11,873 results for Doctoral

  • The efficiency of adaptive cluster sampling

    Brown, Jennifer A. (1996)

    Doctoral thesis
    University of Otago

    xiii, 197 leaves :ill. ; 30 cm. Includes bibliographical references. University of Otago department: Mathematics and Statistics. "January 1996."

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  • Who is God for us? : images of God in a group of Roman Catholic lay women in Aotearoa New Zealand

    Betz, Mary Agnes Ann (2003)

    Doctoral thesis
    University of Otago

    xix, 317 leaves :ill. (some col.), maps ; 30 cm. Includes bibliographical references. University of Otago department: Theology and Religious Studies. "28 November 2003"

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  • Role of iron, siderophores and iron regulation in the Epichloё festucae - Lolium perenne symbiosis

    Forester, Natasha Talei (2015)

    Doctoral thesis
    University of Otago

    Ferric iron-chelating siderophores are produced by microorganisms to compete for and sequester iron, an essential but potentially toxic micronutrient. Epichloё festucae, a filamentous fungus that is mutualistically associated with the grass Lolium perenne, occupies apoplastic spaces between the plant’s shoot cells and relies upon host nutrients to survive. E. festucae synthesises two siderophores, epichloënin A and ferricrocin (FC). A non-ribosomal peptide synthetase SidN was previously found to be required for the biosynthesis of epichloënin A, for iron uptake, for normal colony growth under iron-starved conditions and for normal mutualistic associations of E. festucae with L. perenne. Little else is known about the mechanisms governing iron metabolism in E. festucae or the role of iron in maintaining E. festucae - grass associations. To explore siderophore biosynthesis and iron regulation in E. festucae, iron-related genes were identified and fungal mutants were generated. These mutants, deficient in either siderophore biosynthesis (ΔsidA, ΔsidC, and ΔsidN) or iron regulation (ΔsreA and ΔhapX) were characterised and their phenotypes analysed in culture and in planta. The sidA gene encodes the L-ornithine-N5-oxygenase SidA, an enzyme shown to be required for the biosynthesis of both siderophores. The sidC gene encodes an NRPS enzyme, SidC that assembles FC, a siderophore that was only found in mycelial fractions. Mass spectrometry data indicated that epichloënin A and FC are synthesised under low and high iron availabilities, respectively. Intriguingly, the findings of significant quantities of epichloënin A in mycelial fractions of the wild-type strain Fl1 (WT), combined with the observation that ΔsidN colonies lacked iron-dependent pigmentation suggested that epichloënin A functions in intracellular iron management, in addition to extracellular iron uptake. In the presence of iron, increased ferricrocin production and vacuolar-iron uptake occurred in ΔsidN compared to WT cultures, suggesting an increased intracellular iron pool in the ΔsidN colonies that might fuel the observed increase in aerial hyphal growth. Iron starvation impaired growth of all siderophore mutants in culture, but could be repaired by supplementing iron-deprived media with FC, which was shown to be required for aerial hyphal growth. Iron-bound ferriepichloënin A could not recompense for the loss of FC, and repressed ΔsidN colony growth in excess, suggesting that epichloënin A modulates iron accessibility intracellularly. The ΔsidN fungi grew profusely in hosts around meristematic tissues and correlated with a host-stunting phenotype, which could only be induced by loss of SidN (and epichloënin). These results suggest interplay between siderophores in moderating in planta fungal growth, which might prevent over-colonisation of important host organs such as meristems whose development affect plant architecture. The sreA and hapX genes encode two iron-responsive transcription factors that are involved in regulating iron homeostasis in E. festucae under iron-sufficient and -deficient conditions, respectively. Gene expression analyses showed an iron-dependent mutual control mechanism exists between SreA and HapX, and an alternative splicing mechanism may control SreA activity. Loss of SreA resulted in growth defects and de-repression of siderophore biosynthesis in the presence of iron, while loss of HapX raised FC levels during iron deficiency indicating repressor functions of these proteins. Associations of regulatory mutants with L. perenne were not stably maintained long term and hyphae displayed atypical morphology. The ΔsreA fungi could induce chlorosis during low iron supply to host plants indicating that ΔsreA mutants compete with the host for iron. E. festucae appears to have a tightly regulated iron management system for balancing growth and survival, preventing over-competition for iron in the intercellular niche thus promoting mutualistic associations. Mutations that interfere with Epichloë iron management negatively impact iron-dependent fungal growth and can destabilise mutualistic plant - fungal associations to the detriment of either symbiotic partner.

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  • Exploring the development of biological literacy in Tanzanian junior secondary school students

    Juma, Zawadi Richard (2015)

    Doctoral thesis
    Victoria University of Wellington

    Internationally, scientific literacy is a major goal of science education in the twenty first century. In Tanzania, where there is a widespread lack of public understanding about major health issues, biological literacy is needed so that people can make decisions about the socio-scientific issues that confront them. To that end, the Tanzanian school curriculum aims to connect students’ understandings of Biology to their everyday lives but few studies have been conducted that show whether these aims have been achieved, especially in junior secondary school. This ethnographic case study investigates the ways in which the junior secondary school Biology curriculum in Tanzania supports or constrains the development of biological literacy and how institutional context, particularly as it relates to urban and rural schools, influences the delivery of the Biology curriculum. Teachers’ and Year Four students’ of secondary schools views about school Biology were sought in the course of this study and the issues that emerged were analysed using social constructivist and social constructionist theoretical frameworks. Data were collected through student questionnaires, student focus group interviews, teacher interviews, and classroom observations. The research sites included rural and urban schools, and government and private schools. The findings suggest that the Biology curriculum and the ways it is delivered do not adequately address the students’ needs and therefore is unlikely to enable them to become biologically literate. Rural schools are less well equipped than urban schools to deliver the curriculum and teachers and students face bigger challenges. A key finding was that Tanzanian young people have a strong desire to learn more about reproductive Biology and health issues but these are not prioritised in the current curriculum. In light of these findings, curriculum changes are recommended to provide learning opportunities for students to gain biological knowledge and skills that are relevant to their daily lives.

