1,601 results for Thesis, 2013

  • Development, Validation and Preliminary testing of A Novel Indwelling Wireless Intraoral pH Telemeter

    Lee, Jennifer Jae Won (2013)

    Doctoral thesis
    University of Otago

    Maintaining intraoral pH is important in protecting both hard and soft tissues from acids. When this balance is breached, some detrimental effects can be expected such as demineralisation, tooth erosion and reduced buffering capacity. Telemetric measurements have been previously used for monitoring changes in the intraoral pH in the past but most of the studies included bulky leads in the mouth, limiting optimal measurements outside the laboratory setting. The aim of the current research was to develop a novel wireless device that transmitted data real-­‐time to a smart phone to allow continuous monitoring of changes in the intraoral pH. A number of preliminary in vitro and in vivo (although in one participant) experiments have been carried out to validate the measurements of the wireless device. In vitro experiments included determination of drift over 24 hours and temperature effects to validate the pH probe. In vivo experiments investigated measurements during the daytime and sleep as well as following swallows of acidic drinks. Among various appliances constructed, the clear-­‐retainer type appliance turned out to be of the most time-­‐efficient and successful way of enveloping the wireless device. A distinct difference was observed between the pHs of the upper and lower arches. During sleep, there was a great deal of fluctuations of the pH values in the upper arch, while the recordings from the lower arch showed little change. When an acidic drink was introduced, a pronounced drop in pH in the upper arch was obvious with gradual increase to normal level, compared to minimal changes in the lower arch. An excellent cross-­‐correlation was demonstrated between the reference pH measurement system and the wireless device. The development of the wireless device will lead to exciting applications in the future in the areas of erosive tooth wear, gastro-­‐esophageal reflux and orthodontics.

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  • Evaluation of utilisation of the Prevention of Mother-to-Child Transmission of HIV Programme in Central province, Kenya

    Ngugi, Catherine Njeri (2013)

    Masters thesis
    The University of Auckland Library

    Background: The PMTCT HIV programme has been one of the most successful HIV preventive interventions towards HIV-free future generations. However, even though the programme is virtually effective in developed countries, many developing countries are reporting child HIV infections due to the MTCT. The programme has existed in Kenya for more than a decade, yet in 2011, 12,894children were HIV infected due to MTCT Objective: To evaluate the PMTCT programme, especially the HIV testing from the antenatal period to the postnatal period among expectant parents attending Nyeri Provincial General Hospital in Central Province, Kenya. Design: Retrospective analysis of the hospital registers. Methods: Three hospital registers were analysed for the period from July 2009 to September 2012. The registers were for antenatal, intrapartum and postnatal care respectively. Each register documented the utilisation of PMTCT services by the expectant parents. Descriptive and inferential statistics were produced to analyse data from the registers. Results: The PMTCT services utilisation was sub-optimal. Of the 504 expectant mothers who attended the antenatal clinic, 59.9% came once, 80.4% had their first visit in the third trimester (between weeks 28 and 40) and only 6.9% were accompanied by their partners. All the women were HIV tested in their first visit but only 12.1% were rescreened after three months, and only 3.8% had been tested prior to the current pregnancy (p=0.000). No expectant mother was tested for HIV intrapartum or postpartum. The children of the 504 mothers who were HIV tested were those whose parent/s were known to be HIV positive or who had presented to a child welfare clinic with recurring symptoms suggestive of a failing immune system. Conclusion: Public health programs need to strengthen the PMTCT and HIV prevention programmes to ensure that HIV testing preconception and in pregnancy is fully implemented and strengthened, alongside continued education of the public through community programmes and the media. To avert further horizontal and vertical transmission of HIV, there is a need to address urgently the identified missed opportunities in the PMTCT program. These programmatic challenges require health system redesign and strengthening, resource allocation, addressing research gaps and reassessing the current PMTCT policies.

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  • Synthesis of Organic Carbon Monoxide Releasing Molecules and their application in Palladium-catalysed Aminocarbonylation

    Cho, Kyulee (2013)

    Masters thesis
    University of Otago

    This thesis describes research carried out towards the synthesis of organic carbon monoxide releasing molecules (CORMs). Analyses of their ability to release carbon monoxide (CO) and to be employed in palladium-catalysed aminocarbonylation reactions are also reported.

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  • Communal consciousness: Thread of lies as composite novel and literary depiction of homophobia

    Ojabo, Idoko (2013-07-18)

    Masters thesis
    Auckland University of Technology

    Thread of Lies is a work of fiction that deals with homophobia; the trauma and dejection homosexuals face in the twenty-first century. The death of a lesbian couple is the background behind the plot. The exegesis explores the genre (the composite novel) of the creative work, the impacts of religion and politics on homosexuality, and the societies that gay novelists, James Baldwin and Sarah Waters, portray in their fiction. [Note: The novel “Thread of Lies” is embargoed until 19 November 2019]

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  • Effects of vessels on the surface and vocal behaviour of bottlenose dolphins in Doubtful Sound, New Zealand

    Guerra, Marta (2013)

