School of Agriculture, Food and Ecosystem Sciences - Theses

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    Some critical determinants of goat meat quality
    Payyanakkal Ravindranathan, Archana ( 2023-11)
    Goat meat serves as a major source of meat in developing countries while it is less popular in western countries. Nevertheless, the perceptions about goat meat are changing due to the health benefits of consuming lean meat with reduced fat and cholesterol content. Australia is the largest exporter of goat meat globally. Although there is increasing demand for goats domestically the supply chain is highly inconsistent. There is a significant knowledge gap in understanding the factors influencing goat meat quality and these factors that need to be explored to ensure consistent and better quality goat meat. Therefore, this PhD project was designed to investigate some of the critical factors affecting goat meat quality such as slaughter age, post-mortem ageing, retail storage, muscle type, cooking temperature and electrical stimulation. This PhD thesis consists of three animal experiments and one meta-analysis study. The first experiment compared two age groups (Adult goats, n=12, 2 years of age; Young goats, n=12, 6-9 months of age) of farmed Boer goats. This was a preliminary study to understand the meat quality of goats slaughtered in a commercial plant in Australia. This chapter demonstrated that post-mortem ageing for 14 days could reduce the toughness of goat meat in two age groups of goats. The retail color stability was also assessed from 0 to 10 days on the retail shelf, which was validated using Thiobarbituric acid reactive substances (TBARS) analysis. The second study was a meta-analysis research on the effect of electrical stimulation (ES) on small ruminant meat quality, including sheep, lamb, and goat. The meta-analysis provided statistical evidence of the positive impact of electrical stimulation (ES) on the meat quality of small ruminants. This was evident in terms of ultimate pH, tenderness, increased proteolysis, and elevated colorimetric values. It was observed that pH24 and WBSF showed a decrease in electrically stimulated goat carcasses, compared to non-stimulated carcasses through the forest plots. Overall, the research indicates that ensuring the optimum quality meat in Boer goats involves managing factors from the farm to the abattoir and incorporating considerations such as the ideal age of the animal, post-mortem ageing, and specific cooking methods or temperatures specific to the muscle, should be developed and implemented. The third experiment compared meat quality of three muscles namely, longissimus thoracis et. lumborum, semimembranosus and psoas major, representing different muscle fiber types, to understand the association between fiber type and goat meat quality. The variations observed in the muscle fiber composition and cross-sectional areas (CSA) of type I, IIA, and IIB muscle fibers are reflected in the meat quality of Boer goats. A higher percentage of type I fibers and a lower CSA of all three fibers contribute to reduced toughness in goat meat. This experiment also elucidated the effect of cooking end -point temperature on goat meat quality. Furthermore, the underlying mechanism associating fiber type and cooking temperature has been explained by the protein denaturation at different temperatures in the three muscles using differential scanning calorimetry (DSC). The cooking end-point temperature is a critical factor influencing the quality of cooked goat meat. As the cooking temperature rises, parameters such as WBSF, cooking loss, and volume shrinkage increase, leading to tougher meat. The fourth experiment explored how certain crucial factors, such as intramuscular fat, collagen content, and muscle fiber characteristics, influence the meat quality attributes in two distinct age categories of Boer goats (Adult, n=10, 24 months of age; Young, n=10, 6 months of age). For this study, four muscles, namely longissimus thoracis et lumborum (LTL), semimembranosus (SM), cutaneous trunci (CT) and biceps femoris (BF) were harvested from 20 Boer wether goats. The muscle data obtained will enable well-informed decision-making to improve muscle-specific marketing approaches, aiming to enhance the consumer acceptability of goat meat. Overall, adult goats had a higher type I fiber percentage, but a lower type IIB percentage compared to young goats, and animal age increased the CSA of the fibers in different muscles. Higher type IIB fiber number % and higher CSA were correlated with increased toughness.
