1,023 results for Doctoral, 2011

  • 'An education system characterised by equity' : a critical evaluation of educational change in Samoa, 1995-2005 : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Education at Massey University, Palmerston North, New Zealand

    Male, Alan G R (2011)

    Doctoral thesis
    Massey University

    The problem investigated in this thesis arose from my professional practice as a consultant with regard to educational reforms in a number of countries, including Samoa. This created an initial interest in why different policy options were chosen by different countries in response to similar problems. Observation of the implementation of reforms in various contexts also created questions as to why the implementation of reforms often seemed to lead to new formulations of the original arrangements, resulting in development but little change. A prior review of evaluations of educational reform programmes showed that many educational evaluations are confined to matters of technical advice inputs, resource management and the achievement of milestones. This study however, considers other factors relevant to the successful achievement of an educational reform programme situated within a particular social, political and historical context. In particular, this thesis reports on a critical evaluation of the development, between the mid-1980s and 1994, of a policy aimed at producing an education system “characterised by equity” (Department of Education, 1995) in Samoa and then on the results of the implementation of that policy between 1995-2005. The study focused first on the differences in the performance of student groups based in the national Year 8 secondary school selection examination and in their subsequent access to secondary schooling and to the achievement outcomes in Year 12 over the period between 1994 and 2008. Information was gathered through analysis of national examination results databases. Additional information was gathered through interviews and questionnaires from senior educational system managers and from the principals of a sample of four secondary schools. Questionnaires, aimed at gathering socio-economic data, were administered to 2000 students and their families from Years 9, 11, 12 and 13 at the sample schools. The evidence showed little change in the patterns of achievement between advantaged and disadvantaged groups. The system had expanded but the patterns of inequity remained unchanged. The reasons for the selection of the reform options that resulted in the maintenance of disparities through the 1995-2005 programme were found in the history, culture and political setting of Samoa. Because of the small size and ethnic and cultural homogeneity of the population, the evaluation was based on the theories of Pierre Bourdieu. Bourdieu’s concepts of field practice and habitus showed how the policy options included in the reform programme were influenced by an underlying habitus that generated the desire for change but also constrained the achievement of the stated aim of a “system characterised by equity”. The research showed how the historical background to the patterns of advantage within the system and the structure and patterns of advantage that resulted from the reforms continued beyond the reform.

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  • The effects of digestion resistant carbohydrates on the colon microbiota and colon tissue transcriptome of weanling rats

    Young, Wayne (2011)

    Doctoral thesis
    University of Otago

    Digestion-resistant carbohydrates (DRC) in the diet pass to the terminal ileum and large bowel where they may be fermented by resident bacteria. The bacterial communities in the bowel of young animals undergo dramatic shifts in composition following weaning. These compositional and associated biochemical changes may have long-lasting impacts on the host. However, the mechanisms by which diet induced changes in the microbiota influence host physiology requires further investigation. This study examined whether bacterial community compositions could be engineered by supplementing the diet of newly-weaned rats with different forms of DRC and the subsequent effects these altered microbial communities had on host physiology. Newly weaned conventionally raised or germ-free male 21-28 day old Sprague-Dawley rats were fed a basal diet or basal diets supplemented with DRC at concentrations up to 5% for 14 or 28 days. Colonic digesta was collected from each rat for analyses to determine short chain fatty acid (SCFA) concentrations and to compare bacterial community structure by temperature gradient gel electrophoresis (TTGE) and 454 pyrosequencing analysis of the V3 hypervariable region of the 16S rRNA gene. DRC induced alterations in the host transcriptome were assessed by microarray analysis of RNA extracted from colon tissue. Feeding DRC significantly increased concentrations of SCFA in the colon digesta of young rats. The DRC induced changes in SCFA concentrations were also accompanied by alterations in the colonic microbiota structure. Each type of DRC altered the microbiota in a distinctive manner, which could be clearly differentiated from those of rats fed the basal diet. Feeding DRC also resulted in more uniform microbiota compositions compared to the basal diet. The alterations in microbiota composition were associated with changes in host colon gene expression profiles. Each form of DRC altered colonic gene expression in a distinct manner with profiles from rats fed the same diet showing greater similarity than those fed different diets. Differentially expressed genes in the colon were involved in a number of biological functions including energy metabolism, immune function, and cellular growth and differentiation. Comparisons of the effects of DRC on host gene expression between conventionally raised and germ-free rats showed that the resident microbiota was a determining factor of the host response to DRC. Feeding DRC to conventionally raised rats resulted in the differential expression of different sets of genes compared with feeding DRC to germ-free rats. The results of this study show that the bacterial communities in the colon of newly-weaned rats can be engineered by supplementing the diet with DRC. Using this approach, unique bacterial communities with enhanced fermentative capacity, increased uniformity, and distinct effects on host gene expression were selected. The findings from this study provide support and future scope for the development of different dietary supplements that target different parameters of large bowel function.

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  • The effect of intermittent and continuous hypoxia on cerebral vascular function in humans

    Peebles, Karen Clendon (2011)

    Doctoral thesis
    University of Otago

    The extent to which systemic hypoxia may compromise cerebrovascular function is likely to depend on the intensity and duration of the hypoxic insult. This thesis presents four studies that used a range of intermittent and continuous hypoxic paradigms that examined i) whether hypoxia alters cerebrovascular reactivity during acute alterations in the partial pressure of end-tidal CO2 (PETCO2) and end-tidal O2 (PETO2); and ii) whether reductions in cerebrovascular reactivity were mediated by changes in nitric oxide (NO). As a secondary goal, the impact of alterations in peripheral chemoreceptor (PCR) activity on cerebrovascular function, and on ventilatory (VE) sensitivity were also explored. Blood flow velocity in the middle cerebral artery (MCAv) and cerebral oxygenation, provided indices of cerebrovascular function. Study one demonstrated that acute hypercapnia was associated with the net release of NO from the brain. Therefore, in subsequent studies, cerebrovascular reactivity to hypercapnia, along with complementary NO metabolites (plasma nitrite and NOx [nitrite + nitrate]), was used as a surrogate index of NO bioavailability. Study two examined the effects of chronic (years) intermittent hypoxia (CIH) on cerebrovascular function in patients with severe obstructive sleep apnoea (OSA, apnoea-hypopnoea index > 30 events/h). When compared to a group of appropriate controls, hypercapnic cerebrovascular reactivity was reduced in OSA patients. Since plasma NOx was also reduced, it would seem feasible that this compromise in reactivity was due to a reduction in NO bioavailability. Nevertheless, correlative analysis revealed that the presence of OSA was not the only factor associated with a reduction in hypercapnic cerebrovascular reactivity; a novel finding was that increased age and body mass index were linked as well. Alleviating CIH with 5-6 weeks of continuous positive airway pressure (CPAP) caused no alterations in hypercapnic cerebrovascular reactivity or NO metabolites, but caused a small (4 mmHg) reduction in mean arterial blood pressure (MABP). Study three examined the effects of short-duration intermittent hypoxia [SDIH] and short-duration continuous hypoxia [SDCH]) on cerebrovascular function in healthy participants. For SDIH, participants performed 2 h of repetitive hypoxic apnoeas to mimic OSA (20 s apnoeas; nadir peripheral oxygen saturation [SpO2] ~84%; 30 times/h). For SDCH, participants were exposed to a single hypoxic episode matched in duration (i.e., 20 min) and intensity (i.e., SpO2) to SDIH. Cerebrovascular reactivity and ventilatory sensitivity were assessed during acute PETCO2 alterations under hyperoxic and hypoxic rebreathing in order to provide insight into PCR activity. SDIH (but not SDCH) led to a selective reduction in frontal cerebral oxygenation during hypoxic rebreathing; no concomitant alterations in MCAv or in NO metabolites were observed. One interpretation of these findings is that oxygenation of the frontal lobe was compromised to ensure perfusion of more vital regions of the brain (e.g., brainstem) after SDIH. SDCH (but not SDIH) led to elevations in MABP at rest and MABP reactivity during hypoxic but not hyperoxic rebreathing, likely mediated via PCR activation. No concomitant alterations in VE sensitivity during hypoxic rebreathing were observed possibly due to different rates of recovery for MABP and VE post SDCH; there were no alterations in VE sensitivity during hyperoxic rebreathing. Lastly, in study four, the effect of ~3 weeks of continuous hypoxia on cerebrovascular function and ventilatory sensitivity was examined in healthy sea-level participants following ascent to 5050 m. The main findings were that ascent to 5050 m led to an increase in resting MCAv, and enhanced MCAv reactivity during hypoxic and hyperoxic rebreathing. Alongside a high-altitude induced increase in resting VE , these cerebrovascular responses might serve to maintain oxygen delivery to the brain in the face of hypoxia until other adaptive mechanisms (e.g., an increase in capillary density) that aid oxygen extraction become manifest. Collectively, these findings indicate that the precise effect of systemic hypoxia on cerebrovascular function was contingent on the hypoxic paradigm. Shorter durations of hypoxia (i.e., 2 h intermittent hypoxia and ~3 weeks continuous hypoxia) evoke cerebrovascular responses that may serve to preserve oxygen delivery to vital regions of the brain whereas longer durations of intermittent hypoxia (i.e., CIH, in patients with OSA), is associated with a reduction in cerebrovascular function that may compromise brain function. Furthermore, the findings of this thesis suggest that: i) a reduction in NO bioavailability may contribute to a reduction in hypercapnic cerebrovascular reactivity in patients with OSA; and ii) that alteration in PCR activity may contribute to the elevated MABP after 2 h of continuous hypoxia. Irrespective of the hypoxic paradigm, the cerebrovascular, cardiovascular and ventilatory responses to acute alterations in PETCO2 and PETO2 are complex and inter-related.