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  • Family Language Policies of Refugees: Ethiopians and Colombians in New Zealand

    Revis, Melanie Sandra (2015)

    Doctoral thesis
    Victoria University of Wellington

    There has been a surprising dearth of research on language maintenance and shift in New Zealand over the last decade. This thesis addresses this gap by examining incipient patterns of language maintenance and shift in families in two refugee communities in Wellington. Earlier research suggests that immigrants may maintain their ethnic languages in spite of societal factors pressuring language shift for up to three generations. By then, however, language shift is often completed, with the third generation using the majority language only (Fishman 1991). In a largely monolingual country such as New Zealand, this shift may be accomplished in only two generations (Holmes et al. 1993). Understanding the language dynamics at the micro level that eventually lead to language maintenance or shift requires more research into actual language use among family members than traditional methods provide. This investigation therefore uses ethnographic observations, semi-structured interviews and recordings of naturally-occurring interactions between mothers and their children to highlight the challenges involved in transmitting a minority language. Using Spolsky’s (2004) tripartite model of language policy, I investigate family language beliefs, practices, and management in the refugee-background Ethiopian and Colombian communities. The Amharic-speaking Ethiopian community consists mostly of first and second generation members. They first settled in New Zealand in the 1990s and now display awareness of the challenges of maintaining their language. Most Ethiopian parents consider it their responsibility to teach their children Amharic in the home and many have introduced explicit language policies to promote Amharic use. These families exhibit an ‘impact belief’ (De Houwer 1999) which links their positive beliefs about Amharic with their management of family language practices. Nevertheless, in some cases children subvert and contest explicit language management and become primary agents of language shift. Supporting the parents’ efforts, the Ethiopian Orthodox Church provides a social space where Amharic may be used backed by an explicit policy which requires all members to use the language when at church. This policy provides valuable institutional support and cultural capital for Amharic and contributes to the vitality of the language in Wellington. The Colombian community has had a relatively shorter stay in Wellington, with the first members arriving as recently as 2008. Colombian mothers want to transmit Spanish and many seem confident that their children will maintain the language. In particular, they consider the Colombian variety of Spanish to be a source of pride and a core value (Smolicz 1992), as many participants closely link this variety to their Colombian identity. They further capitalise on the prestige of Spanish as a world language that motivates them to use it even outside their ethnic community. However, few families have put in place explicit language policies to use Spanish in the home; instead, many regard it as a more urgent concern that their children learn English. Overall, despite the community members’ positive attitudes towards their ethnic languages, their efforts to transmit these languages appear to be constrained by the fact that English is invested with considerable cultural capital (Bourdieu 1977) in New Zealand. English acquisition often takes priority, particularly for many newly arrived Colombian families. The participants’ refugee experiences, length of residence in New Zealand and the societal status of their ethnic languages seem influential factors on the degree of control they assume over their children’s language practices. Families also dynamically adapt their language policies to the circumstances, for example by introducing an explicit minority language policy after their children have acquired what they consider to be enough English. Despite a strong desire for their children to continue speaking the ethnic language, the parents have many other (non-linguistic) responsibilities and they frequently lack knowledge about “success strategies” for minority language transmission. Moreover, the children often take significant agency by introducing English into the home domain, in some cases even influencing other family members to use it, and thus initiating language shift. The detailed interactional data in this research provides insight into the different ways parents have instantiated their varying language policies and negotiated home language choice with their children. In sum, this research provides insight into language transmission efforts at the family level, and, using data from observations, interviews and recordings of mother-child interaction, describes in detail the unfolding of language maintenance dynamics. The thesis presents valuable insight into the underlying beliefs about Amharic and Spanish, the role of explicit language management strategies, parental socialisation and discourse styles and children’s agency. As the first such research covering two recent refugee communities it will hopefully assist the individual families to socialise their children in a way that enables them to become proficient minority language speakers. This will ensure a linguistically rich future for New Zealand.

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  • Being musical : teachers, music and identity in early childhood education in Aotearoa/New Zealand

    Bodkin, Sally (2004)

    Doctoral thesis
    University of Otago

    ix, 294 leaves ; 30 cm. Includes bibliographical references. University of Otago department: Music.

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  • The Southland variety of New Zealand English : postvocalic /r/ and the bath vowel

    Bartlett, Christopher Mark (2002)

    Doctoral thesis
    University of Otago

    xiii, 177 leaves :ill. ; 30 cm. Includes bibliographical references. University of Otago department: Anthropology. "13 December 2002" -- T.p.

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  • Designing oligoarginine-associated PECA nanoparticles for enhanced cellular uptake

    Chiu, Jasper Ze Siong (2015)

    Doctoral thesis
    University of Otago

    Introduction: Polymeric nanoparticles can be used as carriers to improve oral bioavailability of therapeutic peptides or proteins. These polymeric carriers can be formulated with cell-penetrating peptides such as oligoarginine to further enhance uptake. Such a combined formulation could deliver bioactive effectively, using less oligoarginine than required for effective cell permeation using oligoarginine alone. The aims of this study were to formulate poly(ethylcyanoacrylate) (PECA) nanoparticles with oligoarginine, characterize the resulting nanoparticles and investigate their in vitro uptake. Methods: PECA nanoparticles were produced by in situ polymerization in a water-in-oil microemulsion. Various oligoarginines were dissolved in the aqueous phase of the microemulsion prior to the addition and polymerization of monomers, to produce different oligoarginine-associated nanoparticles. The resultant nanoparticles were characterized for size and zeta potential in ultra-pure water and the cell incubating medium (Hanks Balanced Salt Solution, HBSS). The nature of the association between oligoarginines and nanoparticles was investigated by MALDI-TOF mass spectrometry. The uptake of the oligoarginine-associated nanoparticles, loaded with a fluorescent probe, by Caco-2 cells was investigated using fluorescence-activated cell sorting (FACS) and confocal imaging. Uptake studies were conducted in both undifferentiated cells and fully differentiated cell monolayers. The uptake of radiolabeled oligoarginine nanoparticles by Caco-2 cells was quantified by scintillation counting and the accumulation of nanoparticles on the cell surface was evaluated with a mathematical simulation model. Results: PECA nanoparticles formulated with di-arginine-histidine (RRH) and tetra-arginine-histidine with an aminocaproic acid spacer (R4acaH) were cationic (zeta potential of +35 and +33.5 mV, respectively) and approximately 200 nm in diameter. Mass spectrometric studies revealed that RRH was covalently tagged to the PECA nanoparticles via histidine but R4acaH was not. Because these RRH-tagged nanoparticles aggregated in HBSS, poloxamer-407 surfactant was added to stabilize the colloidal system. However, the addition of surfactant was found to neutralize the positive zeta potential of the nanoparticles. RRH-tagged nanoparticles associated with a higher proportion of undifferentiated Caco-2 cells after 2 h incubation than unmodified nanoparticles and confocal imaging showed that they were mainly located on the cell surface. Association of RRH-tagged nanoparticles in fully differentiated Caco-2 cell monolayers was not increased compared to that of unmodified nanoparticles. The accumulation trend of PECA nanoparticles on the cell surface predicted by a mathematical simulation model was consistent with the cellular experimental data. Conclusions: PECA nanoparticles associated covalently with RRH via histidine anchoring to produce cationic nanoparticles, which were neutralized in the presence of surfactant. These nanoparticles adhered to undifferentiated Caco-2 cells to a greater extent than unmodified PECA nanoparticles. However, scintillation counting data revealed that the greater tendency to adhere did not result in greater uptake of the RRH-tagged nanoparticles in fully differentiated Caco-2 cell monolayers, which was consistent with the findings of flow cytometry. Mathematical simulation modelling was able to predict the low accumulation of the nanoparticles at the bio-interface but did not account for the adherence tendency of the nanoparticles and the initial contact adherence that occurred during convection mixing upon introduction of the formulation to the cells. Further surface characterization of the RRH-tagged nanoparticles is required to gain deeper insight into the nature of the interaction at the cellular bio-interface. Although fluorescence analysis (such as FACS and confocal imaging) was able to quantify the proportion of cells associated with the polymeric nanoparticles and verify internalization, scintillation counting data complemented the cellular association with invaluable information on the proportion of nanoparticles associated with the cells. Therefore, these techniques should be used together to critically assess cellular association and uptake.