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    The Logic of Innovation: How Institutional Logics Shape Innovation in Australian Agriculture
    Kenny, Sean Nicholas ( 2023-12)
    This research aimed to improve how institutional dimensions of innovation in agriculture are described and enhance the understanding of their impact on innovation. By exploring systems perspectives on innovation within industrial and agricultural contexts, I explain how institutions are predominantly defined as functional and structural elements of innovation systems (IS). This demonstrates how innovation has been rendered technical in agriculture, and I argue for an institutional turn to rebalance IS towards the social and political. By applying a new institutionalist lens, I expand on the current view of institutions to define them as socially constructed, recursive, material, symbolic and political. I use this expanded definition to highlight the lack of approaches for institutional analysis in agricultural innovation systems (AIS) and introduce the institutional logics (IL) perspective as a basis for my research design. This research is a case study of the influence IL have on managing nutrient pollution in agriculture. It draws data from two contexts that have grappled with this issue for decades, namely the Australian sugarcane industry and agriculture in the Netherlands. My analysis centred on the discourse surrounding each context, drawing on data from unstructured interviews with 22 innovation actors, 119 submissions to an Australian senate inquiry, and 59 documents. Interviews covered actors in the policy, program management, intermediary and farming practices, while documents included those addressing the cases technical, policy and strategy dimensions. My analytical framework draws on the foundational elements of IL and seeks to describe the interrelationship between problem framing, chosen theories of action and justifications used to legitimise action. This was used to develop an initial position on IL observed in the case. I then used qualitative content analysis of data from two discursive hotspots to explore how IL impact innovation activity and performance. Through this process, I describe a dominant discourse within the Australian context anchored in what I label a scientific logic. While this logic dominates the discourse, another competing logic drives an alternate discourse. This I label the experiential logic, which is characterised by a contrasting relativism that questions every aspect of the scientific logic. This resulted in a polarised problem domain leading to diminished action to address the problem and limited progress towards nutrient pollution targets. In the Netherlands, the discourse revealed a dominant societal logic that frames the problem legally and justifies action on the grounds of human and ecosystem health. This precipitates an instrumental theory of action that continually layers expectations for actors in agriculture around compliance with various standards and limits. Sitting behind this instrumental facade was a social process built over centuries and focused on a pragmatic approach to building consensus. This resulted in a fusion of the instrumental approach to defining what must change with a social process of settling on how to achieve this. The polarisation observed in the Australian case was absent in the Netherlands; however, questions exist as to whether the consensus based approach to decision making can withstand the various social, political and functional pressures facing Dutch society. Synthesis of my findings showed how limited awareness of institutional processes, epistemological divergence and weak legal frameworks contribute to poor innovation performance in the Australian context. These insights demonstrate a divergence from the dominant technical and economic interpretations of innovation performance in agriculture and challenge the functional and structural black box approach to representing institutions within AIS. This has implications for the relative emphasis placed upon institutional analysis within AIS. Subsequently, this highlights the need for innovation actors to engage with the institutional dimensions of innovation if progress is to be made in complex problem domains. I propose an enhanced role for innovation brokers to facilitate this process and a representation of AIS that better captures this institutional turn.
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    Nutritional strategies to alleviate heat stress in pigs
    Le, Huu Hieu ( 2023-07)
    Heat stress is a both current and increasing issue for pig production during summer in tropical and sub-tropical regions. Heat stress compromises pig production by increasing the energy cost for maintenance instead of utilising the energy for growth and reproduction. Moreover, HS increases pig’s health issues by causing oxidative stress, blood acid-base disturbance and compromises the physiological function of multiple organs. Various strategies are used to combat HS in pig production, but the use of nutritional strategies are cost-effective and once developed able to be easily incorporated into a variety of production systems. In Chapter 3, the effects of different HS duration (0, 1, 3, and 7 d) on voluntary feed intake, physiological parameters, haematological properties and gut barrier physiology were determined. The Evans blue dye (EBD) technique was also used to quantify plasma volume and tissue damage characterized by increased EBD extravasation in multiple organs. The results of Chapter 3 showed that HS resulted in respiratory alkalosis over 7 days of HS. Unlike some previous studies, HS did not compromise gastrointestinal barrier function, as evidenced by no change in intestinal integrity coupled with no differences in EBD extravasation. Plasma volume was reduced by approximately 10% on d3 and remained at this level until the end of the experiment. The reduced plasma volume, together with unchanged blood haematocrit and haemoglobin, suggest a dehydrated state of the experimental pigs despite ad libitum access to water. Increased concentrations of EBD in kidneys and pancreas may indicate extravasation in these tissues, indicating increased vascular damage and compromised function. Chapter 4 investigated the effects of betaine and isoquinoline alkaloids on the thermoregulatory response and intestinal barrier function of heat-stressed pigs. The findings from Chapter 4 demonstrated that supplementation with betaine and isoquinoline alkaloids reduced the respiration rate and rectal temperature of pigs exposed to HS, indicating improved thermoregulation. Additionally, isoquinoline alkaloids decreased the colonic permeability of pigs under HS conditions. These results suggest that betaine and isoquinoline alkaloids can mitigate the increased physiological responses and intestinal hyperpermeability induced by HS. Chapter 5 investigated the effects of recombinant superoxide dismutase (rSOD) on oxidative stress, inflammation, and intestinal barrier integrity. The results obtained from the experiment conducted in Chapter 5 demonstrated that HS triggered oxidative stress and inflammation. The administration of rSOD ameliorated the consequences of heat stress by reducing oxidative stress and inflammation. However, neither heat stress nor rSOD impacted intestinal barrier function. The findings of Chapter 5 suggest that heat stress-induced oxidative stress and inflammation can be alleviated by recombinant superoxide dismutase. Chapter 6 investigated the effects of chromium and organic acid supplementation on the blood acid-base balance and gastrointestinal integrity of heat-stressed pigs. The results of Chapter 6 indicated that heat stress increased physiological responses and triggered respiratory alkalosis, and compromised intestinal barrier function, as evidenced by reduced transepithelial electrical resistance (TER) and increased permeability. However, neither chromium nor organic acids had any beneficial effects on thermoregulation, blood acid-base balance, or intestinal barrier integrity. Hot weather in summer increases the risk of heat stress (HS) and is associated with compromised growth performance, meat quality, and economic loss in pig production. Chapter 7 investigated the effects of supranutritional levels of antioxidants (Se and VitE) and organic acids on growth performance and meat quality of finishing pigs in late summer to early autumn. The weather data indicated that the pigs were under thermoneutral conditions for most of the experimental periods and had a low risk of HS. No benefits were observed from antioxidant and organic acid supplementation on the growth performance and meat quality of the pigs, except protein oxidation was reduced with high levels of Se and VitE. These results may be attributed to the cool weather during the experiments. In summary, this thesis has shown that nutritional supplements such as betaine, isoquinoline alkaloids and recombinant superoxide dismutase can alleviate the negative impacts of HS in pigs.