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  • Measurement and perceptions: Physical activity in people with low back pain

    Perry, Meredith Amy Claire (2011)

    Doctoral thesis
    University of Otago

    Physical activity (PA) is recommended for the management of low back pain (LBP). This research was undertaken to: establish the use of accelerometers as an outcome measure in studies investigating the free-living PA of people with LBP; explore the free-living PA of people receiving physiotherapy for LBP; and compare patterns of PA between people with acute low back pain (ALBP) and people with chronic low back pain (CLBP). PA was measured with the RT3 accelerometer (Stayhealthy Inc., Monrovia, California, USA) which is an objective measure of PA. In addition, perceptions of being physically active with LBP and the coherence between the lived experience of LBP and physiotherapy management were explored. A review of PA and LBP literature found that while ‘advice to stay active’ is recommended, there is a paucity of research exploring the free-living PA of people with LBP with an objective measure, such as an accelerometer. It is unknown if free-living PA is altered in people with LBP compared to healthy individuals. Likewise, the psychometric properties of many accelerometers are also unknown and this may account for some discrepancies in results. A pilot study was undertaken in healthy volunteers (N = 21) to determine the minimum number of days per week of valid RT3 data required to reliably estimate PA, and the validity and utility of the RT3. The RT3 was found to have acceptable utility and good validity, and a minimum of four days of RT3 data are required to reliably assess PA. A mixed methods (MM) study explored: the responsiveness of the RT3 to measure change in PA, compare patterns of PA between people with ALBP or CLBP (N = 111); and semi-structured interviews were conducted with a sub-group of the LBP participants to explore perceptions of PA (N = 13). The RT3 demonstrated limited responsiveness to perceived change in PA, measured with the Global Rating of Change (GROC), at week six only; perceived PA and measured PA appear to be different constructs. A significant interaction between LBP and week of PA measurement was found. Neither LBP group met the recommendation for sustained bouts of moderate intensity PA per day. Interviewees knew that PA was an important aspect in the management of their LBP. However, being active was dependent on perceived control and this was unrelated to LBP classification. The use of “trial and error” strategies when increasing PA resulted in a flare of LBP, the reinforcement of negative PA beliefs and behaviours, and poor treatment coherence. Further research into the design and psychometric properties of accelerometers is warranted. People with ALBP have different PA patterns to people with CLBP; yet both groups demonstrate an inability to endure sustained and repetitive bouts of moderate intensity PA. People with LBP are unsure how to return to habitual PA. Physiotherapists may need to consider treatment coherence, and provide more time and support for changing unhelpful perceptions and PA behaviours. To conclude, perceptions of PA are not the same construct as objectively measured PA, but both constructs are important.

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  • An Epigenetic Analysis of the Human Placenta

    Macaulay, Erin Cuffe (2011)

    Doctoral thesis
    University of Otago

    The human placenta is a highly specialized organ that is responsible for the survival of pregnancy. During its development, placental trophoblast cells invade into the uterine wall to establish a blood supply for the growing fetus. Previous studies have suggested similarities between the invasive phenotypes of trophoblasts and tumour cells; however, a key difference is that trophoblast invasion is under strict control. Given that epigenetic mechanisms have been linked with the silencing of key regulatory genes in cancer, we hypothesized that the epigenetic regulation of first-trimester placental trophoblasts may provide a mechanistic relationship between placental and cancer growth. Further, although the hypomethylated environment within the pseudo-malignant placenta is unique, its role in facilitating placental function is poorly understood. We sought to document placental-specific epigenetic modifications, taking into account that the origin of the placenta is determined during the earliest stages of embryonic development, when the inner-cell mass is first distinguished from the trophectoderm, and when the inner-cell mass further differentiates into the primitive endoderm and the epiblast. A genome-wide methylation analysis was performed using methylated DNA immunoprecipitation (MeDIP) combined with hybridisation to promoter microarrays to identify differentially methylated gene promoters between first-trimester human placenta and peripheral blood DNA. The promoter methylation of 29 candidate genes was then quantified using Sequenom MassARRAY®. Differential methylation patterns were detected in placental tissues compared to both fetal and adult somatic tissues. The relationship between promoter methylation and gene expression was then assessed using real-time PCR and immunohistochemistry. The promoter methylation of one gene, KCNH5, was found to be lineage-specific: low in all tissues derived from the extra-embryonic lineages (trophectoderm and primitive endoderm) and very high in tissues derived from the embryonic (epiblast) lineage. The dichotomous promoter methylation of KCNH5 was found to regulate the lineage-specific expression of alternative gene transcripts. Interestingly, the KCNH5 promoter that is used in tissues derived from the extra-embryonic lineages, and which shows dichotomous methylation, has recently evolved from a SINE retrotransposon that is present in only humans, old world monkeys and apes. To our knowledge, this the first example of a human transcript derived from the insertion of a SINE element. Finally, the lineage origin of the extra-embryonic mesenchyme has been a topic of longstanding debate. The combined epigenetic and expression profiles of KCNH5 in placental villous stroma provide compelling evidence that the extra-embryonic mesenchyme is derived from the primitive endoderm. Retrotransposons are normally silenced by methylation to prevent genome dysfunction. However, the placenta is becoming increasingly known as a tissue in which retrotransposons are actively transcribed. We observed that the absence of retrotransposon-silencing by methylation permitted the emergence of a placental-specific transcript by allowing the retrotransposon to serve as an alternative promoter for KCNH5. Examination of additional retrotransposon-derived genes in the placenta (INSL4 and ERVWE1) confirmed that dichotomous methylation between embryonic and extra-embryonic lineages is a feature of early development. The finding that the retro-elements in these genes have escaped the normal silencing mechanism suggests that they may have functional roles that are unique to the invasive placentas of humans and recent primates.

