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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Exploring the microbial ecology and energetics of wild and domesticated Atlantic salmon (Salmo salar)
(University College Cork, 2023) Schaal, Patrick Daniel; McGinnity, Philip; Reed, Thomas; Llewellyn, Martin; Biotechnology and Biological Sciences Research Council; Science Foundation Ireland; Higher Education Authority
Since the inception of Atlantic salmon (Salmo salar) aquaculture in the 1970s, millions of domesticated fish have escaped from aquaculture facilities into the wild. This phenomenon raises concerns about the ecological and genetic consequences of farmed fish interbreeding with their wild counterparts. The fitness of hybrid offspring from such interactions has long been recognised as diminished compared to pure wild salmon populations, thereby posing a substantial threat to the overall health and robustness of Atlantic salmon populations.
This study takes a comprehensive approach to investigate the impact of domestication on two vital aspects of Atlantic salmon biology: gut microbial communities and metabolism. Both traits have been identified as critical determinants of fish health and well-being. To disentangle the genetic effects from confounding environmental factors, this study employed common garden experiments. These experiments involved rearing fish with diverse genetic backgrounds, including wild, domesticated and reciprocal hybrids, together from the eyed-egg stage through both freshwater and marine phases. This design allowed us to simulate farmed escape and hybridisation events that naturally occur in the wild.
The first data chapter examines the drivers and sources that shape gut microbial assembly over time in juvenile Atlantic salmon in a natural river system. The study shows that the major contributors to the salmon intestine's microbial taxa come from macroinvertebrates, a potential food source, rather than the water column. Moreover, results suggest a possible role of host genetics in driving inter-individual differences in gut microbial community composition, leading to distinct microbiota assemblages between farmed, wild and hybrid fish. Neutral modelling further revealed that the majority of gut taxa are transient, underscoring the dynamic nature of these microbial communities and emphasizing the need to distinguish between transient and resident taxa within the gut environment.
The second data chapter examines the seasonal dynamics of gut microbial communities and energetics in juvenile Atlantic salmon, considering potential variations among farmed, wild and hybrid fish. The study unveils genetic factors as significant influencers of metabolic flexibility in Atlantic salmon. Wild fish exhibit lower metabolic rates in winter and higher rates in summer compared to farmed salmon, indicating their adaptability to seasonal environmental changes. This metabolic flexibility potentially enhances their chances of survival in variable wild environments compared to their farmed counterparts, which might exhibit less adaptability due to artificial selection for commercially favoured traits. Furthermore, our research unveils shifts in gut microbial communities during the winter months, particularly among the offspring of wild fish, possibly attributable to reduced feeding activity. This reduced activity, in turn, might be associated with their generally lower metabolic demands in winter.
The third data chapter assesses whether survivability, gut microbial structure and metabolic rate of Atlantic salmon reared in marine sea pens are affected by amoebic gill disease (AGD), a parasitic infection that poses a significant challenge to Atlantic salmon reared in aquaculture facilities, and if those effects vary between fish from farmed, wild and hybrid origins. Wild fish exhibited substantially higher mortality rates compared to their farmed counterparts, while hybrids fell in between. All fish, regardless of genetic origin, showed significantly lower metabolic rates with increased AGD infection rates. In addition, gut microbial diversity significantly declined in AGD-infected fish.
In summary, our study significantly contributes to our understanding of the complex interactions between host genetics, environmental factors and gut microbiota in Atlantic salmon. It offers indications that the domestication process in Atlantic salmon has influenced both host-associated microbiota and metabolism. As aquaculture continues to expand, these findings underscore the need for comprehensive conservation strategies to safeguard the ecological integrity of wild Atlantic salmon populations in the face of evolving aquaculture practices and the potential consequences of farmed fish escape events.
Normal hero(ine)s and deviant villains: musical representation of moral archetypes in a selection of Disney films
(University College Cork, 2023) Lozano Velasquez, Camilo Andrés; Gale, Emily; Rollefson, J. Griffith; Fundación para el futuro de Colombia
In this dissertation, I examine the musical representation of hero(ine)s and villains in selected Disney animated films: The Little Mermaid (1989), Beauty and the Beast (1991), Aladdin (1992), The Lion King (1994). While existing scholarship extensively scrutinizes Disney characters, this study provides a musicological approach to elucidate how music complements and underscores insights into the representation of the characters’ particular dimensions. Specifically, this research reveals connections between well-established traits associated with character portrayals, such as morality, gender, and sexuality, and the musical-performative elements within their musical numbers. Notably, the scenes featuring love ballads and villain songs provide intriguing opportunities to identify and assess these aspects, shedding light on the depiction and perception of the hero(ine)s as normal and the villains as deviant.