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    Irrigating urban green space as a cooling strategy – impacts on surface energy balance and microclimate
    Cheung, Pui Kwan ( 2023-08)
    Urban green spaces are an important space for physical and social activities in cites. However, people’s willingness to stay in urban green spaces will decrease with increasing air temperature in summer. It is necessary to find strategies to reduce air temperature in urban green spaces. Irrigating vegetation in urban green spaces is a promising cooling strategy. Irrigation can be a sustainable cooling strategy when non-potable water is collected for irrigation through stormwater harvesting and wastewater treatment. Yet, there is a lack of experimental evidence for the cooling effects of irrigating vegetation in urban green spaces. Also, little is known about how much environmental and management factors can influence the cooling effects of irrigation. This thesis identified and quantified the impacts of four environmental and management factors (background climate, daily irrigation amount, irrigation scheduling and weather) that influence the cooling effects of irrigation using field experiments and a computer model. A meta-analysis of the literature and a stepwise multiple linear regression was used to identify the background climate variables that significantly influenced the cooling effects of irrigation. The final regression model suggested that the cooling effect of irrigating vegetation in summer strengthened with increasing background air temperature and weakened with increasing rainfall. A field experiment was conducted in Melbourne, Australia to measure the impacts of irrigating turfgrass with three different irrigation amounts (2, 4 and 7 mm d–1) on the surface energy balance and microclimate of a small green space (36 m2). The differences in the impacts of the three different irrigation amounts were small because a large rainfall brought the soil moisture contents to the same level. Irrigation significantly reduced daytime air temperature and turf surface temperature, but it did not reduce human heat stress. The measured impacts of irrigation on the surface energy balance were small. Another field experiment was conducted in Melbourne, Australia to measure the impacts of three different irrigation schedules (single night-time, single daytime, and multiple daytime irrigation) on microclimate using the same amount of water (4 mm d–1) in a small green space (36 m2). The afternoon mean cooling effects of the multiple daytime irrigation on air temperature and turf surface temperature were significantly stronger than the single night-time and single daytime irrigation. The afternoon cooling effects were measured to strengthen with increasing air temperature, vapour pressure deficit and incoming shortwave radiation. Moreover, the data from this field experiment were used to assess the performance of an urban ecohydrological model, UT&C, in predicting the microclimate of unirrigated and irrigated turfgrass. UT&C was then used to predict the impacts of different daily irrigation amounts (2–30 mm d–1) on the cooling effect of irrigation on air temperature. The cooling effect only strengthened significantly as irrigation amount increased from 2 to 4 mm d–1. This thesis demonstrated that irrigating urban green spaces is an effective strategy to reduce daytime air temperature and turf surface temperature in summer. However, more cooling strategies, e.g., shading, are necessary to reduce human heat stress in urban green spaces in summer.
