full textAgriculture faces numerous challenges, including increasingly stringent regulatory standards, the effects of climate change, and the emergence of increasingly resistant pathogens capable of overcoming control measures, which can devastate crops. While the use of pesticides remains a major solution to combat many pathogens, their harmful impacts on the environment, biodiversity, and human health have been repeatedly demonstrated.
This thesis, part of the BioCrop project, aims to develop environmentally friendly and effective solutions to combat barley ramularia leaf spot (RLS), a disease caused by the cryptogamic fungus Ramularia collo-cygni. RLS is increasing in Ireland, and effective, environmentally friendly pesticides are unavailable.
Previous research has shown that molecules derived from algae, such as ulvans (from green algae), fucoidans and alginates (from brown algae), and carrageenans (from red algae), can be applied to plants to trigger their immune systems. In this context, three different methods were used to prepare extracts from several seaweed species collected along the West Irish Atlantic coast. The extracts were examined for their potential to stimulate the immune system of barley and to protect against infection by Ramularia collo-cygni, as well as for their direct antifungal potential against this fungus.
The results reveal a diverse range of promising potential biostimulants/bioelicitors, offering interesting prospects for future applications in the sustainable management of Ramularia collo-cygni in barley. Seasonal monitoring of these seaweed molecules allowed the identification of optimal harvesting periods to maximise their effectiveness.Department of Agriculture, Food and the Marin
The lived experiences of secondary Irish-medium immersion teachers: An examination of language-sensitive teaching in content areas
No full textThis multi-phase phenomenological study aimed to examine the lived experiences of Irish-medium immersion teachers. In particular, it focused on their language-sensitive practices as they endeavour to integrate the teaching of language with the teaching of content. During the literature review phase, a research-based pedagogical tool, SIOF, was developed. This tool endeavours to aid immersion teachers in their efforts at language-sensitive teaching and was also used in this study to prompt reflection amongst participants on their immersion practices 28 teachers were recruited for this study from 11 Irish-medium settings and there were some 23 subjects represented. During the analysis of the data, themes were developed around the various aspects of SIOF:the nature of scaffolding; managing the language input; encouraging student output; and grappling with feedback. As the discussions in the interviews and focus groups deepened, a second set of themes was developed. These related to the various challenges, supports and opportunities related to immersion teaching: professional learning and awakenings, teacher language and metalinguistic knowledge, departmental and whole-school collaboration, and the affordances of technology in the immersion classroom. In addition, an underlying theme was developed concerning the interplay of commitment, conflict and examination backwash
Development of patient-derived models to discover therapeutic strategies that target the breast tumour microenvironment
No full textThe intricacy of cellular and acellular components within tumours contributes to significant variation within the tumour microenvironment (TME) as well as the response to anticancer treatment. Heterogeneity and spatial tumour-stromal interactions, including cancer associated fibroblasts (CAFs), endothelial cells and tissue‐infiltrating immune cells, play significant roles in cancer progression and treatment response. Many conventional treatments including chemotherapy and targeted therapies target cancer cells, this approach can be further refined to target pro-tumourigenic stromal cells and tumour-stromal interactions within the TME. In this study, we have developed patient-derived models (PDMs) to model these complexities at the level of the individual patient with the aim of using these unique PDMs to discover innovative strategies to treat breast cancer.
In the first part of this study (Chapter Three) we use two‐dimensional (2D) and three‐dimensional (3D) PDMs to screen a natural compound library to discover anti-tumourigenic compounds. We are able to use these unique PDMs, that incorporate the cellular interactions that take place within the TME, to unravel drug-TME interactions, target identification, and improved efficacy of therapies. This study provides the basis for the integration of autologous PDMs into predictive models for a personalised medicine approach.
In the second part of this study (Chapter Four) we use these PDMs to explore the therapeutic benefit of targeting Wilms Tumour 1 (WT-1)+ CAFs within the tumour immune microenvironment. We describe the molecular mechanisms by which CAF-derived WT-1 promotes tumour growth and immune evasion, and discover therapeutic strategies that inhibit WT-1 within the TME thereby enhancing anti-tumour immunity.
This study highlights the importance of PDMs in precision medicine and drug screening, providing a valuable platform for the interplay between the TME and therapeutic responses for breast cancer. The identification of novel therapeutic targets such as WT-1 and the development of natural products as lead anti-cancer compounds represent significant advancements toward personalised and effective breast cancer treatments