The analytical framework of this research centers on musical elements related to lyrical content, musical performance, and contextual considerations such as genre and style. These musical components play a pivotal role in shaping the processes of representation, supporting and advancing conventionally used musical codes of character portrayal.
Throughout this dissertation, I delineate the perceived normality of the protagonists, characterized by virtues, gender conformity, and heterosexuality, in stark contrast to the deviance embodied by the villains, depicted as evil and queer-coded. This dichotomy is musically reinforced by elements that resonate with Western cultural ideals of identity and alterity. Specifically, I discern dualities pertaining to the musical representation of the natural and the artificial, the familiar and the exotic, as well as the conventional and the unconventional.
This study, then, provides a comprehensive examination of the intricate relationship between music and character representation in Disney animated films. However, this research goes beyond character analysis to unveil cultural intersections between beauty, gender, and sexuality, which serve as markers of morality in popular culture, and elements related to the musical texture of the songs.
Multi-generational dispersal and dynamic patch occupancy reveals spatial and temporal stability of seascapes
(Elsevier B.V., 2024-09-03) Clubley, Charlotte H.; Silva, Tiago A. M.; Wood, Louisa E.; Firth, Louise B.; Bilton, David T.; O'Dea, Enda; Knights, Antony M.; Centre for Environment, Fisheries and Aquaculture Science; School of Biological and Marine Sciences, University of Plymouth
The success of non-native species (NNS) invasions depends on patterns of dispersal and connectivity, which underpin genetic diversity, population establishment and growth. In the marine environment, both global environmental change and increasing anthropogenic activity can alter hydrodynamic patterns, leading to significant inter-annual variability in dispersal pathways. Despite this, multi-generational dispersal is rarely explicitly considered in attempts to understand NNS spread or in the design of management interventions. Here, we present a novel approach to quantifying species spread that considers range expansion and network formation across time using the non-native Pacific oyster, Magallana gigas (Thunberg 1793), as a model. We combined biophysical modelling, dynamic patch occupancy models, consideration of environmental factors, and graph network theory to model multi-generational dispersal in northwest Europe over 13 generations. Results revealed that M. gigas has a capacity for rapid range expansion through the creation of an ecological network of dispersal pathways that remains stable through time. Maximum network size was achieved in four generations, after which connectivity patterns remained temporally stable. Multi-generational connectivity could therefore be divided into two periods: network growth (2000−2003) and network stability (2004–2012). Our study is the first to examine how dispersal trajectories affect the temporal stability of ecological networks across biogeographic scales, and provides an approach for the assignment of site-based prioritisation of non-native species management at different stages of the invasion timeline. More broadly, the framework we present can be applied to other fields (e.g. Marine Protected Area design, management of threatened species and species range expansion due to climate change) as a means of characterising and defining ecological network structure, functioning and stability.
Sustainable food process engineering
(University College Cork, 2023) Bremenkamp, Ina; Sousa Gallagher, Maria J; Oliveira, Jorge C.; European Regional Development Fund; European Commission
Food is a basic need and food packaging plays an important role in providing safe food to the world. Food packaging innovations in the past were important milestones for the development of the food sector, by ensuring safety, prolonging quality, and enabling the current supply chain. Nevertheless, the focus has drifted and innovations in the food sector are starting to be driven by ecological needs. The current food packaging options present challenges due to the dependency on fossil raw materials and the accumulation of durable single used packaging waste. Therefore, food packaging innovations need to be adjusted to the new demands, by not being an environmental burden, but still providing product protection, safety, and supporting various supply chains. Design strategies as eco-packaging design, circular economy design and design for recycling are important drivers. Furthermore, the development, improvement, and standardisation of biopolymers for replacing fossil sourced packaging materials are being widely studied. This opens up opportunities for relieving the current environmental burden of food packaging.