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  • Role of NK cells in DC-based immunotherapy of melanoma

    Bouwer, Anthea Lynne (2011)

    Doctoral thesis
    University of Otago

    Natural killer (NK) cells were first identified by their ability to kill tumour or virally infected cells without prior sensitization. In spite of this, the actual role of NK cells in tumour immunotherapy remains controversial. This study therefore set out to investigate the potential of Streptococcus salivarius K12, a gram-positive bacterium that has a history of commercial application as a probiotic in New Zealand, for use as a NK cell adjuvant, applying the therapy using B16.OVA melanoma as a model. To confirm that S. salivarius K12 was able to induce efficient activation of NK cells, I first screened a number of gram-positive and gram-negative bacteria for their ability to induce IFNγ release from NK cells. Using ELISA and fluorescence activated cell sorting (FACS) I found that gram-positive bacteria stimulated a rapid release ( through interaction with self MHC during development. Therefore having a setting where the addition of S. salivarius K12 activates NK cells, I investigated whether these NK cells were recruited to the draining lymph nodes where they could potentially influence the adaptive immune response. A range of adjuvant-activated and S. salivarius K12-activated DC were injected subcutaneously into the flanks of mice and tested their ability to recruit NK cells to the draining lymph node. The adjuvants differed markedly in their ability to recruit NK cells with S. salivarius K12 being the most effective. To determine if activated NK cells would be of benefit in tumour immunotherapy, I investigated the ability of bacterially activated DCs to elicit anti-tumour responses in a B16.OVA melanoma model. Utilizing a therapeutic tumour model where treatment was started three days following tumour inoculation, I found a significant delay of tumour growth in mice that were immunized with ovalbumin-pulsed DC that had been treated for 4 hours with S. salivarius K12 as opposed to other adjuvants tested. I also determined that in vivo depletion of NK cells completely abolished the benefit of DC immunotherapy. A therapeutic tumour experiment where DC were primed in the presence or absence of tumour antigen showed that while NK cells were critical for the antigen-dependent anti-tumour response they did not appear to exert an effector function. To investigate the role of NK cells in priming the anti-tumour response I next utilized a prophylactic setting, where mice were challenged with tumours sixty days after DC immunization. By depleting CD4+/CD8+ T cells and NK cells before time of priming or challenge, I tentatively showed that all three subsets of cells play a role in the anti-tumour response, although NK cells may play a greater role at time of challenge.

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  • Reservations to Human Rights Treaties and the Diversity Paradigm: Examining Islamic Reservations

    Sawad, Ahmed Ali (2011)

    Doctoral thesis
    University of Otago

    This research is a critique of the universalist theory of international human rights treaty law through an analysis of Islamic reservations to four major human rights treaties i.e., Convention on the Elimination of All Forms of Discrimination Against Women (CEDAW), Convention on the Rights of the Child (CRC), International Covenant on Civil and Political Rights (ICCPR) and the Convention against Torture and Other Cruel, Inhuman, Degrading Treatment or Punishment (CAT). Based on my analysis of international treaty law on reservations and State practice relating to reservations to human rights treaties, I have argued that universalist claims of human rights treaties are more of an idea than an established norm. To this effect, I have examined the concept of reservations under international law as contained in the Vienna Convention on the Law of Treaties 1969 (VCLT) and evaluated its applicability to international human rights treaties. In Chapter Two I have contended, firstly, that the VCLT provides a flexible regime for making reservations to treaties and that it does not differentiate between contractual treaties and normative human rights treaties. Secondly, I have argued that the flexible nature of the VCLT regime confirms that international treaty law supports a diversity paradigm which brings together dissimilar consent, particularly in the case of human rights treaties. In Chapter Three I have scrutinised the theoretical debate on the nature of human rights that centres on whether they are universal, relative or pluralist. I have shown that the natural law theories and other transcendentalist justifications of universality of human rights have no cross-cultural validity. I have also pointed out that a posteriori justifications such as minimalist universality, overlapping consensus and relative universality theories are impractical because they attempt to derive a lowest common denominator which diminishes the efficacy of international human rights regimes. In comparison to such universalist theories, alternative human rights theories espouse more inclusive and cross-culturally legitimate approaches. However, I have submitted that theories of cultural relativism provide inadequate explanations of the pluralist State practice in the area of international human rights treaties. In particular, the thick relativist theories fail to explain the existing level of cultural participation in the international human rights regimes. In practice, States parties from different cultural-legal systems cooperate in international and regional human rights regimes through a diversity paradigm that offers pluralist consent on the various normative standards. I have shown that the legitimacy of the diversity paradigm is evident from the State practice of making reservations to human rights treaties. My critique of the reservations made by Islamic States to CEDAW, CRC, ICCPR and CAT, identifies on the one hand, the particular normative conflicts between these regimes and Shari`ah, and on the other hand, the connection between the issues raised in these reservations and the domestic laws of the reserving Islamic States. This examination is important for two reasons: firstly, it demonstrates the extent to which the Shari`ah-based reservations are actually legitimate within the cultural-legal system of the reserving States, and secondly, it helps in understanding the level of juridical flexibility that is available in these reservations. This thesis establishes that the practice of making reservations to international human rights regimes runs counter to theories of ontological universality of human rights. In the case of Shari`ah-based reservations, it reveals that Islamic States are reluctant to forfeit or bargain on certain precepts of Islamic law that are perceived to contradict normative human rights such as absolute freedom of religion and same rights of married spouses. At the same time, it suggests that Islamic States accept the large majority of human rights norms, and make exceptions to only a few select human rights. In addition, the thesis also proposes that the flexible reservations regime of the VCLT provides an effective mechanism for the Islamic States to engage and participate in international human rights treaties, in spite of the reservations. The principal contribution of this study is that it provides a hermeneutic tool - the diversity paradigm - for understanding the plurality of human rights treaty law. I have established that international treaty law on reservations and State practice of making reservations to human rights treaties confirm the existence and validity of a diversity paradigm in the current human rights discourse. The diversity paradigm approach can play a constructive role in delineating the ontological or philosophical argument for the universality of human rights and the actual State practice of committing to and implementing human rights treaties. With the help of this hermeneutic tool I have established that a flexible, international treaty law based approach to human rights treaties is more effective in the propagation of human rights norms in diverse cultural-legal environments as noted in this case study of the reservations to human rights treaties made by Islamic States.