    Masters thesis
    University of Otago

    Marine mammals in coastal areas are increasingly exposed to boats and noise as nature tourism grows. It is now well known that boat-based tourism has a wide range of detrimental effects on the surface behaviour of cetaceans, although effects on their acoustic behaviour are poorly understood. Measuring these impacts is critical for appropriate management, but translation of research findings into effective management often lags far behind research itself. The impacts of tourism on the endangered population of bottlenose dolphins (Tursiops truncatus) in Doubtful Sound, New Zealand, were first studied in 1999, demonstrating behaviour disruption due to boat presence. A code of conduct was implemented in 2008 to mitigate those impacts, establishing guidelines to leave dolphin encounters to chance and restricting vessel traffic in areas of critical habitat. The present study assessed the current impacts of tour boats and the observing research boat on the surface and vocal behaviour of dolphins, and evaluated the effectiveness of management guidelines in reducing interactions. An information-theoretic approach indicated that groups with mother-calf pairs were especially sensitive, showing significantly less cohesion and coordination when tour boats were audible, and were more vocal when boats were close and while moving away, presumably to re-establish group structure. Furthermore, groups with calves increased their whistle rates when tour boats were faster (i.e., louder) while groups without calves became quieter. These results suggest that elevated noise impairs communication and higher repetition rates are used to increase communication success. In a noisy environment, the need for vocal contact when calves are present seems to outweigh the costs of whistling more often. In addition, different whistle modifications were used in response to increased noise levels from tour boats: groups without calves produced longer whistles shifted towards lower frequencies, while groups with calves produced shorter and higher-frequency whistles. Although whistle rates were unaffected by the research vessel, movement patterns and whistle parameters were mildly affected, highlighting the importance of accounting for observer effects in studies of tourism impacts. The extent of dolphin-boat interactions in Doubtful Sound has decreased substantially since the previous study (1999 - 2002). This decline appears to be in response to the management guidelines established in 2008, showing that science-based management can mitigate potential long-term impacts of tourism. Nevertheless, because the Doubtful Sound population is small and has a history of low calf survival, and because groups with calves are particularly vulnerable to boats, it is crucial to further minimise current anthropogenic impacts. The present study provides recommendations for improving current management.

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  • An investigation into the cannabinoid receptor type 2 as a therapeutic target for childhood cerebral hypoxia

    Rivers Auty, Jack Rocky-Jay (2013)

    Doctoral thesis
    University of Otago

    Cannabis sativa is an herbaceous plant that when consumed produces a number of well-known effects on the body, primarily elicited by two G-protein coupled receptors: cannabinoid receptor type 1 (CBI) and type 2 (CBII). Activation of the CBII receptor suppresses the inflammatory response of the immune system. Research has suggested that inflammation can be pathological in central nervous system (CNS) injuries and during early development the brain may be more sensitive to inflammation. Therefore, this research aimed to assess if CBII selective agonists could be neuroprotective in an animal model of childhood cerebral hypoxia (CCH) through an anti-inflammatory mechanism. A previously established model of CCH, that involved the ligation of the left carotid artery of a P26 rat, followed by a fixed hypoxic period, was chosen because of age suitability and its applicability to both asphyxia and stroke pathologies. Investigations into the variability of infarction in the established model, lead to the development of a new model that ended following a clonic tonic seizure. This new model caused significantly less variable brain infarctions compared to the previously reported model and was named Variable hypoxia ischemia (Variable HI). Two CBII agonists were then tested for neuroprotective properties in Variable HI using a partial agonist (GW405833) and a full agonist (HU910). Both single and multiple drug administration strategies were tested and found to provide no substantial tissue protection. Furthermore, behavioral tests were performed following the multiple administration strategy and no differences were found in any functional outcome. Therefore, the anti-inflammatory effects of CBII agonists are unlikely to be substantially therapeutic following CCH. It was argued that this lack of efficacy was caused by the possibility that inflammation is not truly pathological following CCH.

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  • Development of dietary tools to assess dietary patterns of New Zealand adolescents

    Wong, Jyh Eiin (2013)

    Doctoral thesis
    University of Otago

    Despite the recognised importance of overall dietary patterns for adolescents’ health, dietary patterns have not been assessed by means of a diet index in New Zealand (NZ) adolescents. The lack of a validated adolescent-specific food frequency questionnaire has precluded the collection of dietary information in resource-limited research settings, while the absence of an NZ-specific diet index makes description of index-based dietary patterns impossible. This research aimed to address these gaps by developing valid and practical tools for assessment of dietary patterns among NZ adolescents aged 14 to 18 years. Four studies were conducted using data from the Otago School Students Lifestyle Survey Two (OSSLS2) and 2008/09 NZ Adult Nutrition Survey (2008/09 NZANS). Study I involved adaptation, pretesting and assessing the relative validity of a non-quantitative, 72-item NZ Adolescent FFQ (NZAFFQ) in a pilot sample (n 41) of the OSSLS2. The NZAFFQ was found to be comparable to a four-day estimated food record in ranking participants according to 34 food groups (rs=0.40), and highly repeatable when test-retested within two weeks (rs=0.71). In Study II, this questionnaire provided dietary information required for the development of the food-based NZ Diet Quality Index for Adolescents (NZDQI-A). The NZDQI-A was calculated based on ‘variety’ and ‘adequacy’ for five equally weighted food group components. Achieving a NZDQI-A score in the highest one third, was significantly associated with a higher intake of dietary iron and lower intake of total and saturated fat (P-trend<0.05) also established construct validity of the diet index. Through rigorous development and validation, this research demonstrated the validity and application of the NZAFFQ, NZDQI-A and HDHS-A as dietary tools to assess dietary patterns of NZ adolescents aged 14-18 years. Further validation of these dietary tools (in particular NZAFFQ and NZDQI-A) in larger, more socioeconomically and ethnically diverse samples is recommended to advance dietary pattern methodology and promote better understanding of diet-health relationships among NZ adolescents.

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  • Is Data Snooping responsible for Technical Analysis Rules Success?

    Turei Stanton, Worik Macky (2013)

    Masters thesis
    University of Otago

    Data Snooping is often suspected when effective technical analysis rules are found or presented. It is difficult to tell if a result is due to data snooping, so evaluating technical analysis rules often boils down to detecting data snooping and if it has invalidated the results. Herein we look at several algorithms designed to increase (risk–adjusted) returns for investors, and several techniques for detecting or compensating for data snooping. We find no easy answer to detecting data snooping. Many of the methods we look at are useful, but there is no known way to get around sparse data and the unrepeatable nature of investment decisions. We conclude that data snooping bias is a persistent risk and it is unlikely that there is any effective single solution to the problem. The best that we can do is be aware of the risk of data snooping and to report how we have dealt with the risk as part of our analysis.