This thesis focuses on alternative food packaging for ready to eat (RtE) seafood products, a food category that ultimately provides healthy and convenient food to consumers. RtE is a food product group with increasing turnovers, supporting different life styles, e.g., eating on the go, fast and simplified product preparation as well as healthy eating. Seafood products provide essential nutrients and are a valuable food source, rich in nutrients that are particularly important for elderly people, a growing consumer group all over the world. The objective of this thesis was the investigation of biobased edible coatings as sustainable packaging development for RtE seafood products by using a quantitative methodology. A quantitative packaging development approach, in contrast to the often-used qualitative approach in industry, supports an optimal packaging material selection based on the product characteristics and its potential supply chain.
Currently a challenging task in the development of eco-food packaging systems is the assessment of the environmental burden. Every action or product has an environmental impact, but the environmental impact can be significantly influenced by the selected options. A systematic review of existing life cycle assessments (LCA) for investigating environmental challenges of novel food packaging systems in the field of RtE fish and meat products was undertaken and revealed a significant impact of the selected LCA approach on the evaluated environmental impact, highlighting the importance of transparent LCA studies, using fair comparisons and a holistic scope. A step by step approach by shifting the LCA focus to different objectives, such as the whole food-packaging system, comparing different packaging materials and systems, is recommended to allow a comprehensive understanding of the environmental impact of food-packaging system. This enables industry stakeholders to make informed decisions, taking an active role that balance necessity, wastefulness, and creating efficient and sustainable packaging solutions.
A critical review of edible coatings for chilled RtE food products was also performed to understand the state of the art and identify knowledge gaps for further developments. Edible coatings have been studied for RtE food products mainly to improve the microbiological stability; with other quality parameters receiving much less attention. Only few products within the RtE seafood category were tested in combination with edible coatings. Edible coatings can be sourced from natural resources, including land or marine based biomass. The direct use of food resources as packaging can create a burden on the food supply chain. The conversion of food industry waste products to edible coatings allows an optimal use of the full harvested biomass, but has some challenges, e.g., volume availability, collection, and possible high energy demand during transformation. Also, during the selection of an edible coating material, the supply chain impact should be reviewed, and additionally industrial scale up feasibility should be assessed for a successful industrial application. Biobased materials often have a limited potential, but by combining multiple biobased materials, the coating properties can be optimised. Aspects considered included the methodology for coating application, assessment of coating performance, and edible coating challenges as part of the food system were also discussed. Edible coatings are a complex topic but provide an interesting approach for developing eco-food packaging systems.
Developing a tailored packaging system for a RtE seafood product requires the identification of critical quality parameters and understanding of the influence of environmental conditions on the product quality. Therefore, the degradation process of two RtE seafood products, a RtE baked fish product and a RtE minced fish patty, were investigated by studying the microbiological, chemical, and physical properties. The studied sorption isotherm behaviour showed a sigmodal shape, and the best model fitting was reached with the Peleg model, followed by the Guggenheim-Anderson-de Boer (GAB) model. The storage experiments revealed that water loss and microbial growth are important product quality parameters for both tested RtE seafood products, while fat oxidation was only a critical quality parameter for RtE seafood products with a higher fat content. By understanding the underlying reaction of degradation processes and the effect of environmental factors such as oxygen, light, and relative humidity, the required packaging properties were identified.
The application of chitosan and alginate coatings for RtE baked fish products were studied. A full factorial experimental design was used to investigate the effect of coating material composition on microbial growth, water loss and lipid oxidation under optimal (4°C) and abuse (14°C) storage conditions. A 3^2 full factorial design was used to study the effect of chitosan concentration (1, 2 and 3%), and glycerol concentration (0, 15 and 30% w/w chitosan). The effect of the composition of an alginate coating was studying with a 2^3 full factorial design. The studied factors were alginate concentration (1 or 2% (w/v)), glycerol concentration (0 or 1.5% (w/w) alginate) and crosslinking the alginate coating with CaCl2 to form calcium alginate (yes/no). The results showed that a chitosan coating with 1% (w/v) chitosan in 1% (v/v) acetic acid, and 15% (w/w chitosan) glycerol, or 1% (w/v) alginate coating with no glycerol, and no crosslinking showed the best performance in controlling the tested safety and quality parameters. Additionally, a full experimental factorial design was performed to study the combined effect of an alginate and chitosan coating applied as a double coating, and single coating. The double coating tested did not provide a combined product protection. A desirability method was used to identify the shelf life of chitosan, alginate and double coated RtE products based on multi quality parameters. It was concluded that chitosan coated samples showed the best performance with a three- fold shelf life extension compared to uncoated products.