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  • Interaction between COMMD family proteins and the epithelial sodium channel

    Liu, YongFeng (2011)

    Doctoral thesis
    University of Otago

    The epithelial sodium channel (ENaC) is located at the apical membrane of many epithelial cells throughout the body and mediates Na+ influx into epithelial cells. Classical ENaC is made up of three similar subunits, α, β and γENaC subunits. ENaC provides the rate-limiting step for Na+ reabsorption in the distal nephron and therefore controls the extracellular fluid volume and blood pressure. ENaC activity at the cell surface is tightly regulated to maintain Na+ and fluid homeostasis in the body. A number of regulators of ENaC have been identified, including COMMD1 (copper metabolism Murr1 domain containing 1). COMMD1 belongs to a ten-member COMMD (copper metabolism Murr1 domain containing) family whose members all share a C-terminal COMM domain. Previous work in our laboratory has reported that COMMD1 interacts with the α, β, and γENaC subunits via its COMM domain and down-regulates the amiloride-sensitive Na+ currents generated by αβγENaC. Thus, it was hypothesised that other COMMD family members might also interact with ENaC and down-regulate ENaC activity. Therefore, the aims of this study were (1) to study the interaction between the COMMD family proteins and the ENaC subunits. (2) To investigate the effect of COMMD3 and COMMD9 on ENaC activity and the mechanism by which COMMD3 and COMMD9 regulate ENaC activity. (3) To explore the localisation of endogenous COMMD3 and COMMD9 in cultured cell lines and rat tissues and further ask whether COMMD9 colocalises with αENaC in rat kidney. Here protein-protein interaction studies demonstrated that all COMMD family members interacted with ENaC. Functionally, COMMD3 and COMMD9 were able to down-regulate the αβγENaC current through reducing the expression of ENaC at the cell surface. Western blot studies were used to show that endogenously expressed COMMD3 and COMMD9 were detected in HEK 293 cells and some rat tissues including kidney. Here immunocytochemistry studies in HEK 293 cells were used to show that COMMD3 was endogenously expressed in a perinuclear manner, while endogenous COMMD9 was present throughout HEK 293 cells. In the rat kidney, endogenous COMMD9 was found to be mainly expressed in the cortical and medullary collecting duct cells using single label immunohistochemistry. Moreover, COMMD9 was colocalised with αENaC in the collecting duct cells in the rat kidney. In summary, this study identified the interaction between COMMDs and ENaC and discovered the inhibitory effects of COMMD3 and COMMD9 on ENaC activity. In addition, the regulatory mechanism of COMMD3 and COMMD9 on ENaC was found to be through reducing ENaC surface expression. Immunohistochemistry results provide in vivo evidence for the interaction of COMMD9 and ENaC. Therefore, these data obtained in this study suggest COMMD3 and COMMD9 might be endogenous regulators of ENaC and they may be involved in Na+ and fluid homeostasis and therefore ENaC-related disease, such as hypertension. Lastly, this study may provide an insight into a new target point to treat hypertension.

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  • Multiple-stressor effects along gradients of deposited fine sediment and dissolved nutrients in streams

    Wagenhoff, Annika (2011)

    Doctoral thesis
    University of Otago

    Ecological degradation of streams and rivers as a result of agricultural land-use intensification is a major concern in New Zealand and other parts of the world. Agriculture introduces multiple stressors to streams, presenting a challenge for freshwater managers who must understand the relative strengths of each individual stressor and their combined multiple-stressor effects if they are to implement the most effective management actions and avoid ‘ecological surprises’ that arise from complex interactions between stressors. To investigate patterns of ecological response variables across broad gradients of two major stressors, augmented levels of dissolved inorganic nutrients and deposited fine sediment, I designed a streamside mesocosm experiment with eight levels each of nutrients (36 to 6900 micrograms per litre of dissolved inorganic nitrogen plus 1.4 to 450 micrograms per litre of dissolved reactive phosphorus) and deposited fine sediment (0 to 100 % cover of the streambed), and conducted a field survey in a regional set of 43 streams ranging from 2nd to 6th order. I used multiple linear regression and an information-theoretic approach to select the best predictive models for a series of ecological response variables, including algal, invertebrate and ecosystem variables, and tested (1) the subsidy-stress hypothesis for each stressor (where at low stressor levels an ecological variable responds positively until an inflection point beyond which the effect is negative), (2) whether sediment and nutrients operated as single or multiple stressors and whether they interacted with each other, and (3) whether sediment effects were more pervasive than those of augmented nutrient concentrations. In the 21-day long experiment, subsidy-stress patterns across the nutrient gradient were frequently found for algal and invertebrate taxa and communities, but consistently negative response shapes were more prevalent across the sediment gradient. The subsidy-stress hypothesis was not supported by the response of an ecosystem variable (organic matter breakdown, measured using cotton strips and fresh mahoe leaves). Overall, nutrients and fine sediment acted predominantly as multiple stressors and sometimes in complex interactive ways. The relative strengths of fine sediment and nutrient effects were similar for algal response variables but sediment was the more pervasive stressor for invertebrates, a finding that was also supported by the field survey. My field survey further suggested that nutrients and sediment commonly interact in synergistic ways to affect invertebrate variables, with fine sediment overwhelming any subsidy effects that nutrients may have in isolation. The combined experimental and survey results indicate that augmented levels of fine sediment and dissolved inorganic nutrient concentrations need to be managed together because they mostly act as multiple stressors in their effects on algal, invertebrate and ecosystem response variables. While managers should seek to control both nutrient and fine sediment inputs to streams to achieve good ecological stream condition, measures to reduce or avoid further sedimentation are particularly likely to be effective in mitigating ecological impairment and preventing further harm. Finally, in order to best assess the likely causes of decline in stream health, it will be highly desirable for managers to routinely monitor both nutrients (as currently done) and fine sediment in the future.

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  • In Camera/On Camera: The Re-Presentation of Janet Frame as a Kiwi Icon

    Scott, Corey (2011)

    Doctoral thesis
    University of Otago

    Frequently referred to as New Zealand’s most famous and least public author, Janet Frame occupies a curious place in the nation’s literary and cultural history. With her feted literary production largely overshadowed by her dramatic personal history, Frame is, to paraphrase one critic, an author obscured by her image. The present study takes the form of an analysis of this characterisation of Frame in all its attendant implications: biomythical, socio-cultural, multimedia, and extraliterary. Inverting the traditional mode of analysis, we will frame our subject, as it were, by focusing not on the author’s own literary production, but on the promotion and reception of her work in an increasingly heterogeneous range of media/contexts, examining Frame’s transformation from obscure author to New Zealand icon in relation to an ever expanding range of appropriations. Far from superfluous artefacts subordinate to traditional modes of literary analyses, the ephemeral and ancillary evocations of authorial identity that form the basis of our study have an animating and vitalising influence on Frame’s career and celebrity status, testifying to the integral role of mass media in the perpetuation of her biographical legend and construction of her iconic status. By concealing their inherently discontinuous nature through their re-presentation of the subject as an historically determined presence, these manifold appropriations simultaneously purport to present us with an authentic and incontrovertible image of the author, a guarantee that gains added significance in the case of famously hermetic celebrities such as Frame. The increasingly visual nature of Frame’s authorial construction creates the illusion of the foreclosure of the gap between the visible and the invisible, the knowable and unknowable. Through this process, Frame’s likeness becomes increasingly ubiquitous while retaining the mysterious qualities essential to her appeal as both an experimental author and enigmatic celebrity. But rather than re-present her rise to prominence as ameliorative in its manifestation, our analysis reveals Frame’s authorial imago to be a contended site of cultural production, mediating the impact and influence of artists commercial and political commodities in late twentieth and early twenty-first century New Zealand. Refashioned as a secularised, multimedia re-presentation of irrepressible artistic individuality in the face of social and global impediment, Frame’s remarkable life/story is indelibly etched into New Zealand’s cultural imaginary; the famously reclusive author granted the status of Kiwi Icon.