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    Linking fire, climate, connectivity and animal conservation
    Smith, Amy ( 2023-05)
    Australia’s forests and woodlands have been severely fragmented by agriculture, urbanisation and forestry, resulting in loss of habitat for native species. Habitat loss and fragmentation affect landscape structure, defined as the composition and configuration of land cover types. Species persistence in modified landscapes depends on the landscape structure and the availability of resources, which may be altered through management practices, such as prescribed fire. Fire can be used in the ecological management of many terrestrial ecosystems, where its application or suppression alter habitat structure and the availability and configuration of key resources. Current approaches to ecological fire management do not consider the influence of the surrounding landscape or the effect of fire on animal movement (connectivity) within or among habitat patches. The implications of current fire regimes for long-term population persistence are also overlooked. Connectivity is linked to persistence because it maintains dispersal, gene flow and genetic diversity, helping species combat environmental change and avoid extinction. Incorporating connectivity into fire management will help conserve biodiversity in fragmented landscapes. In my research program I investigated how 1) species richness and mammal community composition and 2) individual species respond to habitat, fire and landscape structure using data from remote-sensing cameras collected in south-eastern Australia. Additionally, I combine fire simulation modelling and connectivity analyses using genetic data to 3) compare future connectivity for two small mammals, yellow-footed antechinus (Antechinus flavipes) and heath mouse (Pseudomys shortridgei) under alternative fire regimes and predicted climate scenarios. These findings will inform an understanding of how fire, habitat and climate influence mammal communities, and species’ distributions, connectivity, and persistence. In Chapter 2, my first data chapter, I evaluate the relative influence of fire (time since fire and fire frequency), vegetation type, land use diversity and annual rainfall on ground-dwelling mammal community composition and species richness. Findings suggest that vegetation type and rainfall have the greatest influence on the mammal community and the vegetation type treeless heath is of great importance to critical weight range mammals. In Chapter 3, I focus on 1) the influence of vegetation structure, fire, and annual rainfall on the occurrence of 18 mammal species in two vegetation types (heathy woodland and treeless heath) at the local and landscape scale and 2) if species’ life history traits influence their responses to local and landscape scale predictors. At the local scale understory complexity influenced the occurrence of nine species in both vegetation types. In the woodland species occurrences were also influenced by annual rainfall and basal area while in treeless heath time since fire and fire frequency were important drivers. At the landscape scale, the extent of mature vegetation was most influential in the treeless heath while fire age-class diversity and the extent of native vegetation was most influential in the woodland. All tested species life history traits (size, diet, nest requirement, mean annual offspring and native status) were found to influence species responses at the site scale while only one trait (mean annual offspring) was found to predict species responses at the landscape scale. In Chapter 4, I combine fire simulations and connectivity analyses to compare future connectivity under four alternative fire regimes (0%, 1%, 2% and 4% of total available area burnt per year) and predicted future climate, for two small mammals, heath mouse (Pseudomys shortridgei) and yellow-footed antechinus (Antechinus flavipes). Genetic modelling found that heath mouse and yellow-footed antechinus considered the early post-fire age class low resistance (high connectivity) and pastural farmland to be high resistance (low connectivity). The results of the simulations suggest that the composition of the future landscape will shift towards more recently burnt vegetation, increasing connectivity for the heath mouse and yellow-footed antechinus. Overall, my research has provided new insights into how vegetation type and structure, fire and landscape structure influence mammal species distributions and contributed new information towards an important knowledge gap; how fire regimes influence animal movement and connectivity. Collectively, the findings will inform how fire regimes may influence species distributions and connectivity for long-term persistence in fire-prone landscapes.
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    Evaluation of Australian industrial hemp hurd (Cannabis sativa L.) as substitute lignocellulosic raw material for ultra-low-density particulate composites
    Fehrmann, Johannes ( 2023-08)
    The growing global demand for wood-based panel products faces significant challenges due to increasing scarcity and disruptions in the supply chains of traditional raw materials. In response to this problem, researchers are investigating the feasibility of agricultural by-products as an alternative source for lignocellulosic fibres. Australia's endorsement of hemp seeds for human consumption in 2017 has sparked a keen interest in hemp cultivation, resulting in a by-product known as 'hemp hurd', which is the xylemic inner core of the plant stem. Due to its low specific gravity and chemical similarities to timber, hemp hurd is an appealing option as a core layer constituent in engineered lightweight composite panels. These panels may be used for ready-to- assemble furniture, cabinetry, and decorative or acoustic wall and ceiling panels in both residential and commercial settings. Additionally, hemp hurd composite panels may be incorporated into prefabricated modular construction systems in response to fire or flood emergencies. However, it was unclear whether the hurd would be compatible with adhesives commonly utilised for engineered wood products and how the hurd would react to a natural modifying agent that had previously been effective in creating environmentally friendly lignocellulosic composites. All ultra-low-density hemp hurd particleboard (ULHPB) was fabricated as single-layer panels with densities ranging from 213 to 309 kg/m3. Decorticated hemp hurd chips (“Frog 1”) from Gippsland, VIC served as the raw material. Three synthetic adhesives were used as binders: bio-epoxy (EPX; Change Climate, SA), phenol-resorcinol- formaldehyde (PRF; Jowat Adhesives, NSW), and emulsifiable methylene-diphenyl- diisocyanate (MDI; Huntsman Polyurethane, VIC), respectively. The fourth panel type was an 'eco-friendly' ULHPB (320 - 338 kg/m3), primarily dependent on auto-adhesion and citric acid, which is free from formaldehyde or petrochemicals. The study aimed to determine the impact of hemp hurd particle dimensions on the physico-mechanical panel performance and identify optimal panel compositions in terms of particle and adhesive contents resulting in ULHPB with satisfactory performance characteristics. Furthermore, a subset of MDI-bonded panels was laminated with sheets of aluminium, Masonite hardboard, and Kraft liner, respectively, to explore the effects of surface reinforcement on the flexural properties. Specimen preparation and assessments of all ULHPB followed AS/NZS 4266.1 (2017) for Reconstituted wood-based panels - Methods of testing. The main assessments included internal bond strength, bending strength and stiffness, screw withdrawal resistance, water absorption, thickness swelling, thickness variability, compression ratio, and panel density. Where applicable, the results were evaluated for compliance with AS/NZS 1859.1 (2017) for Reconstituted wood-based panels - Specifications. Additionally, thermo-chemical analyses were conducted on both the untreated raw hemp hurd and the eco-friendly ULHPB to comprehensively study the characteristics of the raw material and understand the citric acid binding mechanisms. The techniques employed were pyrolysis-gas chromatography-mass spectrometry, Fourier-transform infrared spectroscopy, and thermogravimetric analysis. The results demonstrated that certain ULHPB configurations performed very well, considering their homogeneous structure, lack of surface densification, and an exceptionally low-density range. MDI-ULHPB exhibited remarkable dimensional stability, with all configurations passing the AS/NZS 1859.1 thickness swelling limit of 15% after 24h water immersion for moisture-resistant particleboard. Similarly, all MDI- ULHPB configurations with high particle loading and adhesive content surpassed the 0.30 MPa minimum internal bond strength threshold for standard particleboard, irrespective of particle size. The findings also highlighted a significant impact of particle dimensions on various physical and mechanical properties. Moreover, the binder application method and pressing temperature were identified as key factors influencing the overall performance of the produced panels. Nevertheless, the findings showed that the efficiency of raw material utilisation could be enhanced by addressing the adverse effects of smaller particles through the optimisation of processing parameters. The thermo-chemical analyses conducted on both retted and unretted hemp hurd revealed notable structural differences between the raw materials. The analyses also provided evidence of ester linkages in the eco-friendly panels, confirming the bonding mechanism described in previous studies. Additionally, all laminated substrates significantly improved the flexural capacities of the MDI-bonded panels, suggesting that ULHPB using Australian industrial hemp could be a suitable core layer in lightweight sandwich composites. The integration of agricultural by-products, specifically hemp hurd, into engineered building materials presents a promising opportunity to mitigate the depletion of finite timber resources and aligns well with circular economy principles. Moreover, this approach may bolster the cultivation of industrial hemp in Australia, further advancing the environmental and economic sustainability of novel building materials.
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    The state of data sharing in oncology research: an examination of policies, practices and perspectives of key research stakeholders
    Hamilton, Daniel George ( 2023-08)
    Over the last decade or more, there have been increasing efforts to evaluate and improve the transparency of scholarly research across many fields of science. Part of these efforts include lobbying for greater investment in data stewardship, as well as increased public and private access to researchers’ data. In the context of cancer research, this would bring numerous benefits to the research community. For example, greater access to data provides researchers with opportunities to validate discovered findings, answer questions not originally considered by the data creators, and accelerate research through the synthesis of existing datasets. However, transparency also brings challenges, such as the navigation of privacy legislation, increased demands on time and resources, development of infrastructure and expertise, and substantial concerns among researchers such as fears about misinterpretation and misuse of shared data. In this thesis, I present research from five empirical studies that have explored the state of data sharing in oncology. These constitute Chapters 2 to 7. In Chapter 2, I report findings from a survey of journal editors, observing that journals report a wide variety of policies and practices on peer review and data sharing; even within different disciplines, norms are far from fixed. In Chapters 3 and 4, I present the protocol and the findings of a systematic review and individual participant data meta-analysis of over 2.1 million medical publications. At the end of these studies, I estimate that only 8% of medical articles published between 2016 and 2021 declared that the data were publicly available, and only 2% actually shared data. I also estimate that only a third of researchers comply with mandatory data sharing policies of journals, and even fewer – only a fifth – comply with policies requiring researchers to share with others on request. In Chapter 5, I narrow my focus down to data sharing in oncology research, and report that while one in five articles declare that data are publicly available, less than 1% share in accordance with the FAIR Guiding Principles. In this chapter, I also observed similar levels of non-compliance with mandatory data sharing policies of journals to Chapter 4. In Chapter 6, I report the results of a survey of cancer researchers, asking them about their experience with, and thoughts on data sharing. In my final empirical chapter, Chapter 7, I turn to individuals affected by cancer to ask their opinions about whether data from cancer research should be shared, and with whom. Together my work indicates that while both cancer researchers and patients support sharing data, the practice is still uncommon, and that current policies which aim to increase sharing are often wanting. A stronger commitment from key research policymakers such as publishers, funders, and research institutions are needed if we are to improve both the frequency and quality of data sharing in oncology.