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  • Investigation of the Factors that Limit the Shelf Life of Fresh Chilled Pasteurized Milk

    Alothman, Mohammad (2015)

    Doctoral thesis
    University of Otago

    The stated shelf life of fresh chilled pasteurized milk (FCPM) in New Zealand is 14 days, which although considered long enough to meet the needs of the domestic market, limits its export potential. The shelf life of FCPM is usually limited by the growth of microorganisms including Gram-positive spore-forming bacteria that survive the pasteurization process and psychrotrophic Gram-negative bacteria (particularly Pseudomonas sp.) that can re-contaminate the milk during bottling. During growth, microorganisms produce different combinations and concentrations of volatile organic compounds (VOCs) in FCPM, some of which are perceived as off-flavours and influence the sensory quality and shelf life of FCPM. The total number of microorganisms in milk is used as a broad indicator of quality by the dairy industry. However, FCPM containing high microbial numbers can be palatable, while FCPM with lower microbial numbers can be rejected by consumer depending on the activity of the contaminating microbes. Therefore, to ensure the production of FCPM with an export potential (i.e., shelf life > 14 days), a better understanding of the effect of microorganisms (types and numbers) on the sensory quality and the shelf life of FCPM is required. The present study was comprised of 5 experiments that covered three broad tasks. The first task focused on studying changes in the microbial population and the VOC composition (using proton transfer reaction – mass spectrometry (PTR-MS)) in three types of FCPM, namely whole fresh chilled pasteurized milk (WFCPM), high protein – calcium fortified milk (HP-Ca), and skim (Trim) milk during extended storage for up to 26 days (Chapter 4). This experiment was followed by two sensory studies which examined the relationship between changes in the microbial quality, the VOC composition, and the sensory quality of FCPM during storage using firstly a consumer based method (Chapter 5) and then a trained descriptive panel (Chapter 6). The experimental work was concluded by two inoculation studies (Chapter 7 and 8), which investigated the spoilage potential of a number of microorganisms, isolated from aged FCPM (3-21 days) and inoculated into FCPM as either pure or mixed cultures of microorganisms. It was found that post pasteurization contamination (PPC) with Gram-negative bacteria is what primarily limits the shelf life of FCPM in New Zealand. In the absence of PPC, the milk maintained a good quality and had a shelf life of beyond 14 days. The initial microbial population in FCPM was mainly comprised of spore-forming bacteria, however, Gram-negative psychrotrophic microorganisms dominated the microbial population as the milk aged. The different species and numbers of microorganisms entering the milk via PPC caused batch-to-batch and within batch variations in the shelf life of FCPM, due to differences in their initial numbers at the time of contamination, growth rates, and spoilage potential. Owing to this variation in the species and numbers of microorganisms in the milk, it was determined that storage time correlated poorly with VOC and the end of shelf life. Rather, microbial numbers correlated well with increases in VOC concentrations and the end of shelf life which was determined at an estimated rejection threshold (RjT) by consumers occurring when microbial numbers exceeded > 107 CFU.mL-1. The RjT (end of shelf life) was defined as when a unanimous decrease in consumers’ preference occurred due to changes in the sensory characteristics of FCPM. At the same RjT, significant changes in the signal intensities for a number of spoilage-related volatile mass ions occurred in the headspace of FCPM (p≤0.05), including m/z 33, 45, 47, 61, 63, 71 and 89, which were tentatively identified as being methanol, acetaldehyde, ethanol, acetic acid, dimethyl sulfide, butanoic acid or 2-pentanol respectively. Extended storage of WFCPM (26 days) resulted in significant changes in a number of the key sensory characteristics of the milk determined by descriptive sensory analysis namely cheesy odour, cultured odour, barny odour, cheesy flavour, cultured flavour, creamy flavour, sweet taste, mouth coating, sweet after swallow, and creamy after swallow (p≤0.05). These changes had a weak relationship with the microbial quality due to the low number of microorganisms detected in WFCPM throughout the storage period. However, a better relationship between changes in the sensory characteristics and the VOC composition of WFCPM was found suggesting that the contaminating microorganisms had strong spoilage potential despite their occurrence at low numbers. Inoculating FCPM with microorganisms isolated from aged FCPM showed that microorganisms varied in their ability to grow in FCMP at 4.5 °C ± 0.5 and to cause changes in its VOC composition (i.e., had differing spoilage potential). In addition, inoculating milk with different combinations of mixed bacterial cultures of two strains of Pseudomonas fluorescens and Chryseobacterium sp. resulted in VOC composition that is similar but not equal to that inoculated with pure cultures of the dominating bacteria. This could be ascribed to the interaction (competition and/or synergism) that occurs between bacteria during growth. In conclusion, in the absence of post pasteurization contamination FCPM had a shelf life (time before RjT), which exceeded 14 days. However, depending on the spoilage potential of the contaminating microorganisms, PPC could result in changes in the VOC composition and the sensory quality of the FCPM that result in its rejection by consumers if microbial numbers exceeded approximately 107 CFU.mL-1 regardless of the storage time. Preliminary trials carried out in the bottling plant identified a number of potential sources of PPC and it is suggested that eliminating these potential sources will enable the production of milk, which consistently has a shelf life exceeding 14 days.