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  • Reduced Representation Bisulfite Sequencing of Human Neutrophils Reveals Widespread Inter-Individual Epigenetic Variation

    Chatterjee, Aniruddha (2013)

    Doctoral thesis
    University of Otago

    Methylation of DNA molecules is a fundamental mechanism for regulating gene function that is prevalent in all vertebrates. Although, the role of DNA methylation is well recognised in the disease context, the knowledge of variable DNA methylation patterns in healthy individuals is very limited. To our knowledge, there was no study available investigating inter-individual DNA methylation variation in healthy individuals in a homogenous cell population. Identification of epigenetic variation in a normal population is an important step towards understanding phenotypic variation, altered disease susceptibility and drug response. Therefore, we sought to generate reference methylomes from neutrophils of 11 healthy individuals and then identify and document inter-individual variation in DNA methylation between them. We adopted the technique of Reduced Representation Bisulphite Sequencing (RRBS) to profile methylation pattern of the individuals. We optimised, improved and streamlined the process of RRBS library preparation. Next, a robust bioinformatic pipeline was established to analyse large-scale epigenomic data as part of the project, which could be efficiently applied to other large-scale epigenetic analysis. Several novel tools and new strategies were developed during the course of the study to facilitate genome-scale DNA methylation analysis. From the 11 individuals, 344 million sequenced reads were obtained and successfully aligned with the reference genome using our methylation pipeline. From the high quality methylation information available from the fragments, we were able to detect 12851 autosomal Variably Methylated Fragments (iVMFs) associated with 6353 protein coding genes. Almost 51% of the variably methylated fragments were found to be present in gene bodies, i.e., exons, introns and exon-intron boundary and overall 64% of them were located within CpG islands and CpG island shores. Integrating our results with recently released ENCODE data revealed that variably methylated fragments strongly overlap with active regions of the genome. It was observed that the variably methylated fragments strongly overlap with RNA polymerase II, CTCF binding sites and showed enrichment of active histone marks, DNase hypersensitive regions and strong enhancers. Further, upon ranking, we found 83 genes associated with 10 or more variably methylated fragments. Functional analysis of top candidate genes indicated that they disproportionately involve in neuron function, memory formation, and RNA metabolic processes. Pathway analysis indicated their involvement in melanogenesis, calcium signalling, neoplasms and carcinogenesis. Examples of the novel variably methylated genes include FBRSL1 (involved in would healing and a potential marker for alcohol-induced liver injury), STY10 (involved in immune dependent memory performance and circadian timing system), DLGAP2 (in organisation of synapse and neuronal cell signalling, implicated in autism spectrum disorders), CDH4 (a cell adhesion protein and putative tumour suppressor gene), SALL3 (regulation of DNA methylation, embryonic development and congenital disorders), TERT (involved in maintenance of telomere length). This study provides the first genome-wide, base-pair resolution DNA methylation profiles in a homogenous, human cell type to document inter-individual variation in DNA methylation. The results from this work will serve as a resource for future studies aiming to understand the nature and mechanism of altered phenotypic traits and disease susceptibility due to variable DNA methylation in normal individuals.

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  • As I Exemplify: An Examination of the Musical-Literary Relationship in the Work of John Cage

    Edmeades, Lynley (2013)

    Masters thesis
    University of Otago

    This thesis examines the ways in which John Cage negotiates the space between musical and literary compositions. It identifies and analyses the various tensions that a transposition between music and text engenders in Cage’s work, from his turn to language in the verbal score for 4’ 33’’ (1952/1961), his use of performed and performative language in the literary text “Lecture on Nothing” (1949/1959), and his attempt to “musicate” language in the later text “Empty Words” (1974–75). The thesis demonstrates the importance of the tensions that occur between music and literature in Cage’s paradoxical attempts to make works of “silence,” “nothing,” and “empty words,” and through an examination of these tensions, I argue that our experience of Cage’s work is varied and manifold. Through close attention to several performances of Cage’s work— by both himself and others—I elucidate how he mines language for its sonic possibilities, pushing it to the edge of semantic meaning, and how he turns from systems of representation in language to systems of exemplification. By attending to the structures of expectation generated by both music and literature, and how these inform our interpretation of Cage’s work, I argue for a new approach to Cage’s work that draws on contemporary affect theory. Attending to the affective dynamics and affective engagements generated by Cage’s work allows for an examination of the importance of pre-semiotic, pre-structural responses to his work and his performances. At the same time, this thesis demonstrates the importance of music and literature as frameworks for interpretation even and especially where Cage attempts to undermine these frameworks. The thesis, then, identifies the tension between pre-interpretative affective response and preconceived frameworks for understanding as part of a dynamic that drives the interplay between music and literature in Cage’s work.

