University of Galway Research Repository
Open access to publications, including peer-reviewed articles, conference papers, working papers, reports, and other scholarly communications by University of Galway researchers.
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Publication Enrichment and expansion of human umbilical cord mesenchymal stem cells as an angiogenic therapy for critical limb ischemia(University of Galway, 2025-02-12)Critical Limb ischemia (CLI) or which is otherwise known as Chronic limb threatening ischemia is the advanced form of PAD, which can lead to ischemic rest pain, non healing wounds, ulcers gangrene, and in its worst form to limb amputation and consequent death. CLI occurs due to atherosclerosis in the arteries supplying the lower extremities. This causes the tissues below the plaque to be deficient in oxygen and nutrients; and leads to micro and macro vascular complications. Among the CLI patients, the non-revascularizable percentage of 10%-50 % or the “no-option” segment has poor prognosis with high mortality rates and reduced quality of life. The no-option patients have to undergo limb amputation; even upon amputation in addition to loss of quality of life, 50% die in 5 years and 70% die in 10 years of amputation. There is no effective treatment for CLI; hence a therapy for CLI is an unmet medical need. In response, a scalable, reproducible sterile system using 3D microbioprinting methodology was developed, to allow high-throughput bioprinting of GMP compliant, sorted and Quantum closed bioreactor expanded 3D UC-362- MSC-gel platforms. Innovative devices were developed and prototyped in this approach, and their proof of concept was sought. An invention disclosure form (IDF) for the novel innovative device was prepared and filed at the University of Galway Technology Transfer Office. The system received an Enterprise Ireland feasibility grant for obtaining IP rights and a startup development. The IP application process was initiated in this regard. The novel innovation will benefit numerous 3D bioprinting applications in different fields by enhancing their capacities. An in vivo randomized study was carried out in a nude BALB/c HLI mouse model for evaluation of the angiogenic capacity of the umbilical cord derived CD 362-MSC-bioprinted-cell gel platform and consisted of four groups with 12 animals in each. The treatment groups included saline/ sham, UC-362-MSC-IDO cells alone, UC-362-MSC-IDO-gel platforms, and acellular-gel platforms. Although the perfusion imaging methods of laser Doppler imaging and the novel HLI-MSOT used for the first time ever in HLI perfusion imaging did not detect increases in perfusion among treatment groups, the highest gains in capillary density with greatest significance (p<0.0001) were observed in the calf muscle of UC-362-MSC-IDO-gel platform recipients (368 BV /mm2 ± 197 s.d.). Muscle analysis of the ischaemic posterior calf muscles revealed high capillary densities in UC-362-MSC-IDO-gel treated animals (368 BV /mm2 ± 197 s.d.), and in UC-362-MSC-IDO cell treated animals (341 BV /mm2 ± 293 s.d.) compared to the saline treated group (p<0.0001). On average, the UC-362-MSC-IDO-gel treated animals developed 2.6 times more blood vessels per unit area compared to that of the saline recipients. The muscle fiber diameter analysis revealed the average of the median Feret fiber diameter was significantly higher in UC-CD-362-MSC-IDO cell treated (p<0.0001) and in UC-CD-362-MSC-IDO-gel platform treated (p<0.05) mice compared to the saline treated mice. The nature of added benefits the UC-362-MSC-IDO-gel platform can confer over UC-362-MSC-IDO cells alone warrants disease-specific application analysis. Therefore, based on the present study, the high-throughput 3D microbioprinted UC-362-MSC-IDO-gel platform with potent in vitro and in vivo proangiogenic capacity may require further dose-based fine-tuning through HLI in vivo studies for more amplified therapeutic benefit, before its use in critical limb ischemia. Additionally, a novel three-dimensional imaging modality for mouse hind limb ischemia based on multi-spectral optoacoustic tomography (MSOT) was developed and compared against the standard laser Doppler imaging modality. A comprehensive description of methodology, process, benchmark values for ischemia HLI-MSOT, and dos and don’ts were introduced for conducting MSOT in mouse HLI studies based on the learning experience and results. In the proof of concept studies, the novel mouse HLI-MSOT method was successful in detecting all ischemic events with 100% specificity and sensitivity relative to the standard LDI system in the ischemic mouse foot pads. The novel HLI-MSOT imaging modality would enhance the accurate determination capabilities of small animal-based HLI perfusion studies particularly in the thicker denser tissue 3D space which is not sufficiently addressed by the LDI based imaging. Thus, the novel MSOT based HLI imaging system could therefore be utilized successfully as either a stand-alone three-dimensional perfusion data acquisition modality instead of the LDI system, for more accurate perfusion information acquisition; or as a complementary system to the standard LDI already in use in a conjunctive manner in mouse HLI studies. Abbreviations-: Indoleamine-2,3-dioxygenase (IDO); umbilical cord derived CD-362-MSC and IDO secreting cells: UC-362-MSC-IDO;3D bioprinted umbilical cord derived CD-362-MSC and IDO secreting cell-hydrogel platforms: UC-362-MSC-IDO-gel; blood vessels: BV; Standard deviation: s.dPublication Designing educative curriculum materials for primary mathematics teachers for use during curriculum reform(University of Galway, 