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  • The Formulation of Titanium - based Metal Feedstocks and the Fabrication of Parts using the Powder Injection Moulding Process

    Ewart, Paul Douglas (2015)

    Doctoral thesis
    University of Waikato

    Development of a profitable titanium industry for New Zealand will not come about without innovative technologies. Plastic injection moulding has long held a place in NZ manufacturing to produce large quantities of complex parts and holds the key to such innovation. Titanium metal parts were fabricated by injection moulding titanium based metal powder feedstock followed by a debinding process and subsequent sintering. The fabrication process in its entirety was investigated in four distinct steps. Feedstock formulation involved combining the metal powders with various carrier components. Injection moulding enabled the shaping of the feedstock into geometries approximating the final part. Debinding being the process whereby the carrier/binder system is removed from the part to create a powder compact retaining the required geometry. Sintering being the final step where the metal powders are consolidated into a fully dense metal part of net shape. The feedstock binder consisted of water soluble polyethylene glycol that reduced feedstock viscosity, improved particle wetting, aided greenpart shape retention and eliminated toxic solvents in debinding. Carnauba wax and bees wax aided dispersion, lubricated particles, were safe to handle and better for the environment (than petroleum waxes). Their low melt temperatures aided removal during thermal debinding and supported residue elimination. By optimising the ratio of water soluble, wax and polyolefin binder components (3: 2: 1 respectively) for melt flow and pellet formation, greenparts defect free with uniform particle distribution were made. The optimal binder system proved suitable for titanium alloy and irregular shape pure titanium powders (hydride-de-hydride). Increasing powder loading (wP = (0.60 to 0.65)) had no appreciable effect on viscosity while enabling feedstock with good uniformity and pellet formation. Dimensional change was not affected by uniformity of the feedstock however molecular weight, volume and dispersion of binder components affected interparticular distances. Low processing temperatures reduced disruption to part geometry, benefitted particle bonding and helped retain handling strength. The use of low temperatures for thermal debinding (t = 250 °C) enabled removal of the binder below the temperatures that facilitate interstitial diffusion and oxide/carbide formation, although part thickness, mass and overall volume effected the processing time. A strong correlation was seen between handling strength of the greenparts and defects, such as non-uniform density distribution and cracking after sintering. Sintering was essential to produce the final part and showed that a binder free brownpart was not the only criteria for eliminating impurities. The furnace atmosphere must remain free from contamination to eliminate transfer back to the parts. This was addressed using an argon sweep gas, however, the design and efficacy of the system was considered inadequate. Decomposition products need to be removed quickly from the furnace as they evolve before impurities from the sweep gas diffuse back into the parts during the extended duration at sinter temperatures (t = 1300 °C). The combination of an optimised titanium feedstock and the use of a low temperature thermal debinding technique produced a consolidated MIM part of relatively large dimensions. The parts were seen to have uniform microstructure throughout the cross-section with density comparable to that of MIM standards. In difference to the literature, a high powder loading (φp = 0.65) of HDH powders was used and shown to be readily mouldable. The higher powder loading also eliminate separation defects and shape distortions evident using lower amounts of powder.

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  • Governance of International Rivers: Threats, Gaps and Challenges

    Raman, Durgeshree Devi (2015)

    Doctoral thesis
    University of Waikato

    In light of the growing water shortages world-wide and concerns over freshwater disputes arising from essentially a growing world population, an increase in per-capita consumption and the limited supplies of freshwater resources, this thesis looks at issues of governance of international rivers in terms of threats to them, gaps in their governance regimes and challenges associated with closing those gaps. International river basins globally are currently threatened with over-extraction, pollution, damming and infrastructural development as well as the impact of climate change. If left unaddressed, the pressure on the international river basins, as riparian States compete for its limited supplies, is only going to exacerbate any chances of freshwater disputes between them. The United Nations Convention on the Non-Navigational Uses of International Watercourses offers a guidance framework to enable riparian States of international rivers to achieve ‘equitable utilization’ of water resources as well as management of the basin in order to avoid freshwater disputes. This thesis analyses the adequacy of the Convention to address the four main threats. The analysis is supplemented by the Berlin Rules, international cases and arbitral awards. The thesis has also undertaken a study of the European regional framework as an example of best regional practice, given that it not only has a similar Convention to the UN Watercourses Convention being the United Nations Economic Commission for Europe’s Convention on the Protection and Use of Transboundary Watercourses and International Lakes, but it also has other pieces of legislative and policy documents to guide the European Union States to achieve the paramount objective of the EU water policy, which is ‘good ecological status’ for all its water bodies by 2015. This is to ensure sustainable water supply for its current and future populations. In order to test the viability of the UN Watercourses Convention against individual basin’s legal regimes, the thesis has taken the Jordan, the Nile and the Indus River Basins as case studies as they are already considered to be ‘hot spots’ for freshwater disputes and the four main threats to them, which if not adequately addressed, will only aggravate the already existing tension. The analysis of the case studies’ legal regimes involve an examination of the extent of the specific threats in each river basin and the strengths and weaknesses of each governance regime in order to ascertain where it is lacking. In order to enable an international legal framework that is apt to guide riparian States to deal with any of the four main threats to any international river basin, this thesis proposes recommendations for changes to the UN Convention based on other sources of international law and policy, the EU framework as well as the strengths of the governance regimes of the case studies. In order to minimize any chances of freshwater disputes and increase water security in the case studies, the thesis also makes recommendations for improvement to each legal governance regime based on international law and policy, the EU framework as well as the strengths of the governance regime of the other case studies. In doing so, this thesis provides a comprehensive overview of the current international law, policy, case law and arbitral awards relating to each major threat that has been identified. It also highlights the progress being made in addressing these threats in the European region through the practical application of the relevant treaties, directives and policy documents. Finally, it puts together the legal responses that are required to effectively address the four main threats in the Jordan, the Nile and the Indus River Basins.