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    Mapping for Sustainable Livelihoods: using cultural mapping to clarify community shared visions and livelihood options in natural and cultural resource planning and development
    Field, Jennifer Joi ( 2023-04)
    Abstract The development of sustainable livelihoods and sustainable growth is a key challenge for society. While there is often the best of intent, many opportunities for sustainable development are not realised. The goal of this research was to understand the reasons for overlooked or lost opportunities for sustainable livelihoods and sustainable growth. The research was undertaken in the Kimberley region, a contested landscape in the north of Western Australia. This region includes a diverse range of industry, government and community stakeholders, all with vested interests in its natural and cultural resources. The region is rich in resources, and Indigenous people’s intergenerational knowledge of the area is keenly sought after from sectors such as tourism, mining, national parks, education, health and environment. However, despite the amount of private investment and government funding for development that is poured into the area, it results in little change for its at-risk Indigenous communities of the Kimberley despite the constant demand from academic, industry and government sectors to engage with them and address their needs. The intent was to learn their perspectives about the constraints when engaging with communities and to identify opportunities for improving interactions and more sustainable outcomes for all parties. The study explored research questions related to this goal using personal ethnography, interviews, a workshop and tailored cultural mapping practice, and engaged with a large range of sector leaders. Another focus was to explore an approach to sharing of knowledge between Indigenous communities and the many stakeholders they engage with, and the benefits that might come from this. A bespoke designed method of cultural mapping was refined and accredited and used as a research framework. Bespoke is when a training method is designed to address a real-world issue or concern. This method was used to design the research questions and a workshop involving interviewees. This method was also used to develop multi sector engagement scenarios that make sustainable livelihoods, and the constraints to achieving them, more visible. The study found livelihood and growth opportunities were missed because: 1. cultural knowledge was not specifically recognised to be of value in sustainable development; 2. time poor community leaders cannot fully evaluate potential opportunities arising from the huge amount of investment; 3. Kimberley Indigenous communities do not feel heard or included in culturally appropriate ways in the large-scale development being implemented by others; and 4. knowledge collected from communities rarely had any benefits for the communities, yet that knowledge benefited those collecting it. Further, the study found that development proponents from the public and private sectors predominantly work in silos. The consequence for communities is the effort expected when each stakeholder knocks on their door to ‘consult’ or gather information. This commitment takes time and effort that communities could invest into their own initiatives. More broadly, these findings indicate that community livelihood opportunities are not being realised because culture, and its complexity, are being ignored, which points to the need for including culture in a more practical and realistic way into the existing sustainable development paradigms. Culture remains ambiguous in these paradigms, indicating the lack of clarity that underpins efforts to incorporate it. As a result of this disconnection, decision makers and investors fail to acknowledge the urgency of reversing the loss of cultural knowledge. This knowledge is potentially critical to addressing major challenges such as climate change, language loss, and loss of biodiversity. These findings, and findings of prior studies underpinning this one, show that for communities to have the chance to achieve sustainable livelihoods, their single most important cultural asset, their practices and knowledge of their region and its natural environments, must be protected and acknowledged. These findings have wider implications for achieving sustainable livelihood and development objectives in Indigenous communities across Australia and in many other communities around the world. It is recommended that ‘culture’ be incorporated as the first pillar of the sustainable development paradigm, and become a standalone Sustainable Development Goal
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    Identification of long non-coding RNAs in plant reproductive development
    Babaei Gharahghani, Saeid ( 2023-07)
    Linear and circular long non-coding RNAs (lncRNAs, and circRNAs) are regulatory RNA molecules that do not encode proteins but play critical roles in biological processes in responses to internal and external factors. These non-coding RNAs can originate from various genomic regions, including exonic, intronic, or intergenic regions and function based on their specific nucleotide sequences and structures. This thesis aims to advance our understanding of circRNA and lncRNA expression patterns and functional roles in plants during flowering, employing RNA sequencing and plant transformation techniques, with a focus on soybean flowering and Brassica rapa pollen development. Pollen development is a crucial process that plays a pivotal role in fertility and subsequent seed production. In-depth RNA sequencing investigations were conducted to examine circRNA expression during five distinct stages of pollen development in B. rapa. A total 1180 circRNAs were identified. These circRNAs were generally small, ranging from 100 to 600 nucleotides in length, comprised of one to two exons, and displayed an uneven distribution across all chromosomes. Further analysis demonstrated differential and stage-specific expression patterns of circRNAs, primarily showing an upregulation