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  • Characterisation of Compounds Contributing to Kina Roe Colour

    Garama, Daniel James (2011)

    Doctoral thesis
    University of Otago

    Sea urchin roe is a highly valued product in the international marketplace. New Zealand’s coastal zones, have significant stocks of sea urchin (Evechinus chloroticus; local name Kina), but quality issues including colour, taste and texture limit export opportunities. The objective of this study was to investigate compounds which contribute to desirable (bright yellow to orange red) as opposed to undesirable (brown or black) roe coloration, to contribute to an understanding of Kina roe pigmentation and the establishment of a Kina roe export industry for New Zealand in the future. The current belief is that carotenoid compounds are responsible for sea urchin roe pigmentation. Sea urchins cannot synthesise carotenoids de novo, and are therefore dependent upon dietary carotenoid intake. It is reported that dietary carotenoids may be assimilated selectively or transformed to other forms. Echinenone and β-carotene have been identified as the main carotenoids found in Kina roe and also in 10 of the 11 other sea urchin species studied globally. In this study, carotenoids were extracted from differently pigmented Kina roe and from sections of Kina digestive tract gut wall tissue. The carotenoids were analysed by RP-HPLC. Comparison of the carotenoid profiles revealed that echinenone was the predominant carotenoid in both light and dark pigmented roe, with increases in fucoxanthin, astaxanthin and β-carotene being detected in dark brown compared to light coloured roe. The predominant carotenoids detected in Kina gut wall were fucoxanthin, violaxanthin and echinenone. The collected Kina were feeding predominantly on Macrocystis pyrifera (kelp) that contains mainly fucoxanthin, and minor amounts of β-carotene and violaxanthin. The source of echinenone in the Kina roe is uncertain, as it is not present in kelp, which forms the major component of sea urchin diet. Results from this study suggest that echinenone is generated from β-carotene, which is present in low levels in kelp. It has been suggested in the literature that the conversion takes place exclusively in the roe, however, this study found high concentrations echinenone present in the gut wall of Kina. This study suggests that the gut wall is therefore directly involved in the metabolism of carotenoid compounds and that separate carotenoid modification events are occurring in different tissues. The results of the carotenoid analysis in this study suggest that carotenoid content may not be entirely responsible for the colour variation observed in Kina roe. It is now the belief that other non-carotenoid compounds are also affecting coloration. To obtain information about the Kina roe proteome, Kina roe proteins were displayed by large format 2-D PAGE and analysed by an in-gel digest/mass spectrometry/informatics workflow, involving interrogation of the Echinodermata and Strongylocentrotus purpuratus genome databases. A number of proteins in the Kina roe proteome were identified from homologues in the databases, and some of these proteins appear to be unique to either light or dark pigmented Kina roe. The results of this study indicate that some proteins in Kina roe are capable of contributing to roe pigmentation by association with other compounds. In addition, a diet trial was undertaken with Kina to evaluate the effect of the introduction of carotenoid compounds on Kina roe colour. Although the lack of availability of carotenoids in quantity limited the scope of this trial, the results indicate the potential for roe colour manipulation via the diet. Overall, the results of this study have contributed to the knowledge of colour development in Kina and have indicated possible future research directions.

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  • Cooperation of Calcium Ion Transport Mechanisms for Cerebellar Synapse Physiology

    Roome, Christopher Joel (2011)

    Doctoral thesis
    University of Otago

    The cerebellum has often been referred to as the "neuronal machine", so called for the elegant architecture of neuronal circuitry and necessarily clockwork precision of signal transmission therein (Eccles 1967; Ito 2006). To maintain such precision, many synapses within the cerebellar micro-circuitry are highly plastic and frequency dependant. In particular, short-term synaptic plasticity (STP) at an important excitatory synaptic pathway between cerebellar granule cells (CGCs) and Purkinje neurons (PN), called the "parallel fibre to Purkinje neuron synapse" (PF-PN), is an integral feature of the synapse and for cerebellar function as a whole (Dittman, Kreitzer et al. 2000; Boyden, Katoh et al. 2004). During transmission at PF-PN synapses, the dynamics of elevated pre-synaptic calcium (or residual calcium) dramatically impact the STP exhibited by the synapse (Zucker and Regehr 2002). Multiple cellular mechanisms function cooperatively to carefully control residual calcium dynamics and two principle pre-synaptic mechanisms expressed in CGCs include the sodium calcium exchanger (NCX) and plasma membrane calcium ATPase (PMCA) (Blaustein, Juhaszova et al. 2002; Ivannikov, Sugimori et al. 2010). Both PMCA and NCX proteins function to remove elevated intracellular calcium and their cooperative activity is thought to be critical for maintaining PF-PN synaptic behaviour (Regehr 1997; Empson, Garside et al. 2007). However, characterisation of NCX activity in pre-synaptic calcium control, its influence on synaptic transmission, and how it might interplay with PMCA activity at PF-PN synapses remains to be established. This research aimed to understand the cooperative activity of NCX and PMCA2 and its functional impact on PF-PN synaptic behaviour. To do this, calcium fluorescent imaging and electrophysiological recordings were made from the mouse cerebellum in vitro, whilst PMCA2 and NCX were sequentially removed by either pharmacological or genetic manipulation to assess their individual and combined activities. Two fluorescent calcium imaging techniques using a genetically encoded calcium indicator, GCaMP2 and a conventional calcium indicator, Calcium Green-1 Dextran, were utilised to determine the influence that cooperative NCX and PMCA2 activity has on PF pre-synaptic calcium dynamics. The impact that cooperative NCX and PMCA2 activity had on PF-PN synaptic behaviour was addressed using patch clamp electrophysiology to record PF-PN post-synaptic currents and assess STP of the synapse. To supplement experimental studies, a computational modelling approach was used throughout to aid interpretation of calcium fluorescent imaging experiments. The model simulated pre-synaptic calcium dynamics to provide a theoretical basis for how calcium efflux characteristics exhibited by NCX and PMCA2 dictate their cooperative interplay for pre-synaptic calcium control. This investigation has provided strong evidence for an important cooperative interplay of pre-synaptic NCX and PMCA2 activity, capable of influencing PF-PN synapse behaviour. The extent of cooperation between NCX and PMCA2 activity depends upon on pre-synaptic calcium load (hence pre-synaptic activity) and this influences the behaviour of the PF-PN synapse. It is proposed that the kinetic balance for this cooperative activity within the PF pre-synaptic terminal is predominantly governed by the kinetic properties that each mechanism exhibits, including their calcium affinity for activation and maximal efflux capacities.

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  • Genomic Analysis of Early Hereditary Diffuse Gastric Cancer

    Nasri, Soroush (2011)