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  • Elucidating the Origin of Tetrodotoxin in Pleurobranchaea maculata and Stylochoplana sp.

    Salvitti, Lauren R. (2015)

    Doctoral thesis
    University of Waikato

    Tetrodotoxin (TTX) is an extremely potent neurotoxin that acts by selectively targeting voltage gated sodium channels blocking propagation of action potentials. Long believed to be present only in pufferfish, TTX has now been detected in a wide range of phylogenetically unrelated terrestrial and aquatic taxa. Despite decades of research the exact origin of TTX remains a mystery. Current literature supports three hypotheses: endogenous, symbiotic bacteria, or bioaccumulation through a dietary source. In 2009, the opisthobranch Pleurobranchaea maculata (grey side-gilled sea slug) was found to contain high concentrations of TTX in New Zealand. A large collaborative project, of which my research was a major part of, was initiated to explore the origin of TTX in P. maculata. During extensive benthic surveys conducted to identify possible dietary sources of TTX, high concentrations (ave. 380 mg kg-1) were detected in Stylochoplana sp. (Platyhelminthes) from Pilot Bay (Tauranga, New Zealand). Tetrodotoxin concentrations were found to vary temporally, peaking between June and August. The co-occurrence of Stylochoplana sp. and P. maculata in Pilot Bay raised the possibility that Stylochoplana sp. could be a dietary source of TTX for P. maculata. A real-time PCR assay was developed, and detected Stylochoplana sp. in seven out of nineteen P. maculata foreguts. Symbiotic bacterial production of TTX in the tissues of P. maculata and Stylochoplana sp. was also explored. Isolated strains (102; 17 unique strains - identified using 16S rRNA gene analysis) were analyzed using a recently developed method to detect the C9 base of TTX. In addition to enhanced sensitivity, this method has the advantage that it might detect precursor and degradation products. To explore the possibility that TTX is produced by a consortium of bacteria, experiments were undertaken where homogenized tissue was spiked into marine broth and samples were collected over two weeks for toxin and molecular analysis. No C9 base or TTX production was detected in isolates or from bacterial communities, suggesting that a symbiotic microbial source of TTX is unlikely in these organisms. The ability of non-toxic P. maculata to sequester TTX from an environment known to contain toxic populations of the same species was also assessed. Sixteen non-toxic specimens were kept in mesh cages (eight anchored to the benthos and eight suspended 0.5 m above it) for eight weeks and fed a non-toxic food source. Toxin analysis revealed that more ‘benthic’ specimens (4 verses the 2 from suspended specimens) sequestered TTX and were shown to retain higher concentrations (max. 0.79 versus 0.43 mg kg-1). These data suggest a localized microbial source of TTX that is more readily available from the benthos. Diet analysis, utilizing next generation sequencing of toxic and non-toxic P. maculata identified their diet comprised a wide array of organisms, with Thelepus sp. and Plumularia sp. being prevalent in toxic individuals, and further testing of these organisms is suggested. Lastly, immunohistological methods, employing a monoclonal antibody targeting TTX, were conducted with tissues from P. maculata and Stylochoplana sp.. Strong TTX signals were detected in the mantle and oocytes of P. maculata and the ova and pharynx of the Stylochoplana sp.. These data suggest ecological roles for TTX including: defense in adults, protection in progeny, and prey capture in Stylochoplana sp.. A synthesis of the studies presented in this thesis, and those that were conducted as part of the larger project, are also presented and future studies to elucidate the origin of TTX in New Zealand taxa are suggested.

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  • The Moriori. The integration of Arboriculture and Agroforestry in an East Polynesian Society

    Maxwell, Justin James (2015)

    Doctoral thesis
    University of Otago

    The Chatham Islands were a challenging environment for East Polynesian colonisers. The successful long term settlement of these islands can be attributed to the first people applying and adapting Polynesian strategies to the colonisation of an unfamiliar environment. Previous studies have suggested that settlement and subsistence practices were entirely focused upon the collection of wild plants and fauna, throughout the Moriori sequence with a heavy dietary reliance on one marine species, the New Zealand fur seal (Arctocephalus forsteri). This interpretation is not consistent with the results of this research. In this thesis a holistic multi-proxy research design is used to identify terrestrial plant use by Moriori and the landscape modification which is associated with the introduction of East Polynesian subsistence practices. The primary data sets employed are the ethnographic and historical accounts of Moriori subsistence, archaeological investigations of the broad-leaved forests and associated sites, anthracological and palynological analyses to identify past vegetation regimes and the anthropogenic effects, and to date when humans began to modify the environment. The results suggest that after an initial period of rapid population growth, even though marine mammals were still available in large numbers, the first settlers began to modify the environment to increase terrestrial production. It is argued that the environmental changes occurred in part to increase the productivity of wild plants, particularly bracken fern (Pteridium esculentum). The most important change to the vegetation was the intentional introduction and management of the mainland New Zealand endemic tree Corynocarpus laevigatus. The broad-leaved forests, a previously under-researched component of Moriori subsistence, are shown to have been actively managed by Moriori. They were an integral component of the subsistence practices in the ‘late’, post-1650AD, Moriori sequence. The introduction and cultivation of Corynocarpus laevigatus was essential to the long term colonisation of the Chatham Islands in the absence of the standard tropical East Polynesian cultigens.