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  • Clinical and Psychosocial Aspects of The Long Face Morphology

    Antoun, Joseph (2013)

    Doctoral thesis
    University of Otago

    Introduction: The long face morphology is a relatively common presentation in orthodontic patient populations, although the clinical and psychosocial features of this condition are still unclear. Objectives: To investigate and compare the: (1) cephalometric features; (2) oral behaviour patterns; (3) and, oral health-related quality of life and functional limitations between long (case) and normal (control) face individuals. A longer-term objective was to establish a craniofacial database that could be used to investigate the association between vertical facial patterns and selected candidate genes. Materials and Methods: Eighty cases with a distinctively long face (mandibular plane angle greater than 2 standard deviations, or 42 degrees) and eighty controls were individually matched on age, gender, ethnicity, and treatment stage. Self-report and clinical data were collected using an online database (www.longface.ac.nz). The self-report measures included the oral behaviour checklist (OBC), the Oral Health Impact Profile (OHIP-14), and the Jaw Functional Limitation Scale (JFLS-8). Moreover, a comprehensive cephalometric analysis was carried out for each study participant. Results: The sample had a mean chronological age of 17.2 years (SD = 4.6), with the majority of the participants being female (65.0%), and of New Zealand European origin (91.3%). In comparison with controls, long face individuals were characterised by a significantly reduced posterior facial height and increased anterior facial height (P < 0.001). Nearly one-fifth of the long face sample had an anterior open-bite. In general, the long face morphology was found to consist of at least 3-4 clusters (i.e. sub-phenotypes). There were no significant differences in either the prevalence or mean number of reported oral behaviours between long and normal face individuals. Long face individuals had small but significantly higher overall and social domains scores of the OHIP-14. On the other hand, there were little differences in functional limitations scores between cases and controls (P > 0.05). Conclusions: The long face morphology is not a single clinical entity but consists of several distinct clusters that can be characterised using cephalometrics. Facial morphology is not necessarily associated with jaw function or oral behaviour patterns. Long face individuals, however, are more likely to self-report poorer oral health-related quality of life, especially with respect to social interactions.

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  • Rivers of Peace: Third Party Conflict Management of Transboundary River Disputes

    Bobekova, Elvira (2013)

    Doctoral thesis
    University of Otago

    There is a growing body of literature explaining agreements over international river disputes. However, beyond individual case analysis, no quantitative study has been undertaken on the role of third parties in settling river disputes in the regions of the world that are most vulnerable to global climate change. Moreover, there has been no study that combines quantitative and qualitative approaches and provides a systematic explanation within a single analytical framework. This study aims to fill these gaps by combining quantitative and qualitative methods, developing a novel theoretical framework called transcendency, and conducting the first large-n study examining the role of third parties in the emergence of river agreements in Asia and Africa during the time period 1948-2007. Through utilising new data on the role of third parties in river disputes, this study shows that third party involvement in the conflict management of river disputes increases the likelihood of reaching river agreements. Through a process tracing case studies of third party engagement in international river disputes in Central Asia, this study also identifies how and why third parties reach agreements. Drawing on the transcendency framework, I argue that third party actors facilitate riparian cooperation by addressing three transcendency problems: securitisation of river systems, legal ambiguity and credibility problems. River water has a superordinate value, therefore river issues are often perceived as zero-sum security issues. At the same time, however, river water also has utilitarian value due to its use in addressing the development and economic needs of states. One of the reasons why third parties are able to advance cooperation is because third parties can assist in the de-securitisation of the water issue and shift the focus towards the utilitarian aspects of river disputes. Secondly, third parties can address issues related to legal ambiguity and help to clarify the positions of riparian states from a normative perspective. Thirdly, where upstream/downstream relationships exist, third parties can assist in obtaining and providing the necessary information to address issues of information asymmetry and incentivise parties to commit to their agreements through promises of financial support. In addition to identifying the effect and outcome of third parties in riparian disputes, this study also explains why some riparian disputes attract third party assistance whereas others do not, although this is not the major focus of the study. The study demonstrates that a third party’s strategic interest in the resolution of a dispute as well as a riparian state’s openness to the international community, particularly a riparian state’s relationship to powerful Western states, will determine if riparian states are willing to engage third party assistance in managing riparian conflict. Given the current uncertainty around the security challenges of climate change and water stress, this research contributes to our understanding of how to respond to conflicts concerning transboundary waters.

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  • Extended Care Paramedic clinical guideline compliance, does it have potential for harm?

    Hoyle, Sarah Raewyn (2013)

    Masters thesis
    University of Otago

    Background Extended Care Paramedic (ECP) practice is aimed at managing more patients at home or in the community under a delegated scope of practice applying pre-determined clinical guidelines. These clinical guidelines have been carefully developed to mitigate the increased risk associated with treating more patients in the community. This study aimed to evaluate the compliance of the ECPs in applying the clinical guidelines for lower back pain and syncope and to analyse the risk associated with non-compliance. Methods: Cases of syncope or lower back pain attended by ECPs were reviewed for compliance in a two stage evaluation. Based upon the documented clinical record written by the ECP, the compliance with the clinical guideline was determined. In cases where the guideline was not followed, two independent experts assessed the potential risk of harm for a patient utilising the Ministry of Health clinical incident risk scoring system. Results: There were 23 lower back pain and 25 syncope cases collected between April 2011 and Feb 2012 that were assessed. In 16 (64%) of the syncope cases the patient was managed in the community, although in 7 (44%) of these the case documentation did not demonstrate guideline compliance. The most commonly missed components of the guideline were headache, recent head injury and valvular heart disease. In 17 (74%) of the lower back pain cases the patient was managed in the community, however in 13 (76%) of these cases the case documentation did not demonstrate guideline compliance. The most commonly missed components of the guideline were weight loss and the presence of osteoporosis. The clinical risk associated with non-compliance was assessed differently by the two experts. One expert rated 3 (43%) of the syncope cases and 9 (69%) of the lower back pain cases as being a potential sentinel risk of harm to a patient, while the second rated 1 (14%) of the syncope cases and 2 (15%) of the lower back pain cases as a potential sentinel risk. Conclusion This study raises significant concerns regarding documentation of guideline compliance in cases where ECPs are choosing to manage patients in the community. It is not clear whether this reflects a failure in clinical care, or a failure in the documentation of the care provided. In either case, the risk to the patient, the ambulance service and the paramedic associated with the failure in documentation is considerable. In a significant proportion of these cases the risk associated with the missing documentation was classified as sentinel, although the variance in risk classification was considerable. The discrepancy associated with the risk assessment observed demonstrates the difficulty in evaluating risk purely on the basis of documentation of cases. The level of non-compliance appears to be different for the two clinical conditions studied. Quality improvement initiatives will be required to ensure that the ECP clinical evaluation of patients and the corresponding documentation are more compliant with the current operating guidelines.