    Doctoral thesis
    University of Otago

    Diffuse gastric cancer (DGC) is one of the two main types of stomach cancer. Histologically, DGC can be subdivided into poorly differentiated carcinoma and signet ring cell carcinoma (SRCC). Carriers of germline mutations in the gene encoding E-cadherin (CDH1) are predisposed to DGC (hereditary DGC, HDGC). Essentially all asymptomatic mutation carriers present with occult, multifocal SRCC confined to the gastric mucosa before they develop advanced disease. Initial characterisation of these early HDGC foci (referred to as eHDGC) suggests an indolent nature of these lesions, contrary to their current pathological definition as malignant disease. The main aim of this study was to determine if genomic instability is an early event in HDGC and how it might lead to disease progression. We assessed chromosomal aberrations in the early intramucosal eHDGCs by using array comparative genomic hybridisation (CGH). Taking advantage of possibly the largest eHDGC collection worldwide, we analysed tissue from twelve members of one HDGC family, all carrying the same CDH1 mutation. All specimens were formalin-fixed paraffin-embedded (FFPE), as eHDGC is generally identified in resected stomachs by microscopy due to both its intramucosal location and the small size of the foci. As a result, the first part of this study focussed on the optimisation and establishment of techniques for the genomic analysis of degraded DNA from minimal amounts of laser-capture microdissected (LCM) neoplastic cells. In the first step, we assessed several histological stains for their suitability in identifying neoplastic cells found in eHDGCs, followed by an optimisation of the LCM procedure to obtain consistent dissection of individual cells. Next, we evaluated different DNA extraction parameters to obtain sufficient amounts of DNA for genomic profiling and established a multiplex PCR reaction as a quality control for the prediction of successful profiling. Since no agreement exists on the most suitable platform for the profiling of FFPE-DNA, two different array CGH systems were compared. DNA from FFPE and matched fresh-frozen (FF) tissue was separately analysed on both a SNP-based array (Affymetrix) and on an oligonucleotide-based array (Agilent), and resulting profiles were evaluated for the level of agreement between matched pairs of FFPE and FF samples. On the SNP-array, a substantial increase in apparent copy number alterations was observed in all FFPE tissues relative to their matched FF counterparts. In contrast, FFPE and matched FF genomic profiles obtained via the oligonucleotide array were highly concordant, indicating the reliability of this platform for the analysis of degraded DNA. We then proceeded with the genomic analysis of the early HDGC foci. For all twelve HDGC patients, 30,000 cells from each of three tissue types, signet ring cells (SRC), poorly differentiated cells (PDCs) and non-malignant epithelial cells were dissected and analysed using the Agilent platform. Chromosomal aberrations were found in SRCs and PDCs, and confirmed by multiplex ligation dependent probe amplification (MLPA). No changes were detected that were common to all patients. Accordingly, no common genes, pathways, or miRNAs were identified to be altered in eHDGC, suggesting the aberrations had not yet undergone clonal selection. Importantly, no aneuploidy or other large-scale chromosomal rearrangements were detected. Instead, all aberrations affected small regions (< 4.8 Mb) and were predominantly deletions. Analysis of DNA sequence patterns revealed that essentially all aberrations possess the characteristics of common fragile sites. The presence of genomic instability at the fragile sites in the absence of widespread genomic instability was highly consistent with eHDGC being relatively indolent. We therefore examined by immunohistochemistry the activity of key DNA repair proteins in eHDGC. ATM-H2AX-CHK2 were consistently expressed and activated in all examined eHDGC foci, indicating an intact and activated DNA repair system accompanying genomic instability at fragile sites. Altogether, this study has established the methodology for the successful CGH profiling of FFPE tissue and has provided the first genetic characterisation of the earliest stage of DGC development. This analysis and subsequent immunohistochemical examination has shown that early stage intramucosal DGCs are (unlike advanced DGC) typified by low levels of genomic instability at fragile sites. Moreover, they express an active DNA damage response (DDR), providing a molecular basis for the observed indolence of eHDGC.

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  • The development and evolution of supergene gold and sulphide mineralisation in quartz pebble conglomerate deposits.

    Falconer, Donna Marie (2011)

    Doctoral thesis
    University of Otago

    The development and evolution of supergene gold and sulphide mineralisation that occurs in quartz pebble conglomerates (QPCs) from two contrasting environments is investigated. The contrasting sites in this study represent a progression in the development of supergene conditions that occur in relatively high energy fluvial settings. Mineralisation at two separate localities from a Miocene-Pliocene aged QPC in southern New Zealand is examined in detail. In contrast to this, gold mineralisation from an Eocene aged palaeochannel from the deeply weathered lateritic regolith of the Yilgarn Craton, West Australia, is also investigated. Although from vastly different geological settings, both occurrences of supergene mineralisation are in fluvial environments characterised by anomalous gold (Au-Ag alloy) and fine-grained diagenetic sulphides. Given the analogous fluvial environments, they have undergone similar processes and consequently a more complete picture of gold and sulphide diagenesis has been built up. A number of gold precipitation and dissolution textures are distinguishable in the active supergene environment at Belle-Brook (New Zealand). Precipitation textures include a variety of semi-spheroidal gold forms that are variously aggregated, budded and occasionally crystalline. Dissolution textures are associated with the loss of Ag from the Au-Ag alloy and are characterised by preferential grain boundary dissolution along subgrain boundaries. Fresh dissolution textures are observed as a well-defined line occurring between subgrains, however with increasing evolution and modification to the surface early textures are often obliterated. The diagenetic sulphide suite at Belle-Brook shows a progression of sulphide diagenesis from detrital sulphides through to fine-grained framboidal pyrite and spheroidal marcasite that may also develop into a pervasive cement or large (cm’s) lumps. The low pH surface waters at Belle-Brook preclude the oxidation of these sulphides to goethite. The sulphide suite is predominantly marcasite in which extensive precipitation periodically occurs most likely in response to fluctuating redox conditions associated with the alluvial mining operation that occurs at the site. At Sunrise Dam coarse-grained chunky palaeochannel gold is interpreted to be supergene. A high-grade hypogene source intersects the palaeochannel and hypogene gold is observed but is readily identifiable based on morphology. Supergene gold in the palaeochannel occurs as distinctive highly irregular grains characterised by embayments associated with detrital quartz grains, or filled with clays that host fine-grained microcrystalline gold. Episodic gold precipitation is inferred from microcrystalline gold that forms lineations or bands. Fluctuating redox conditions are most likely responsible for what may be episodic gold precipitation. In the hypersaline lateritic regolith at Sunrise Dam, gold is strongly redox controlled as indicated by enrichments associated with palaeo-redox fronts. With evolving aridity associated with the change in climate from wet and tropical in the Eocene, to the present arid climate, the resultant drying out of the profile and lowering of redox fronts has resulted in a redistribution of gold enrichment and depletion zones. With the exception of fine-grained marcasite and pyrite preserved in the reduced basal lags of the palaeochannel, these changing redox conditions have resulted in the oxidation of the original diagenetic sulphide suite to goethite and iron-rich clays. Whilst entirely supergene gold particles are rare in the QPCs in New Zealand, they are common in the palaeochannel at Sunrise Dam where there is a nearby high-grade hypogene gold source. Despite a lack of hypogene source, examples of entirely supergene gold do occur in the QPCs indicating that in very specific environments supergene conditions are conducive for mobilising and precipitating significant amounts of gold. In contrast to the lateritic regolith where supergene processes are responsible for and control gold enrichment, physical processes are the most significant for gold enrichment in QPCs from New Zealand. The main site at Belle-Brook is characterised by actively occurring supergene processes and as such provides valuable insight into early diagenetic processes that are often obscured or not preserved in other more modified settings. This study finds that gold in the supergene profile behaves in a similar fashion, regardless of whether it occurs in an arid weathered regolith profile in Western Australia or a quartz pebble conglomerate gold placer in southern New Zealand. Morphological features and geochemical textures on gold from all sites indicate that electrochemical refinement of the Au-Ag alloy is a major processes that drives the coupled dissolution and precipitation of gold that occurs in the supergene environment.

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  • Sheep Fat Bingo: A comparison of subcutaneous adipose-derived mesenchymal stem cells with infrapatellar adipose-derived mesenchymal stem cells with regard to their chondrogenic ability in a sheep model of osteochondral defect repair.