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  • Life history and distribution of mysid species in a large open estuary

    Bierschenk, Beate Monika (2015)

    Doctoral thesis
    University of Otago

    In the highly dynamic environment of an estuary, environmental factors such as salinity, temperature, light and hydrodynamics as well as biogenic factors such as predator/prey interactions influence the population dynamics of estuarine species. The aim of my study was to explore the potential for resource partitioning between four commonly co-existing estuarine mysid species, Tenagomysis chiltoni, Tenagomysis novae-zealandiae, Tenagomysis macropsis, and Gastrosaccus australis, by investigating their life histories, seasonalities and distributions within an estuary. Mysid samples were collected along the shoreline (water depth: 0.5 – 0.6 m) of the Taieri Estuary (South Island, New Zealand) using a sweep net and in the deeper water (water depth: 4 – 6 m) with a set of 3 drift nets. A lateral segregation in the estuary was found between the two hyperbenthic species, T. chiltoni and T. novae-zealandiae, and the two benthopelagic species, G. australis and T. macropsis with hyperbenthic mysids mainly occurring in the shallow waters along the estuary shoreline and benthopelagic species in deeper central-channel waters. The life cycle and breeding dynamics of all four mysid species were similar to those described in the literature for other temperate estuarine mysid species, although the breeding period in the study estuary was noticeably shorter than in estuaries of lower latitudes in New Zealand and elsewhere. The observed seasonal migrations and life-stage specific segregation between adults and juveniles may reduce competition, inter-specific predation, and cannibalism by allowing different life stages to utilise the same habitats or food sources, but at different times. Water temperature seems to play a key role for the timing of the breeding season, abundance, and reproductive effort, whereas salinity, total suspended solids and phytoplankton biomass (measured as chlorophyll a) were associated with the distribution of the mysid species. Thus, the spatial distribution of these four mysid species within the Taieri Estuary reflects the complex linkages and interactions between favourable temperature and salinity conditions, food availability and reproduction. As a consequence of confirming the lateral and longitudinal segregation of species and life history stages within the estuary, the question arose of how relatively small aquatic organisms, such as mysids, orient themselves in a large three-dimensional body of moving water. Therefore the role of turbulence as an orientation aid was investigated in a flume tank experiment, using Gastrosaccus australis as the test organism. The mysids actively tracked areas of shear, when turbulence was present, but favoured reduced flow in the absence of turbulence. These different swimming responses might be an adaptation of G. australis to its pelagic habitat. By moving to reduced flow areas in an absence of mid-water turbulence, mysids could avoid seaward displacement. Change in riverine management such as by water abstraction, damming for hydropower plants, or extreme weather events associated with climate change will impact distribution, densities and population dynamics of the resident mysid species in estuaries. These changes in abundance or, in the worst case scenario, even the loss of mysid species could potentially have severe consequences for estuarine food webs, which may result in decreased food availability and therefore impact the nursery function of estuaries for commercial fish species.

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  • Screening for Antisocial Development

    Tyler-Merrick, Gaye Margaret (2014)

    Doctoral thesis
    University of Canterbury Library

    Teachers report that there are an increased number of students engaging in persistent antisocial behaviour in their classrooms. Teachers need to identify these students early because if there is early identification then there is the potential for early intervention, which in turn may prevent negative long-term outcomes for these students as well as long-term costs to society. The aims of this study were (1) develop a psychometrically sound, cost effective, three-step multiple gating behaviour screening procedure that teachers could use in their kindergarten/classroom so that they could identify those students at-risk of antisocial development, (2) examine if the third gate of this procedure was necessary for the accurate identification of these students, and (3) could such a screening procedure be adapted for classroom teacher use in New Zealand kindergartens and schools. Forty eight teachers from three kindergartens and 10 primary/intermediate schools volunteered for the study, of which 34 teachers completed all three gates of the screening procedure. Results indicate the three gate screening procedure was easily adapted for kindergarten and classroom use with, at Gate 3, teachers’ self-recording 30 direct observations of a nominated and control student during their normal teaching lesson with good accuracy. All three gates were effective in identifying those students at-risk of antisocial development but Gates 1 and 2 were the most effective in terms of accuracy, time and resourcing. The teachers found the three gate procedure manageable, required very little training and did not interrupt classroom routine or schedules. The implications of these findings are discussed.

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  • International Student Mobility and Internationalisation of Universities - The role of serendipity, risk and uncertainty in student mobility and the development of cosmopolitan mind-sets through knowledge and intercultural competence. Employability, students’ future mobility aspirations and the EU’s support of international student mobility

    Weibl, Gabriel (2014)

    Doctoral thesis
    University of Canterbury Library

    The background to this study lies in the discrepancy between the perceptions of international student mobility in the context of the internationalisation of higher education by the EU and universities on one hand and international students themselves in terms of their motivations to study abroad on the other hand. This is a comparative study based on three main case studies, of six universities in New Zealand, Oxford University in the UK and the Charles University in the Czech Republic. It explores the students’ experiences abroad in terms of their intercultural competence, the shaping of identities, the acquisition and transfer of knowledge, the possible forming of cosmopolitan mind-sets and empathy, perceptions of employability and their future mobility aspirations. This thesis also considers the barriers and ‘push and pull’ factors of mobility, perceptions of risk and uncertainty in regards to mobility and the role of serendipity in student mobility, which has been overlooked in the literature on mobility and migration. The theoretical framework of the study builds on social capital theory, Europeanisation and the ‘do-it-yourself biography’ theory. The nature of this topic, however, suggested the employment of the concepts of globalisation, transnationalism and consideration of other forms of capital, such as the total human capital, mobility capital and transnational identity capital. This is predominantly a qualitative, mixed-method and longitudinal research project, which uses surveys, case studies, interviews and the data collecting tool called grounded theory. It triangulates data to support and enhance the analytical validity of the thesis. This research concludes that student experiences abroad as well as the internationalisation efforts of universities and the EU would benefit from the introduction of education for global citizenship, which should focus on the intercultural competencies of students. The thesis suggests sociocultural elements for example the cosmopolitan mind-set can enhance the economic, academic and political rationales of internationalisation, such as employability.