2025-02-11)Mathematics curricula internationally and in Ireland are undergoing significant changes to ensure students possess critical 21st-century skills. Teachers must develop the necessary pedagogical knowledge to enact reformed curricula. Unfortunately, time, capacity, school culture, and choice often impede teachers’ participation in continued professional development (CPD) beneficial to their pedagogical growth, issues often exacerbated by reform. Existing design models for CPD do not fully describe their effectiveness during reform, signalling a need to further understand and identify effective CPD models for use during periods of change. Educative curriculum materials (ECMs) are one method of CPD that aims to support teachers in progressing their practice while improving student learning. While research suggests that ECMs can positively impact teachers’ professional learning, limited research exists on how they can be designed and used during curriculum reform. Employing a design-based research (DBR) methodology, this study collaboratively investigates the design and implementation of ECMs for primary teachers in Ireland. ECMs were designed and refined throughout four iterative design cycles by combining relevant literature, educational theories, and stakeholder input. The ECMs targeted questioning in mathematics lessons to promote students’ critical thinking skills development. The emerging theoretically informed MACE design framework and data from surveys, focus groups, and observations guided the design. Findings indicate that the ECMs taught teachers the value of questioning and how to implement it in lessons. Teachers appreciated the non-prescriptive nature of the ECMs and their simplistic design. Moreover, individualised support from the researcher was identified as invaluable to professional learning. This project’s contributions include the identified potential for ECMs to be a practical approach to CPD, particularly during curriculum reform. In addition, the emerging MACE design model provides four key design criteria and five design informants for developing and implementing ECMs. Although beyond the immediate scope of this research, the MACE design model could be adapted to inform the design of other forms of CPD.Publication Shotgun metagenomics based exploration of Irish soil microbiome(University of Galway, 2025-02-11)The soil microbiome plays a crucial role in an array of important ecological processes, such as biogeochemical cycling, drought resilience, and the formation of soil structure. Metagenomics has revolutionised our understanding of diverse and predominantly unculturable microbial communities in soil, shedding light on their essential ecosystem functions. However, metagenomic techniques for soil microbiomes remain relatively new, and broader applications require considerable optimisation of pipelines. This thesis examines the Irish soil microbiome through metagenomic analysis of 131 soil samples. Taxonomy classification for soil metagenomics was first optimised by developing an in-silico mock community comprising all known soil-specific bacteria, archaea, and fungi. In-silico metagenomic datasets created using this mock community facilitated the identification of optimal taxonomy classification parameters, including tools, thresholds, and a custom database, which were then applied to map the Irish microbiomes comprehensively. Comparing these taxonomic profiles from shotgun and corresponding amplicon sequencing data, we found that both methods provide moderately similar results, including consistent identification of major phyla, similar patterns of community differentiation, and a similar relationship between nitrogen functions and phyla. Differences between the two methods mainly stemmed from differences in reference taxonomy, underscoring the need for a unified taxonomic framework to ensure reliability and comparability of metagenomic analyses. Next, 107 Metagenome-Assembled Genomes (MAGs) were recovered from 32 deeply sequenced subsamples, revealing antimicrobial resistance in unculturable yet abundant microbial fractions. Alongside elongation factor Tu, K+ transport activator, and arsenic resistance transporter, abundant genes conferring resistance to antibiotics like isoniazid, spectinomycin, and rifamycin, common antibiotics used in cattle, were identified, indicating potential bidirectional transfer of genes between soil and its surrounding environment. This study also recovered a novel Thaumarchaeota MAG that encodes an ammonia-oxidising gene, enhancing our understanding of ammonia-oxidising archaea in agricultural soils. Overall, this thesis, advances knowledge in soil metagenomics as well as microbial diversity and potential functions in Irish soils and identifies novel genomic assemblies, crucial for updating soil-specific databases and managing microbial activity amid global environmental changes.Publication Is youth mentoring beneficial for child and adolescent mental health service users? A multi-stakeholder perspective(Springer, 2025-02-07)Background Internationally, the number of young people who experience significant mental health issues is increasing. It is argued that flexible, community-based initiatives can help support mental health services to address the mental health needs of young people. Youth mentoring is a community-based model, which has been found to act as a supportive resource for vulnerable and at-risk youth. Objective This research examines the benefits and challenges associated with the provision of mentoring within a youth mental health context. The study explores the rationale guiding the partnership between a community-based mentoring