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  • Spatial and temporal variation in beach-cast Durvillaea antarctica rafts

    Bussolini, Laura Taylor (2013)

    Masters thesis
    University of Otago

    Durvillaea antarctica is a robust, buoyant macroalga which is found growing throughout the high latitudes of the Southern Hemisphere. This kelp grows on exposed, rocky coastlines, and their holdfasts act as an important habitat for a wide variety of intertidal invertebrates. The internal structure of the blades traps air and gasses, allowing the entire structure to remain highly buoyant for extended periods of time. Thus, when kelp becomes detached following storm surges or intense wave action, floating rafts of D. antarctica can traverse the Southern Ocean, acting as an important transport vector for the associated invertebrates which inhabit the holdfasts. Previous work investigating the phylogeographic structure of growing, attached D. antarctica populations has revealed a high degree of genetic variation throughout the species’ range. The mitochondrial marker, cytochrome c oxidase subunit 1 (COI), is highly variable in attached populations, displaying a number of unique haplotypes, some exclusive to narrow geographic areas. With this molecular knowledge of attached populations, it is possible to assign a probable source location to rafts of D. antarctica which have washed ashore on the New Zealand coastline. This study collected beach-cast rafts of D. antarctica from a number of sites along New Zealand’s east coast and assigned each sample to a known haplotype (and thus, source population) by using established information regarding the species’ phylogeographic structure. By examining the assemblage of haplotypes sequenced from a particular beach, general patterns in rafted assemblages were evaluated. In particular, this study attempted to investigate how haplotype frequency found at a particular location changed across both space and time in relation prevailing weather patterns and ocean currents. On a spatial scale, significant changes were detected in haplotype assemblages across New Zealand’s east coast. Two distinct genetic breaks were found; one at Cape Campbell, and one in Pegasus Bay. A similar genetic break has previously been documented at Cape Campbell for a range of intertidal invertebrates with dispersing larval life-stages (e.g. limpets, sea stars, mussels, chitons). Data from this study confirm this genetic break; beach-cast D. antarctica assemblages showed dramatic genetic turnover between sites on a very fine scale, suggesting that the currents in this area act as a significant dispersal barrier to both D. antarctica rafts (and associated invertebrates) and intertidal invertebrates with larval life-stages. A second genetic break in the haplotype assemblages of beach-cast D. antarctica rafts was found in Pegasus Bay. Again, this break in haplotypes found mirrors a change in ocean currents of the region. This study demonstrates how the prevailing ocean currents of a particular region are intrinsically linked to the assemblage of beach-cast D. antarctica found on any given stretch of coastline. When changes in haplotype assemblages were examined across time, temporal patterns were only detectable after spatial variation was accounted for. The Cook Strait region showed the largest changes in haplotype assemblages found over time, which was expected, due to the variable nature of the ocean currents in this region. Changes in prevailing wind patterns can have profound effects on the flow of water in the Cook Strait region; prolonged shifts in prevailing wind direction can actually reverse the net flow of surface water. Therefore, the temporal shifts in quantity and source location of D. antarctica assemblages observed in this study are most likely a result of fluctuating wind patterns. This study found that the haplotype assemblages of beach-cast D. antarctica rafts show significant patterns across both space and time. D. antarctica rafts travel with major current systems, and thus, different assemblages of haplotypes are found in different regions of the country, reflecting the input of local currents. However, prevailing wind speed and direction are also critical components that influence which assemblages of D. antarctica are found on a particular beach at a particular time. The genetic breaks and temporal shifts identified in this study have profound implications for a wide variety of marine taxa, including the ‘hitch-hiking’ invertebrates present on D. antarctica rafts.

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  • Evaluation of clinical ethics support needs and service provision at a tertiary hospital in New Zealand

    Dai, Libby (2013)

    Undergraduate thesis
    University of Otago

    Doctors often face ethical challenges in the course of clinical practice. Clinical ethics advisory services (CESS) provide a mechanism for supporting doctors facing these ethical dilemmas. In New Zealand, CESSs are relatively new and have emerged as a clinician-led initiative. This is an exciting time for CESSs in New Zealand, as their availability increases and their systems become increasingly formalised and integrated into the health care system. This thesis is the first in New Zealand to explore the clinical ethics needs of doctors and to evaluate how their clinical ethics needs could be most effectively met. The Capital and Coast District Health Board (CCDHB), comprising a major tertiary hospital and its satellite hospital, is used as a case study. Doctors at CCDHB have had access to a clinical ethics support service since 2010, when the CCDHB Clinical Ethics Advisory Group (CCDHB CEAG) was established. Many of the findings of the research would be applicable to CESSs throughout New Zealand. I developed a methodology to understand the clinical ethics needs of senior doctors at CCDHB and to evaluate how their needs could be better met. In-depth, semi-structured interviews were conducted with 14 senior doctors. The data were analysed using an iterative inductive strategy combining conceptual and normative analysis. My analysis draws on the current international literature of clinical ethics support, as well as my experience as a clinical medical student and my period of observation of the CCDHB Clinical Ethics Advisory Group. This study found that in the absence of formal services, doctors use ad hoc strategies of peer consultation to manage ethical issues. Not all doctors were equally able to access informal support, particularly junior doctors. Many participants were unaware that formal clinical ethics support was available to them and most did not know how formal ethics support worked. Some participants felt that to seek case consultation was to abrogate clinical responsibility and thought that doctors should be able to manage ethical issues themselves. Participants identified a need for improved strategies for clinically relevant ethics education. This study identifies five key recommendations to enhance clinical ethics support at Capital and Coast District Health Board: 1. CCDHB CEAG should formalise its activities, particularly case consultation, using a procedural justice model. 2. CCDHB CEAG should involve clinicians in the process of case consultation to increase user trust and to take advantage of case consultation’s educative value. 3. CCDHB CEAG should allow patients and their families and advocates the option of being involved in the process of case consultation, to ensure that patients feel that their perspectives have been adequately taken into account. 4. CCDHB CEAG should conduct monitoring and evaluation of its service to ensure that it achieves and maintains clinical relevance and normative robustness. 5. CCDHB CEAG should actively disseminate accurate and appropriate information about its aims and processes to all users and potential users to enhance trust in their service and to clarify misunderstandings about their role.