Improving product safety and quality by combining different protection methods, known as hurdle technology, is a common approach. The applied hurdles can differ. Well applied examples are sanitizing, packing and cold storage for fruits and vegetables. A novel sanitizing system consists of the use of cold plasma treatment, avoiding the use of chemicals to reduce microbiological contamination and increase safety. The combination of cold plasma treatment and an equilibrium modified atmosphere packaging (EMAP) for cherry tomatoes was investigated under controlled temperature (10 and 20°C) throughout storage. Statistical analysis of the results showed that plasma treatment did not negatively affect the quality of the product. A higher microbiological growth was detected within the packed cherry tomatoes, while a plasma treatment before packing reduced growth of microorganism during the early days of storage. Package was important to prevent weight loss and changes in total soluble solid content over 14 days of storage. The combination of cold plasma, temperature and EMAP design ensured the quality retention of cherry tomatoes, which suggests that they have potential to be used as hurdle technology.
A packaging based on an edible coating, requires a second packaging component which can be a packaging film. Combining the edible coating and an outside layer should provide an optimal product protection over the required shelf life. A mathematical modelling approach was taken to estimate the required water barrier properties for the packaging film material. The water loss was identified as the remaining most critical quality parameter after a chitosan coating was applied. Film materials were selected based on their properties and end of life options, and the water vapour barrier properties at lower storage temperatures were tested. The water vapour transmission rate (WVTR) allowing a water loss of 10% within 21 days was calculated using the GAB model, and using a linear approximation of the isotherm was estimated to be 94 and 81 g/m2 day, respectively. The simplified linear model showed similar results to the GAB model approach for predicting moisture loss of a high moisture food product. When increasing the required shelf life only a small reduction of the WVTR was seen. Testing the WVTR at chilled storage conditions showed that depending on the material selected, the temperature can impact the water vapour barrier of the packaging film materials, especially for biobased materials. The recommended film material in combination with a chitosan edible coating for a RtE baked fish product was a cellulose based compostable film.
Food packaging is essential but only with efficient solutions, an open mind and with various approaches the negative effects of food packaging on the environment can be tackled. Special emphasis should be given to food packaging that allows to use naturally available protection systems. It was highlighted that including circular economy aspects and environmental considerations during all development stages of a food packaging improves the sustainability of a packed food product. An integrated precision packaging, based on an edible coating and a film layer, for RtE seafood products can be an eco-packaging solution, without compromises in food safety and quality.
I-LOFAR observations of the transient universe at low frequencies
(University College Cork, 2023) Kyprianou, Jake; Callanan, Paul
This work concerns using the Irish radio telescope, I-LOFAR, to observe the recent astronomical phenomenon of Fast Radio Bursts. Fast Radio Bursts are a novel type of radio transient, extremely powerful radio bursts that last only a few milliseconds. All but one of these bursts has come from beyond our Galaxy. The discovery of a repeating FRB source FRB180916B that produces bursts in a 5-day long window every 16 days prompted the question, could we use the Irish LOFAR telescope to observe these bursts? Recent detections of FRB180916B by a variety of telescopes across a range of frequencies has seen abnormal behaviour in bursts at low frequency. If I-LOFAR could be used to observe FRBs we could investigate this behaviour in other repeaters.
In this thesis I investigate using I-LOFAR to make such a detection. Using 72 hours on FRB180916B and 8 hours on Galactic magnetar SGR1935+2154 which was found to be a Galactic FRB source. No bursts were detected above fluence thresholds of 200 Jy ms and 273 Jy ms respectively at 150MHz. I present theoretical arguments on the viability of detecting an FRB, based on observational properties of FRBs and the limitations of I-LOFAR. I also discuss the other implications of our non-detection based on new knowledge of the activities of these two sources. The consequences of a potential successful detection in the future are discussed as are possible strategies to maximise our chances of a detection.
The data processing is performed using the REALtime Transient Acquisition cluster, REALTA, located at the site of I-LOFAR in Birr, Co. Offaly.