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  • Discovery of novel circular replication-associated protein encoding single-stranded DNA viruses in ecosystems using viral metagenomic approaches

    Dayaram, Anisha (2015)

    Doctoral thesis
    University of Canterbury Library

    The introduction of next-generation sequencing (NGS) technologies has dramatically changed the field of virology, with many significant discoveries of novel circular replication-associated protein (Rep) encoding single-stranded (CRESS) DNA viruses. Traditionally, most research into CRESS DNA viruses has often focused on investigating plant and animal pathogens that are of significant economic importance. This research has led to the discovery and establishment of three different CRESS DNA families including Geminiviridae, Nanoviridae and Circoviridae, which infect eukaryotes. CRESS DNA viruses can have single or multicomponent genomes, with the latter requiring all components for infection. CRESS DNA viruses have circular single-stranded DNA (ssDNA) genomes with at least one protein encoding a Rep which is responsible for viral replication. It has been shown that CRESS DNA viruses are able to evolve rapidly with nucleotide substitution rates that are similar to those observed in RNA viruses. The Rep gene has conserved regions known as motifs which are often used to determine relatedness between CRESS DNA virus. NGS has expanded our knowledge on the diversity of novel CRESS DNA viruses. Viral genomes are now routinely recovered from different sample types without any prior knowledge of the viral sequence. This has led to the development of the field of viral ecology. This field places an emphasis on viruses being one of the most abundant organisms on earth, and are therefore likely to play a major role in ecosystems. Environmental metagenomic studies have isolated CRESS DNA viruses from sea water, freshwater, faecal matter from various animals, soil, the atmosphere, sediments and sewage; dramatically increasing the known CRESS DNA viral genomes in the public domain. These studies are shedding light on the distribution of CRESS DNA viruses, as well as providing baseline data for future studies to examine virus-host interactions, community structure and ultimately viral evolution. Vector enable metagenomics (VEM) is another novel approach utilising NGS techniques for discovering CRESS DNA viruses. As many plant-infecting CRESS DNA viruses such as geminiviruses and nanoviruses are vectored by insects, this approach exploits this mechanism by using insect vectors as a surveillance tool to monitor and survey these viruses circulating in ecosystems. Recent studies have used these methods to identify known viral plant pathogens as well as novel viruses circulating in insect vectors such as whiteflies and other higher order insects such a mosquitoes and dragonflies. These approaches successfully demonstrated that VEM can be used as a unique method, with the first mastrevirus discovered in the new world being recovered from dragonfly species Erythrodiplax fusca using this approach. The research in this thesis uses metagenomics to survey CRESS DNA viral diversity in different organisms and environments. Two hundred and sixty eight novel CRESS DNA viruses were recovered and verified in this study from a range of sample types (adult Odonata, Odonata larvae, Mollusca, benthic sediment, water, Oligochaeta and Chironomidae) collected in the United States of America, Australia and New Zealand. All viral genomes isolated had two major proteins encoding for a putative Rep and coat protein (CP), with major Rep motifs identified in most Reps. Phylogenetic analysis of the Reps encoded by the viral genomes highlighted that most were extremely diverse falling outside of the previously described ssDNA viral families. A top-down approach was implemented to recover CRESS DNA viruses and possible viral pathogens from Odonata and their larvae. Thirty six viral genomes were recovered from terrestrial adult dragonflies as well as the twenty four from aquatic larvae. Dragonfly cycloviruses were isolated from the some adult Odonata species which were closely related to the isolates previously described by Rosario et al. (2012). The viruses isolated in the aquatic and terrestrial ecosystems differed substantially indicating that different CRESS DNA viromes exist in both land and water. The diversity of CRESS DNA viruses in seven different mollusc species (Amphibola crenata, Austrolvenus stutchburyi, Paphies subtriangulata, Musculium novazelandiae, Potamopyrgus antipodarum, Physella acuta and Echyridella menziesi) from Lake Sarah and the Avon-Heathcote estuary both in New Zealand, were also investigated. One hundred and forty nine novel viral genomes were recovered. Two CRESS DNA genomes were recovered from molluscs which have Rep-like sequences most closely related to those found in some bacterial genomes. Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) was originally isolated from fungal species Sclerotinia sclerotiorum in china and was later found in benthic sediments in New Zealand. As part of this study, SsHADV-1 was recovered from dragonflies (Erythemis simplicicollis, Ischnura ramburii and Pantala hymenaea) collected in Arizona and Oklahoma, USA suggesting a larger distribution of these viruses and not surprising given the near global distribution of S. sclerotiorum. Dragonfly larvae-associated circular DNA viruses (DflaCVs) that were originally isolated in Odonata larvae samples from three New Zealand lakes were later recovered from water, benthic sediment, worms and molluscs from one of the lakes initially sampled, suggesting that these viruses are ubiquitous in freshwater environments. This study has attempted to generate baseline data of CRESS DNA viruses in certain environments using NGS-informed approaches. This data was used to try and establish whether viral distribution in different samples types can potentially be explained by the food web interactions between different samples types. Although the analysis did not show any significant relationships between sample type interactions and viral distribution a few common associations between Odonata larvae and benthic sediment were evident. This was expected as the larvae live within the sediment so it could be assumed that they potentially have similar CRESS DNA viral distribution. Although the distribution of viruses varied across sample types, molluscs proved the best sampling tool for isolating largest numbers of CRESS DNA viruses in an ecosystem with extensive diversity. Overall, this research demonstrates the applications of NGS for investigating the diversity of CRESS DNA viruses. It demonstrates that some sample types such as Odonata in terrestrial systems and molluscs in aquatic environments, can be used as effective sampling tool to determine the diversity of CRESS DNA viruses in different environments as well as detecting previously isolated viruses. The CRESS DNA viruses isolated in this body of work provides baseline data that can potentially be used in future research to investigate hosts of these viruses and their interactions with hosts and potential flow in their environments.

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  • From Disordered Bosons to Dipolar Fermions - Theoretical Studies in Ultracold Atoms

    Towers, Joseph (2015)

    Doctoral thesis
    University of Otago

    We use numerical simulation to study ultracold, quantum degenerate, atomic gases. In the first part of the thesis we study the effects of disorder, introduced via a bichromatic optical lattice, in one and two dimensional systems. We employ the Aubry-Andr\'{e} model and use time-dependent numerical simulations to investigate the disorder dependent transition to strong localisation present in the model. Weak s-wave interactions are added to the model and we observe the interaction between localisation and interaction induced self-trapping. We then add a tilted lattice potential to the model. In the homogeneous model this induces Bloch oscillations. While one might expect that a strong enough force will break the strong localisation or self-trapping, within the bounds of the single-band model, the trapping effect of the Bloch oscillations reinforces both of the other effects leading to increased confinement, albeit lacking the clear single frequency oscillation signature of pure Bloch oscillations. Along with the two dimensional bichromatic optical lattice we add a term to the Hamiltonian equivalent to that of a uniform external magnetic field on charged particles. Since the experimental realisation of this model would employ neutral atoms, the magnetic field is synthetic, the equivalent effect being produced by an appropriate set of lasers and magnetic fields. We show that in the ballistic regime (weak bichromatic disorder) the system displays positive magnetoresistance. Conversely in the strong localisation regime the system exhibits negative magnetoresistance. In the latter part of the thesis we use density functional theory to calculate the ground-state density of a harmonically trapped dipolar Fermi gas. We then use these to calculate the lowest energy collective mode oscillation frequencies under the hydrodynamic approximation. We find that increasing the strength of the dipoles has the effect of increasing the mode frequencies. The increase saturates for large dipole strengths. We verify this analytically and show that such is due to the local nature of the two dimensional energy functional and not dependent on the specific equation of state. We employ an average density approximation to construct an energy functional for the inhomogeneous, 2D degenerate Fermi gas. The ground-state densities for a cylindrically symmetric harmonic trap are compared to the Kohn-Sham results, showing extremely good agreement in the tail region and good agreement with the exact ground-state energy. We then do the same for higher order polynomial traps and obtain improved agreement for higher degree.