    Milazzo, Christopher (2011)

    Doctoral thesis
    University of Otago

    Articular cartilage is an avascular, aneural, alymphatic tissue that has a very low capability for intrinsic repair. Injuries to the tissue often lead to progressive degeneration, leading to painful joint disease. The most successful biologically-based treatments for articular cartilage lesions are cell-based therapies that introduce new cells to the lesion with the intention that they produce and replace lost extracellular matrix. Adipose-derived mesenchymal stem cells (ASC) are an attractive source of graft cells for their ease of collection, ease of expansion, and ability to differentiate into the chondrogenic phenotype and produce cartilage-specific extracellular matrix. While many studies report the inferiority of ASC with regard to their chondrogenic ability, the vast majority of these authors isolate ASC from subcutaneous (SC) fat harvested during lipoaspiration procedures. Few studies have studied the chondrogenic potential of ASC isolated from the infrapatellar (IP) fat pad and none have compared the chondrogenic potential of ASC from these two sources. This study compared ASC isolated from IP and SC fat in an ovine model. Adipose tissue was harvested surgically from both SC and IP fat sources. ASC were isolated from each source and expanded by monolayer culture in vitro. Monolayer cultures were induced to pellet formations using a chondrogenic medium and then cultured in the mechanically-loading environment of a three-dimensional rotary cell culture system. Neocartilage pellets from each source were compared for their ability to produce the phenotypic cartilage extracellular matrix proteins collagen type II and aggrecan as well as pericellular collagen type VI. Qualitative analysis was performed with immunohistochemical evaluation of pellets by stain with antibodies against these matrix proteins. Quantitative assays for total collagen, total glycosaminoglycan (GAG), and DNA content of pellets were performed to confirm qualitative results. Pellets were then autologously implanted into osteochondral defects surgically created in the articular surfaces of sheep knees. After four and twelve weeks of recovery, post-mortem examination of defect repair was performed and defects removed by dissection for fixation and subsequent processing for histopathology and immunohistochemical analysis. Qualitative comparison of SC and IP pellets revealed that IP pellets produced greater relative amounts of all extracellular matrix proteins studied than SC pellets. IP pellets were significantly larger than SC pellets and contained more total collagen and total GAG per unit of DNA than SC pellets. When implanted, none of the pellets contributed substantially to defect repair, but IP pellets remained within the defects at twelve weeks while SC pellets were absent. In conclusion, this study shows that IP ASC have greater chondrogenic ability than SC ASC, suggesting potential for the use of IP ASC in tissue-engineered constructs for repair of articular cartilage injury.

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  • Messenger RNA Data Mining

    Pollock, Robert (2011)

    Doctoral thesis
    University of Otago

    Messenger RNA (mRNA) is the molecular intermediary carrying genetic information from the nucleus to the cytoplasm. All the information about cellular localisation, efficiency of translation and message stability must be found within the sequence of the mRNA molecule. Very little is known about the sequence elements that must direct many of these processes. De novo computational methods have been extremely useful in characterising the molecular determinants of function at the protein level. Similarly much has been learned about the functional elements at or near transcription start sites (TSSs). Computational methods have not yet been as successful in finding elements within the messenger RNA sequence. There is much evidence to suggest such elements exist. Conservation in genomic sequence corresponding to the mRNA 30 untranslated region (3'UTR) is greater than it is in the intergenic region. In addition there are a large number of proteins in the eukaryotic cell that contain RNA binding domains. In this study, predicted 3'UTR regions for all genes from the budding yeast Saccharomyces cerevisiae were extracted from the downstream region of each gene. Yeast makes a powerful platform for this purpose because of the vast repository of functional data available for cross checking results, and thereby validating methodology. In this work, the 3'UTR sequences of yeast were interrogated using computational methodology to find statistically significant patterns within the sequences. Such patterns (or sequence motifs) can be over-represented words—either contiguous words or regular expressions—or collections of locally aligned sequences (typically expressed as matrices of positional letter counts). Two methods were chosen here: the first, MEME, searches for statistically significant local alignments. The second, TEIRESIAS, enumerates words (allowing for wildcard letters) present in the sequence database, subject to certain constraints. The goal of this project was to find significant words using as naïve and unsupervised an approach as is possible, utilising little or no functional data upstream of the analysis. Through doing this, it was possible to illustrate the power of computational methodology to decipher the molecular details of cellular control, with little or no additional information. This approach represents a significant challenge for computational biology tools. The sequence dataset was searched for elements under two scenarios: the first, completely unsupervised (using all of the sequence data), and the second partly supervised. The partly supervised approach utilised mRNA halflife values were obtained from a genome-wide study of mRNA stability to bin the sequences before conducting the search. This study examines the performance of both MEME and TEIRESIAS when applied to these difficult problems, and considers ways of improving the sensitivity of the analysis (to find the maximum number of motifs). The effect of repetitive and duplicated sequences, and appropriate parameters for searching, on the output of TEIRESIAS is examined. Secondly a methodology for converting text-pattern motifs (from TEIRESIAS) into alignments that can be compared with MEME results, is developed. The partially supervised approach was conducted using MEME. MEME was not able to find many motifs when executed with default parameters, typically finding only low complexity elements, duplicated sequences, and alignments of only 2-3 sequences. After a concerted effort was made to optimize MEME, which is documented here, some 18,000 statistically significant alignments were found. After filtering and testing of the motifs, 3311 motifs comprising 1324 motif clusters were found to be associated with stability. Using the fully unsupervised approach, MEME was also able to find a large number of motifs, though (notably) slightly fewer than were found using the partially supervised approach. TEIRESIAS was also able to find many statistically significant patterns using the unsupervised method. The large number of motifs found during this analysis were tested for likely biological validity in several ways: by testing whether or not motif-containing sequences were biased towards stable or unstable sequences; by testing whether or not motif-containing sequences were enriched in functional and localisation classes of genes (Gene Ontology) and by testing for motif enrichment in the target mRNAs associated with known RNA binding proteins. These approaches confirmed that the motifs found were likely to have biological significance and leads to their consideration as candidates for likely components of functional elements.

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  • Response inhibition and properties of its underlying processes : evidence from behavioral and electrophysiological measurements

    Ko, Yao-Ting (2011)

    Doctoral thesis
    University of Otago

    I attempted to further our understanding of response inhibition by examining three questions concerning how it works. The first question that I examined was what determines the success of response inhibition. This question was examined with the stop-signal paradigm, a prominent experimental setting for the study of response inhibition. I hypothesized that the relative strength of activation and inhibitory processes is a determinant, which led to an examination of graded action of response inhibition. To examine graded response inhibition, several continuous measurements including response force, electromyography (EMG) and the lateralized readiness potential (LRP) derived from electroencephalography (EEG) were employed; and new methods of comparing conditions and of controlling for contributions from response activation were introduced. Results in the present study indicated that response inhibition works in a graded manner. The second question that I examined was how specifically targeted response inhibition is. In line with previous studies, results in the present study indicated that response inhibition works globally to some extent, at least when speeded responses were required. New information about global response inhibition in the present study was that global response inhibition was considered with two distinct lines of research – one line concerns selective response inhibition, where global response inhibition was indicated previously, and the other line concerns the psychological refractory period (PRP) paradigm, which has been a prominent experimental setting for the study of divided attention. The third question that I examined was on what level(s) of processing selective response inhibition and global response inhibition produce their effects. Results in the present study with measurements of response force, EMG and the LRP indicated that global effects of selective response inhibition within the stop-signal paradigm are produced at the motor stage of processing, and that global effects of response inhibition within the PRP paradigm are produced at the response-selection stage of processing.