trend during pollen development. Comparative analysis using bioinformatics tools revealed that the identified circRNAs in B. rapa exhibited approximately 35% sequence conservation with circRNAs identified in Arabidopsis thaliana, while only about 3% sequence conservation was observed with circRNAs from other plant species. Functionally, the identified circRNAs in B. rapa were found to regulate pollen development by participating in diverse biological processes, including protein biosynthesis, meiotic and meiosis cell division processes, DNA processing, enzymatic activities, and carbohydrate metabolism. Moreover, the investigation identified 88 circRNAs containing binding sites for microRNAs (miRNAs), indicating their potential role as miRNA sponges in post-transcriptional gene regulation. Specifically, the circRNAs expressed in B. rapa pollen exhibited binding elements for various flowering miRNAs, such as miR156, miR164, and miR172, suggesting their potential involvement in pollen developmental processes. To validate the presence of circRNAs, nine circRNAs were selected and confirmed through experimental procedures, including the verification of back-splicing junctions using divergent primers and Sanger sequencing experiments. Soybean (Glycine max) is considered the world's major source of vegetable oil and protein. The transition from vegetative growth to flower development in soybean is triggered by exposure to short-day photoperiod, as it is a short-day plant. During floral transition in soybean, RNA sequencing data was generated from Shoot Apical Meristem (SAM) samples dissected from plants subjected to short-day treatment at four time points: 0, 2, 4, and 6 days after treatment. The expression profiling of circRNAs identified 384 circRNAs in soybean SAM, which were found to be predominantly short in length (300-600 nucleotides) and composed of two to four exons. Furthermore, an uneven distribution across the 20 chromosomes of soybean was observed. CircRNAs exhibiting short-day treatment-specific expression patterns were noted during the floral transition processes in soybean, with a greater number of circRNAs displaying upregulation following six days of short-day treatment. An analysis of circRNAs expressed in soybean SAM revealed that they possess longer flanking introns, which were significantly enriched with reverse complementary elements, potentially facilitating circRNA biogenesis. Additionally, circRNAs derived from genes involved in flowering-related hormones such as abscisic acid and auxin were also identified. The involvement of circRNAs in diverse biological processes, including SAM development, adaxial/abaxial axis specification, reproductive shoot system development, and the regulation of flower development, was unveiled through in-silico functional analysis. Furthermore, miRNA binding sites were found in 38 circRNAs, including those associated with development and flowering, such as miR156 and miR172, suggesting their potential function in circRNA-miRNA-mRNA networks that regulate gene expression during floral transition. The backsplicing of 26 selected circRNAs was validated through divergent primer amplifications or Sanger sequencing. The intricate gene regulatory network underlying the floral transition in soybean was illuminated by these findings, which highlighted the unique characteristics and potential functions of circRNAs during this process. To explore the role of lncRNAs in soybean flowering, a specific flowering-associated lncRNA known as NC_GMAXST00046315 was introduced into soybean via Agrobacterium-mediated transformation. PCR screening of the obtained transgenic lines was performed using specific primers for the reporter gene beta-glucuronidase (GUS), which successfully confirmed the presence of the transgene in the transgenic lines. The quantitative PCR (qPCR) analysis revealed that the inserted lncRNA in the soybean genome exists in a copy number ranging from one to three copies. Moreover, qPCR analysis validated successful overexpression in selected transgenic lines, with expression levels ranging from 1.8- to 2.35-fold higher compared to non-transgenic plants. Since lncRNAs typically regulate the expression of their neighbouring genes in cis or trans, further investigations were undertaken to assess whether the expression of neighbouring genes was influenced by overexpression of the lncRNA. Specifically, the impact of lncRNA overexpression was compared between non-stress and heat stress conditions, as the BAG gene (heat-responsive gene) is located downstream of the lncRNA. The results indicated a significant decrease in the expression of BAG in transgenic lines compared to WT plants (non-transgenic Bragg) under non-stress condition. During heat stress, a noteworthy increase in lncRNA expression was observed in WT plants, implying its involvement in stress-responsive pathways in soybean. The expression of the BAG gene exhibited a 270-fold increase in WT plants and up to 680-fold increase in transgenic lines, indicating the potential regulatory effect of the overexpressed lncRNA on BAG gene. The transgenic soybean lines also exhibited notable improvements in seed characteristics, resulting in significantly higher yields compared to WT plants. Specifically, the transgenic lines displayed enhanced seed weight and a higher percentage of undamaged seed coat, while WT plants produced smaller seeds with wrinkled discoloured seed coat. The seed weight of transgenic lines increased by approximately 15%, and the occurrence of intact seed coat increased by 6-9% compared to WT plants. These findings highlight the positive impact of lncRNA overexpression on soybean yield, particularly under heat stress conditions. In summary, the significance of circRNAs and lncRNAs in plant flowering and reproduction is emphasized by this research. The identification of critical regulatory circRNAs and lncRNAs in this study contributes to a deeper understanding of the regulatory mechanisms that control flower development in crop plants. Furthermore, this knowledge has the potential to facilitate the advancement of more efficient and higher yielding seed-producing crops.