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  • An Improved Human Anxiety-Specific Biomarker: Frequency Band, Modality Specificity, Personality, Pharmacology, and Source Characterisation

    Shadli, Shabah Mohammad (2015)

    Doctoral thesis
    University of Otago

    Anxiety disorders are among the most common mental illness in the western world with a major impact on disability. But their diagnosis has lacked objective biomarkers. McNaughton and colleagues previously developed a human EEG anxiety biomarker, goal-conflict-specific-rhythmicity (GCSR) in the stop signal task (SST). However, their version of the SST had some statistical limitations and was not suitable for clinical translation because of the narrow band GCSR and frequency shifts between experiments. Our aim was to modify the SST in a way that would overcome all the statistical limitations and produce larger amplitude GCSR. Go-stop (approach-avoidance) conflict in the SST generates rhythmic activity in the right frontal area as a result of activation of the behavioural inhibition system. We developed an SST in which short and long stop signal delays (SSDs) were controlled by average Go reaction time, while intermediate SSDs tracked 50% correct stopping to maximise goal conflict. This new procedure provides balanced numbers of trials across delay groups and prevents overlap in their values. Right frontal (F8) GCSR was extracted as the difference in EEG Fourier power between matching stop and go trials of a quadratic contrast of the three delay values (subtraction of average EEG power of short and long SSDs from the EEG power of intermediate SSD). Separate experiments assessed frequency spectrum (with both visual and auditory stop stimuli), personality relations, drug sensitivity (both auditory and visual stop stimuli) and source localisation. GCSR had a frequency range (4-12Hz) similar to that of rodent hippocampal rhythmical slow activity (RSA); correlated significantly with trait anxiety scores in initial and later blocks; and was reduced by three chemically distinct anxiolytic drugs in the auditory SST (administered double-blind): buspirone (10mg), triazolam (0.25mg), and pregabalin (75mg) and two chemically distinct anxiolytics; buspirone (10mg) and triazolam (0.25mg) in the visual SST. This anxiolytic drug sensitivity was similar to that of the rodent RSA assay from which GCSR was derived. GCSR was located in the medial frontal gyri, right inferior frontal gyri and superior frontal gyri, known to control SST stopping. GCSR, measured in our new form of the SST should be suitable as a biomarker for one specific type of anxiety disorder in testing of groups of anxiety disorder patients and in the development of measures suitable for individual diagnosis.

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  • Seizure-induced cardiomyopathy: Benefit of Atenolol

    Read, Morgayn (2015)

    Doctoral thesis
    University of Otago

    Epilepsy affects 1-2% of the population in New Zealand and is associated with an increased mortality rate of two to three times that of the general population. This thesis examines the effect of seizures on cardiac function, as it is hypothesised that seizure-induced activation of the sympathetic system produces electrographic (ECG) abnormalities, cardiac dysfunction and structural damage. Using a rodent model, seizures were induced using the excitotoxin, kainic acid, either subcutaneously or via an intrahippocampal drug cannula. The first section of this study demonstrated that systemic kainic acid administration produced generalised seizure activity developing to status epilepticus. Kainic acid administration produced an immediate drop in heart rate (by 28%) associated with bradyarrhythmias. This was followed by a progressive increase in seizure severity which coincided with the development of tachycardia, QTc prolongation and T wave elevation. Heart rate variability analysis demonstrated that seizure activity resulted in significant changes in autonomic function. Prophylactic therapy with atenolol or clonidine attenuated seizure-induced ECG changes and preserved normal cardiac morphology. The second half of this thesis used an improved model of seizure in which kainic acid was administered directly into the hippocampus to prevent possible systemic effects. The results in this study clearly demonstrated that seizures produced cardiac dysfunction, particularly changes in heart rate, QTc interval and blood pressure. Seizure-induced cardiac dysfunction resulted in significant structural damage as early as 48 hours which was still present up to 28 days after the original seizure induction. Assessment of autonomic function using various techniques demonstrated that seizures resulted in an increase in plasma noradrenaline levels and enhanced sympathetic dominance at 48 hours. The seizure-induced tachycardia which ensued resulted in the development of dilated cardiomyopathy with significant cardiac structural injury. The formation of cardiac micro-lesions and fibrotic deposition is suggested to contribute to left ventricular dysfunction and an increased susceptibility to arrhythmia induction. Intervention therapy with atenolol, 60 minutes post seizure induction, preserved cardiac function and structure. Importantly, atenolol reduced the susceptibility to arrhythmia onset, which has been reported as a contributor to sudden death in epilepsy. Interestingly, atenolol treatment during seizures also reduced EEG and behavioural score severity and protected the hippocampus from injury. Attenuation of seizure activity with diazepam did not reduce the extent of cardiac dysfunction. Diazepam-treated animals had significantly higher blood pressure, left ventricular dilation and an increased susceptibility to arrhythmia induction. However, combination therapy with atenolol and diazepam, proved effective at protecting both the heart and brain following seizure activity. This thesis has consistently demonstrated that atenolol administration (prophylactic or intervention) offers significant protection against seizure-induced cardiomyopathy. Atenolol, therefore, should be considered for clinical use, prophylactically in epilepsy or as a rescue intervention during status epilepticus. Importantly, this study clearly demonstrates that atenolol in combination with diazepam offers superior therapeutic benefit, over either monotherapy, in an animal model of status epilepticus.

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