organisation and child and adolescent mental health services (CAMHS) in Ireland, and identifies key practice considerations. Method 40 participants involved with the partnership took part in semi-structured qualitative interviews, which were analysed using a thematic analytic approach. Results Mentoring was viewed as a means of providing relaxed, informal, friendships that could help the young person to socialise more, strengthen their social skills, and become more integrated into their communities. Positive changes in social and emotional well-being were observed among participating youth. Practical challenges included delays in matching young people with mentors and communication issues. Conclusions Findings have relevance for researchers and practitioners interested in the integration of community-based and statutory mental health services, as they indicate that youth mentoring can act as a supportive resource for youth who experience mental health difficulties. Findings also provide insights into the processes that may support/hinder the effectiveness and acceptability of mentoring within a context mental health, which can help inform best practice guidelines. Similar content being viewed by othersPublication Development and evaluation of novel technologies to reduce methane emissions focusing on forage based ruminant production systems(University of Galway, 2025-02-07)Enteric methane, a by-product of feed fermentation in the rumen, accounts for 44.3% of global agricultural greenhouse gas emissions. The agricultural sector is facing increasing pressure due to the need to increase food production to meet the demands of the growing population while meeting the greenhouse gas reduction targets which have been written into legally binding climate agreements. Hence, mitigation of enteric methane from ruminant livestock is now a key research focus. Dietary manipulation through the incorporation of anti-methanogenic compounds in ruminant diets has been the most widely researched and effective strategy to-date. However, the majority of the research has been reliant on offering the anti-methanogenic compound mixed into the animal’s total mixed ration. Considering that grassland and mixed systems account for 97% of global enteric methane emissions, there is a necessity to develop anti-methanogenic strategies that are applicable to predominantly forage-based systems. Seaweeds containing bromoform have consistently reduced methane production in vitro and in vivo. However, there are unresolved concerns regarding animal health and the environment with bromoform supplementation. Therefore, the first objective of this thesis was to screen a range of non-bromoform containing seaweeds in vitro for their effects on methane production and digestibility, using the rumen simulation technique system. None of the seaweeds assessed reduced methane production (Chapter 3). Subsequently, following further in vitro studies which are not presented within this thesis, a range of promising anti-methanogenic compounds were applied in vivo, in sheep (Chapter 4) and beef cattle (Chapter 5 and 6), mixed with concentrate feed and supplemented once or twice daily, respectively. Methane production was measured using portable accumulation chambers and GreenFeed technology, in sheep and beef, respectively. While brown seaweed, Ascophyllum nodosum, failed to reduce methane production in vivo (Chapter 4 and 5), isolating the anti-methanogenic agent (phlorotannins) and offering an Ascophyllum nodosum extract to sheep (Chapter 4) and beef cattle (Chapter 5), reduced methane production by 9 and 8%, respectively. Oils high in polyunsaturated fatty acids, soya oil and linseed oil, were offered to sheep (Chapter 4) and beef cattle (Chapter 5), respectively, resulting in reductions in methane production of 9 and 19%. Finally, calcium peroxide was offered to beef cattle in Chapter 6, reducing methane production by 18 and 28% at a low and a high dose, respectively. Some anti-methanogenic compounds lose their potency if subjected to processing, i.e. formulated into a pelleted feed, which is useful for delivering a homogenous feed to ruminants. Therefore, calcium peroxide was incorporated into both a coarse ration and a pellet to evaluate its processability, resulting in a 28 and 27% reduction in methane production, respectively, when offered twice daily. Surplus to the environmental effects of the compounds, the effects of the diets on animal health and performance, ruminal fermentation and diet digestibility were investigated. Essential oils and soya oil offered to sheep in Chapter 4 were the only compounds assessed that had a positive effect on animal performance. Linseed oil and calcium peroxide increased propionate production in Chapter 5 and 6, respectively. Additionally, calcium peroxide reduced total tract digestibility, which did not result in a reduction in performance. In Chapter 5, microbial DNA was extracted from rumen samples from beef cattle supplemented with linseed oil and the Ascophyllum nodosum extract. The rumen microbiome was sequenced using a metataxonomic approach to investigate the effects on microbial communities (bacteria, archaea, fungi and protozoa), resulting in subtle shifts in bacterial and fungal communities for linseed supplemented animals. The work of this thesis will contribute significantly to the continued development of anti-methanogenic dietary strategies focussing on application at pasture, with the aim of extracting the most effective anti-methanogenic agents and incorporating them in a slow-release bolus to reduce reliance on concentrate supplementation.
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