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  • Overcoming the antifungal drug resistance of biofilms on dental acrylic

    Newsham-West, Kathryn J (2013)

    Doctoral thesis
    University of Otago

    Introduction RC21v3 is an octapeptide derivative that inhibits the drug efflux pump that confers azole resistance on the yeast Candida albicans -an opportunistic pathogen that can cause denture stomatitis. C. albicans often forms biofilms on oral surfaces including denture prostheses, and biofilm cells are more drug resistant than planktonic cells growing as a suspension in liquid medium. Aim The objective of this research was to determine whether RC21v3 acts synergistically with fluconazole (FLC) to inhibit the growth of C. albicans cells in planktonic cultures and during growth as a biofilm. Methods Minimum growth inhibition concentration (MIC) assays were undertaken to measure the inhibitory effect of FLC and RC21v3 on C. albicans cells growing as planktonic cultures. Checkerboard MIC assays were used to measure the effect of combinations of FLC with RC21v3 on both planktonic and biofilm growth. The inhibition of C. albicans biofilm growth on denture acrylic was measured using crystal violet staining of biofilm cells. The effect of FLC and/or RC21v3 on biofilm structure was investigated using confocal microscopy. Results Checkerboard MIC assays showed that RC21v3 acted synergistically with FLC to inhibit the planktonic growth of three C. albicans strains: ATCC 10261 and MML610 which are FLC-susceptible, and MML611 which is FLC-resistant. In addition, the combination of RC21v3 with FLC in growth assays resulted in FLC becoming fungicidal to all three strains. A novel dental acrylic biofilm model was developed. As it demonstrated reproducible growth of C. albicans, it could be used to measure biofilm growth inhibition. FLC inhibited the growth of C. albicans biofilms and checkerboard assays showed that RC21v3 acted synergistically to reduce the growth of ATCC10261 biofilms. Conclusion This is the first demonstration that RC21v3 can chemosensitize C. albicans biofilms to fluconazole, and so may be of use in treatment of patients with FLC-resistant biofilms on denture surfaces.

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  • Regulatory Mechanisms Modulating the Co-Expression of ESR1 and Three Upstream Genes in Breast Cancer

    White, Jackie Anna (2013)

    Masters thesis
    University of Otago

    Breast cancer is the most prevalent form of cancer diagnosed in women with oestrogen receptor α (ERα) positive breast cancers accounting for approximately 80% of all malignancies. Several genome wide association studies have associated breast cancer risk with a number of SNPs located in the 6q25.1 locus just upstream of the ESR1 gene which encodes ERα. More recently, ESR1 was found to be co-expressed with three uncharacterised genes, C6ORF97, C6ORF211 and RMND1 (collectively C6ORFs) situated immediately upstream from ESR1, in ER positive cell lines and tumours. These genes remained highly correlated after treatment with an ERα antagonist, so are unlikely to be regulated via ERα. RMND1 is also transcribed on the opposite strand, excluding the possibility of a single transcript. Alteration of DNA methylation is a common observation in breast cancer. Therefore, this project aimed to determine whether changes in DNA methylation occur at the 6q25.1 locus and whether this influences gene expression. This study hypothesised that changes in DNA methylation would correlate with gene expression of ESR1 and the three C6ORFs. Gene expression of ESR1, the three C6ORFs and alternative ESR1 mRNA isoforms were analysed in vitro using breast cancer cell lines. Long-term oestrogen deprived (LTED) cell lines were also generated and, together with fulvestrant resistant cell lines, were used to model the effects of anti-oestrogen therapies used in the treatment of ER positive breast cancers. These analyses revealed that DNA methylation in the ESR1/C6ORF97 locus, gene expression of the four transcripts and alternative ESR1 mRNA isoforms differed greatly between breast cancer cell lines. ER negative breast cancer cell lines were similar to the ‘non-tumourigenic’ MCF10A cell line while ER positive cell lines were hypomethylated and showed higher expression relative to MCF10A. Additionally, changes were seen in the ER positive cell lines during adaptation to oestrogen deprivation or fulvestrant treatment with the T47D LTED and fulvestrant resistant cell lines displaying an ER negative phenotype. Two putative regulatory binding regions were also discovered which were differentially methylated and correlated with gene expression in the cell lines; one negatively and one positively. To further examine this correlation in a clinically relevant setting, a public breast cancer dataset was analysed. ER positive tumours were found to be hypomethylated relative to normal tissue. In tumours, two differentially methylated regions were shown to have a strong negative correlation with gene expression of ESR1 and the three C6ORFs. These gave correlation coefficients of -0.577, -0.593, -0.600 and -0.454 for ESR1, C6ORF97, C6ORF211 and RMND1, respectively, using Pearson correlation analysis and correction for multiple testing. Further analysis of a normal breast tissue dataset revealed a very uniform DNA methylation pattern and ESR1 expression did not correlate with expression of the three C6ORFs. The differentially methylated regions in tumours coincided with binding sites for ERα and cohesin and long range chromatin interaction sites involving RNA polymerase II. Therefore, reduced DNA methylation seen in the ER positive tumours could facilitate enhanced chromatin interactions and transcription leading to the co-expression of ESR1 and the three C6ORFs. These alterations seen in the 6q25.1 locus, both in vitro and in the dataset, distinguish ER positive tumours and may contribute to resistance to anti-oestrogen therapies.