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    Characterization of phenolic compounds from the selected native Australian flora, their bioaccessibility, bioactivities, safety evaluation, and their reciprocal interactions with the gut microbiota
    Ali, Akhtar ( 2023-08)
    Plants have formed the basis of a traditional medicine system that has existed for thousands of years. The growing interest in phytochemicals for general health to prevent chronic disease and aging fueled nutritionists and other scientists to explore the nature, composition, and presence of bioactive metabolites in plants. Phenolic compounds are diverse bioactive metabolites, including phenolic acids, flavonoids, lignans, stilbenes, coumarins, phenolic terpenes, tyrosols, and other polyphenols. Phenolic metabolites have attracted much interest due to their wide range of proven biological properties. Australian native plants offer a substantial potential source of new antioxidant chemicals for medicinal or functional products. The emerging interest in the food supply required detailed analytical characterization and quantification of antioxidants to collectively understand their role in food and human health. Previously, a few studies were conducted to characterize and identify phenolic compounds from native Australian fruits, herbs, and medicinal plants. However, comprehensive profiling of these plants still needs to be improved due to the complex nature of phenolic and non-phenolic compounds and the expense and non-availability of commercial standards. Considering the potential of phenolic compounds, I comprehensively characterized 19 selected native Australian flora (Kakadu plum, Davidson plum, muntries, quandong peaches, rosella, strawberry gum, lemon aspen, mountain pepper berries, river mint, bush mint, sea parsley, bush tomatoes, lemongrass, wattle seeds, Oldman saltbush, sandalwood nuts, aniseed myrtle, lemon myrtle and cinnamon myrtle were studied for in-depth screening of phenolic compounds and their biological activities. The highest total phenolic content (TPC) was measured in Kakadu plum (74.84 mg GAE/g), while the lowest TPC was quantified in lemon aspen (4.40 mg GAE/g). The other selected plants (bush mint, river mint, quandong peach, strawberry gum, Davidson plum, bush tomatoes, muntries, and lemongrass) were quantified with the TPC (57.70, 46.59, 42.85, 36.57, 32.49, 26.78, 23.04 and 15.09) mg GAE/g, respectively. Kakadu plum, Davidson plum, muntries, and quandong peaches contain diverse phenolic compounds, particularly flavonoids (condensed tannins and anthocyanins). For example, the Kakadu plum contains condensed tannins like ellagic acid, punicafolin, pedunculagin, punicalin, and kurilagin corilagin, potent phenolic compounds. Davidson plums and quandong peaches were measured with higher amounts of anthocyanins than blueberries and blackberries, highlighting that these fruits are highly beneficial for human health. Delphinidin 3-O-sambubioside, delphinidin 3-O-glucoside, cyanidin 3-glucoside, and ellagic acid were measured with a higher concentration in Davidson plum, while isorhamnetin, delphinidin 3-O-glucoside, and cyanidin 3-rutinoside were found with a higher concentration in quandong peach. Moreover, higher concentrations of rosmarinic acid, chlorogenic acid, sagerinic acid, quinic acid, and caffeic acid were measured in bush mint, river mint, bush tomatoes, and mountain pepper berries. Chlorogenic acid, myricetin 3-O-rhamnoside, quercetin 3-O-arabnoside, quercetin 3-(2-galloylglucoside), and epicatechin had higher concentrations than other quantified phenolic compounds in strawberry gum; and delphinidin 3-O-sambubioside, cyanidin 3-rutinoside, cyanidin 3-glucoside, cyanidin-3-sambubioside, cyanidin, epicatechin, and chlorogenic acid had higher concentrations in rosella. In this study, I identified and quantified many new compounds in all studied plants and explained their chemistry. Antioxidant, anti-diabetic, and anti-Alzheimer activities were also measured for selected plants. These fruits provide a potential source of natural antioxidants for various health applications (anti-diabetic and anti-Alzheimer). The function-structure relationship is also described using in-silico molecular docking and simulated pharmacokinetics models. Native Australian fruits have remarkable pharmacological and medicinal values. The effective utilization of native Australian fruits and herbs could help to detoxify reactive oxygen species in antioxidants-deficient individuals and fulfill the antioxidants and nutritional sufficiency in the population. Based on the higher value of the Kakadu plum, Davidson peaches, muntries, and quandong peaches were further analyzed for bioaccessibility of phenolic compounds, their reciprocal interactions with the gut microbiota, and safety evaluation using a zebrafish model. The safety of phytochemical extracts from these selected fruits was evaluated using an embryonic zebrafish model to effectively utilize these plants in drug discovery effectively. Muntries were quantified with the least LC50 value (169 mg/L) compared to Davidson plum (376 mg/L), Kakadu plum (>480 mg/L), and Quandong peach (>480 mg/L), which indicates that muntries extract was more toxic than other fruit extracts. Importantly, we found that adverse effects were not correlated to the total phenolic content and antioxidant potential of these native Australian fruits and cannot simply be predicted from the in vitro analysis. According to the Organization for Economic Cooperation and Development (OECD) guidelines, native Australian fruit extracts are included in the safe category. Additionally, the bioaccessibility and biotransformation of phenolic compounds, the production of short-chain fatty acids, and the impact of native Australian fruits on gut microbiota composition during in-vitro digestion and colonic fermentation were also investigated in this thesis. Quandong peaches were measured with a higher amount of total bioaccessible phenolic compounds than other selected fruits. Native Australian fruits significantly affect the diversity of microbial composition and production of short-chain fatty acids. Kakadu plum and muntries have significantly higher total short-chain fatty acids production than Davidson plum and quandong peaches. These native fruits are beneficial for maintaining gut health by regulating microbial composition. This could also be due to the higher concentration of dietary fiber in these fruits, condensed tannins, anthocyanins, and other flavonoids, which are highly beneficial for gut microbiota. This study addressed many gaps in the selected native Australian flora and added value for native Australian fruits and herbs commercialization. It broadened the knowledge of the complex metabolomic profiling of the selected fruits, their bioactive functions, safety evaluation, and their impact on the gut microbiota. This study will develop further research to explore the phytopharmaceutical potential of these native Australian fruits, herbs, and spices in drug discovery using different in-vivo models.