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  • Assessment of genetic variation in the threatened New Zealand sea lion, Phocarctos hookeri, and its association with fitness

    Osborne, Amy (2011)

    Doctoral thesis
    University of Otago

    The New Zealand sea lion (NZSL) is the rarest sea lion in the world and exists in relative isolation, primarily in New Zealand’s sub-Antarctic islands. Once widespread throughout New Zealand, the species suffered a population bottleneck through subsistence and exploitative hunting. Only 8600 – 11300 individuals remain and pup production has declined by 40% over the last decade. In addition, the species is unusually susceptible to disease and has suffered three seasons of very high pup mortality in recent years (1997 – 2003). As such, it is of high conservation concern. Here we have applied population genetics and molecular ecological methods to address how genetic factors may be impacting the susceptibility of the NZSL to disease. First, since the level of variation at neutral genomic loci is expected to be a reasonably good predictor of overall genomic variation, we dissected the level of variation at a large panel of microsatellite loci, and established that while heterozygosity is maintained, allelic diversity is depauperate. We have also provided genetic evidence of an historical population-size bottleneck, and indicated that the population departs from random mating and panmixia, as expected under Hardy-Weinberg equilibrium. Next, because of the difficulties associated with the anonymity of microsatellite loci in species for which no genome sequence exists, we created a predicted physical map of the pinniped genome using microsatellites, based on demonstrated synteny between species of the Carnivora. We optimised and then utilised a panel of 21 microsatellite loci to show that overall genetic variation in NZSL pups is associated with death by bacterial infection, and that the panel of microsatellites used here is reflective of genome-wide variation, justifying its utility in the context of HFCs. However, the level of variation at neutral genomic loci is not necessarily correlated with variation elsewhere in the genome; therefore it was important to investigate variation at genes with known function in disease resistance or susceptibility. We have illustrated that the gene SLC11A1 (previously NRAMP1) has conserved structural features in the NZSL reflective of its role in macrophage activation; however we lacked the statistical power to associate variations in this gene with disease in this study, despite promising trends. We then demonstrated a high level of variation at one gene of the major histocompatibility complex (MHC), in spite of low allelic diversity at microsatellite loci. The NZSL has been subject to recurrent epizootic events in recent years, attributable to two different bacterial pathogens. We suggest that, as a consequence of recurrent selection pressure exerted by diverse pathogens and multiple epizootic events, balancing selection may be operating at this locus in order to maintain MHC diversity, which is generally vital for an adequate immune response. In addition, certain haplotypes of this gene associated strongly with survival; however these results should be viewed as tentative. In summary, we have presented a thorough assessment of genome-wide variation in the NZSL and conclude that diversity is generally low; however selection appears to be maintaining variation at genes involved in the immune response, and this work provides intriguing preliminary data for further study. This research serves to elucidate overall levels of genetic variation in this endemic, threatened species, and aids in the understanding of the genetic mechanisms of resistance to disease epizootics, which is crucial for their conservation management and population recovery. This work has the capacity to be applied to many species of conservation concern both in New Zealand and globally.

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  • Regulation of E-cadherin by Human Papillomavirus type 16 E6

    D'Costa, Zarina (2011)

    Doctoral thesis
    University of Otago

    The primary risk factor for the development of cervical cancer is a persistent infection with certain high-risk human papillomavirus (HPV) types such as 16 and 18. The ability of these viruses to cause such persistent infections within the host can be attributed to several immune evasion mechanisms. One such mechanism involves adversely affecting the amount of viral antigen presented to the host immune system. It was previously shown that the E6 oncoprotein of HPV16 is capable of actively down-regulating expression of epithelial (E)-cadherin expression which directly correlates with depletion in the number of immune Langerhans cells (LCs) in the infected tissue. In this manner, HPV16 E6 is able to contribute to viral survival and protection. The aims of this study were firstly, to investigate the mechanism of E6 regulation of E-cadherin; secondly, to identify a region of E6 responsible for regulation of E-cadherin; thirdly, to investigate the roles of the other HPV16 oncoproteins in E-cadherin regulation and fourthly, to identify potential therapeutic interventions for early HPV16 infections. The E6 oncoprotein from HPV16 was expressed in HCT116 cells and its ability to regulate E-cadherin promoter, transcript and surface protein was investigated. E6 was found to regulate E-cadherin at a transcriptional level. The E-cadherin promoter was found to be repressed in HCT116 E6 cells through a methylation dependent mechanism that is independent of direct methylation of the E-cadherin promoter. In order to identify the region of E6 oncoprotein important for E-cadherin regulation, a range of HPV16 E6 mutants were tested for their abilities to decrease transcription of E-cadherin. Mutational analysis of HPV16 E6 led to the identification of residues 118-122 and the nearby R124 residue, located within the C-terminal zinc-finger binding domain to be important for transcriptional regulation of E-cadherin by E6. In addition, the other major oncoproteins of HPV16, namely E5 and E7 were co-expressed with E6 and their abilities to regulate surface E-cadherin were assessed. E7 was also found to be effective in decreasing surface E-cadherin levels, and this effect was enhanced when the two oncoproteins were co-expressed in HCT116 cells. Furthermore, regulation of E-cadherin by HPV16 oncoproteins was assessed under conditions of differentiation using a simple monolayer model of differentiation and a three-dimensional organotypic raft culture system. Lastly, in order to identify potential therapeutic interventions for early HPV16 infections, rational design was used to design peptide antagonists of E6 that could potentially interfere with E6 regulation of E-cadherin. Despite efficient delivery of peptide inhibitors of E6 into target E6 expressing cells, no restoration of E-cadherin levels were detected. However, another potential therapeutic compound, Indole-3-carbinol, was identified. This research gives insight into the mechanism of transcriptional regulation of E-cadherin by HPV16 E6. The data presented here suggest that a specific regulatory region of the protein can directly affect regulation of E-cadherin. These data may provide the foundation for an effective HPV16 inhibitor, which would help decrease the burden of HPV-related disease that affects millions of people each year.

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  • Re-conceptualising Sense of Place: Implications for place branding

    Santana, Adriana Campelo (2011)

    Doctoral thesis
    University of Otago

    This thesis is concerned with understanding what constitutes a sense of place and how such an understanding can help in the development of a place brand. Branding theory and techniques have been applied to places in order to promote economic development and to enhance the cultural differentiation of places. The development of a brand for places requires not just an understanding of the elements that create a communal sense of place, but also an understanding of how the place is part of the community it represents. What constitutes a sense of place can help in the development of a place brand. In this endeavour, the research problem is to understand what constructs determine a sense of place. In order to achieve the aims of this research, an investigation was conducted on the Chatham Islands of New Zealand, an archipelago with ten islands with an area of 966 km2 and a population of 609 inhabitants, located 800 km east of New Zealand. In this relatively isolated community that has a distinct cultural history, interactions with the environment are pronounced and relationships between people are critical. The thesis adopts a qualitative philosophical position, positioning research paradigms as interpretivist, postmodernist and constructivist. Accepting the existence of multiple realities, the ontology of this study is relativist leading to a transactional and subjectivist epistemology. The epistemology that guided the entire journey is based on the belief that a collaborative approach is necessary to create knowledge, via a phenomenological hermeneutic methodology. Multi-sited ethnography (Marcus 1995) through participant observation, phenomenological interviews, and videography was used as a strategy for inquiry. The constructs of time, ancestry, landscape, and community, were revealed to be determinants for the Chatham Islanders’ sense of place and they recognised them as elements of major significance in their lifestyle, and in their personal and communal identity. These constructs stand for a set of meanings that influence the habitus, the ways of doing things on the islands, and the significance of doing things in particular ways. In addition, the findings and discussion demonstrated how these constructs bestow meanings on the symbolic representations of the community, which are also reinforced through the sensory perceptions of the place. This thesis suggests a creational place branding approach that adopts a co-creation strategy to identify the constructs that determine the sense of place. A sense of place model is presented as a guide to investigate the set of meanings within each of these four constructs (time, ancestry, landscape, and community), and their importance in other places. The recognition and representation of these constructs are vitally important to brand imagery and brand communication. Equally important, is an understanding of how these constructs should be represented in order to properly express and preserve their meanings. Place imagery encompasses symbolic representations and sensory perceptions of the place. Therefore, this study develops and presents imagery representation criteria to provide procedures to enhance the ethos of the place in portraying a place brand. The creational ethically-driven place branding approach proposed in this thesis embraces the co-creation and recognises the cultural dependency of brand meanings. It requires that the ethos of the place and the people of the place should be positioned at the core of the brand to establish ownership, achieve authenticity and promote brand sustainability.

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