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  • Biochemistry of digestion and algal-biotoxin metabolism in bivalves

    MacKenzie, Angus Lincoln (2013)

    Doctoral thesis
    University of Otago

    This study was primarily focussed on the identification and isolation of enzymes involved in the digestion of phytoplankton in the bivalve gut and the assimilation and biotransformation of secondary metabolites released by these digestive processes within the digestive gland (hepatopancreas). The main hypothesis was that these enzymes play important roles in algal biotoxin sequestration and elimination and an improved understanding of the nature of these enzymes may lead to solutions to the harmful effect of algal toxin contamination on shellfish aquaculture productivity. The function of the crystalline style in these processes was an essential component of this objective incorporating the hypothesis that major matrix proteins play an important role in the gelling properties of the styles. A second objective was to identify digestive enzymes that might be useful as biochemical indicators for the discrimination of superior family traits within a bivalve selective breeding programme, and test the performance of these markers against mussel families selected for differing growth capacities. An endo β-1,4 glucanase (cellulase) that mediates the digestion of dinoflagellate thecal plates in the bivalve gut was tentatively identified and partially purified from the crystalline style of the GreenshellTM mussel Perna canaliculus. This enzyme appears to play a key role in the lysis of the toxic dinoflagellate Dinophysis (spp.) thereby liberating okadaic acid and pectenotoxins for absorption within the hepatopancreas. The enzyme was isolated using dissociated dinoflagellate thecal plates as substrate and assayed by the release of reducing sugars. After selective adsorption/desorption using a thecal plate suspension the enzyme was further purified by gel filtration and an active fraction of 43-44 kDa isolated. One major band of carboxymethyl cellulose (CMC) hydrolysis activity was observed on CMC-zymogram gels corresponding to a Coomassie stained protein of 46kDa on non-reducing SDS-PAGE gels. Under reducing conditions the activity on zymogram gels was maintained (at 46kDa) but the Coomassie stained band was shifted to 30kDa. However de novo amino acid sequencing of bands from heated aliquots on an SDS-PAGE gel revealed the presence of a 63 kDa protein which contained tryptic peptides with close sequence similarity to glycoside hydrolase family 9 (GHF9) cellulases found in a variety of invertebrate taxa including the blue mussel Mytilus galloprovincialis. This demonstrated that the 46 kDa activity bands on the zymograms were possibly artifacts created by complexing of the enzyme with probably at least two other proteins. The enzyme is almost certainly endogenous although this has yet to be confirmed by sequence analysis of cDNA and genomic DNA. An enzyme capable of hydrolyzing pectenotoxins (PTXs) and okadaic acid (OA) esters within the hepatopancreas of the GreenshellTM mussel Perna canaliculus was isolated and characterized. It is believed this is the first report of the purification of any esterase or lipase from the digestive gland of a bivalve. PTX2 and PTX1 were hydrolyzed by the enzyme but it was inactive against PTX11, PTX6 and acid isomerised PTX2 and PTX11. PTX11 and PTX2b competitively inhibited PTX2 hydrolysis. The enzyme also hydrolyzed short and medium chain length (C2-C10) 4-nitrophenyl-esters, okadaic acid C8-C10 diol esters and DTX1 7-O-palmitoyl ester (DTX3). The ability of the enzyme to hydrolyze the diol and acyl esters of okadaic acid, with which PTXs are invariably associated in natural shellfish contamination events, raises the possibility that it may participate in other associated process such as the synthesis of OA and PTX seco acid esters in vivo. MALDI-Tof MS/MS determination of de novo amino acid sequence and BLAST searches of several data bases failed to identify any similarity to known proteins. Partial characterization of the crystalline style matrix proteins of Perna canaliculus and Mytilus galloprovincialis was carried out to attempt to identify the biochemical basis of differences in the physical structure of the styles. P. canaliculus has a crystalline style that is typical of those bivalves with permanent hard-type styles while the style of M. galloprovincialis is typical of bivalves with transient soft-type styles. The consistency of the styles is clearly related to their respective moisture content and both style types contain a suite of high molecular weight (>800 kDa and ~95-170 kDa) heavily glycosylated proteins and medium molecular weight (40-50 kDa) more lightly glycosylated protein duplexes. These protein pairs appear to play a role in gel formation, and differences in the nature of these proteins may determine the difference between hard and soft styles. One and two dimensional SDS-PAGE, MALDI-TOF MS/MS peptide analysis and de novo amino acid sequencing, showed there was a high degree of similarity between the sequences of several peptide fragments of the prominent40-50 kDa protein duplexes and ‘Myosinases’ I and II annotated within a M. galloprovincialis EST data base (“Mytibase”). ‘Myosinases’ belong to a large family of astacin-like metalloproteinases that are widely distributed in nature, although in many cases their function is unknown. This research establishes a new role for this important group of proteins. Analysis of the electrophoretic behaviour of the style proteins from a number of New Zealand endemic bivalve species showed that medium MW lightly glycosylated proteins were a major component of them all. It was hypothesised that astacin-like proteins determine the character of the crystalline styles of all bivalve species. The activities of amylase, laminarinase, cellulase and chitinase enzymes in the crystalline styles of several New Zealand bivalve species were visualised, quantified and partially characterised. Alpha amylase and laminarinase constituted the major activities in Perna canaliculus and Mytilus galloprovincialis. Protein-specific N-acetyl glucosaminidase (NAGase) activity was highest in the style of C. gigas followed by the gastric fluids of P. galloprovincialis and the style of P. canaliculus. NAGase activity was very low in the style and gastric fluids of the surf clam Paphies subtriangulata and the gastric fluids of P. canaliculus. Chitobiase and chitotriase activities also varied in different ways between styles and gastric fluids in the various species. Whether the observed activities represented true chitinase activity was questionable because assays using chitin azure did not relate to the relative activities observed using fluorescently labelled proxy substrates in oyster and mussel style extracts. It was speculated that the NAGase activities observed may more realistically represent lysozymes than chitinases. Assays of chitinase, cellulase and amylase activities in the crystalline styles of selected fast and slow growing families of the mussel Perna canaliculus were carried out on two occasions over six months, during which time the shellfish were growing in a normal mussel cultivation situation. The data did not support the hypothesis that differences in growth rate by these families could be related to the different expression of digestive enzymes leading to improved nutritional efficiency by faster growing families. On the contrary faster growing families in general exhibited lower rates of enzyme activity and these differences between families appeared to be related to the size of the individuals rather than their genetic heritage.

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  • Thermal Hysteresis Proteins in Tenebrio molitor Larvae

    McKellar, James Lawrence Oreti (2013)

    Masters thesis
    University of Otago

    Adaptation to cooler climates is a necessity for the organisms which endure temperatures below freezing. The yellow mealworm beetle, Tenebrio molitor, overwinters in the larval stage and is therefore succeptable to freezing conditions. To reduce the risk of freezing, which can be lethal, T. molitor express thermal hysteresis protein (THP) into their haemolymph that bind to the forming surface of ice crystals and lower the freezing temperature of the organism’s fluids, which allows the larvae to survive temperatures down to −13 ○C. This small, highly disulfide bonded protein is traditionally produced recombinantly for analysis. However there are cleavages in the peptide backbone in the native protein that E. coli cannot produce and potentially play a role in the function. This research outlines the purification of THP from both the T. molitor larvae and a recombinant expression system and the two samples were tested using optical recrystallometry and nanolitre osmometry. The data show the two sources to have similar recrystallometry inhibition activity, however the native protein proves to be more active in reducing the freezing temperature, and therefore increasing the thermal hysteresis, than the recombinant protein. The data also show evidence of the thermal hysteresis proteins forming dimers and other multimers and suggests there are interactions between the many isoforms produced by T. molitor. The difference in activity between the two sources shows the importance of understanding post-translational modifications when using a recombinant expression system and knowing how proteins function in relation to other proteins in vivo.

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  • The Development of a Facebook Concussion Management Intervention for Young Persons with a Sports Concussion

    Ahmed, Osman Hassan (2013)

    Doctoral thesis
    University of Otago

    Background: A concussion is a brain injury caused by direct or indirect forces to the head, and is common in contact and collision sports. The high proportion of younger individuals who participate in contact and collision sports means that a considerable number of concussions involve persons in this demographic group. Medical management of concussion centres on physical and cognitive rest during the early stages post-injury, with the provision of accurate information important in order to facilitate a safe return to sport, education or employment, and recreational activities. The recent advent and continued use of social networking sites (in particular Facebook) amongst the younger population has led this thesis to explore the potential of Facebook to provide best-practice concussion information to individuals recovering from a sports concussion. Aims: Given the absence of any prior examination of the use of social networking sites to assist the recovery from sports concussion, this thesis explored the use of a Facebook concussion management intervention as an adjunct to traditional medical care. The overall aim of this thesis was: - To develop a concussion management intervention to be delivered via Facebook. To achieve this aim, a number of preliminary studies were conducted in order to inform the development of the Facebook concussion management intervention. Methods: A multi-stage approach was used in the development of the interactive concussive management intervention (termed “iCon”). Following a comprehensive review of the related literature, existing concussion-related websites and Facebook groups were evaluated. The subsequent consultation with key stakeholder groups (young persons with a concussion and doctors whose caseload includes persons with a concussion) assisted in identifying the needs of this cohort and further aided the development of iCon. As well as containing best-practice concussion information, key features of iCon include the provision of real-time feedback from a sports physiotherapist and a doctor, links to high-quality concussion-related websites, and the opportunity to share concussion-related experiences with other users. Once iCon had been developed it was necessary to trial this intervention under controlled conditions, and a pilot study was used for this purpose. iCon was evaluated using programme evaluation methodology, with the primary focus of the evaluation being measured by the satisfaction of the individuals using iCon. A participant questionnaire was conducted prior to entering the group and upon exiting the group, and objective symptom measurements were taken prior to and following iCon. Data relating to the participants’ use of iCon and their interactions was also sought during this pilot study. Results: The evaluation of concussion-related websites indicated a variety in the quality, content and readability of the information posted online, whilst the analysis of existing concussion-related Facebook groups showed these to be primarily used by individuals to share experiences relating to their concussion. The stakeholder consultation demonstrated support for the development of iCon, from both young persons who had sustained a concussion (via focus groups), and the doctors responsible for their care after a concussion (via semi-structured interviews). Eleven participants were enrolled into the pilot study, and all of the participants who were symptomatic upon entering iCon (N=9) saw a reduction in their symptom scores. The primary measure of evaluating iCon was the satisfaction of the individuals using it, with the satisfaction scores and accompanying quotes indicating that the participants were satisfied with iCon. All of the participants (N=11) stated that they would recommend iCon to others, and that they felt comfortable in sharing information within iCon. The majority of participants (N=8) also reported their concussion knowledge had increased as a result of iCon and that iCon influenced their return to play decisions. Conclusions: The innovative approach taken in this thesis using a Facebook concussion management intervention to assist the recovery from concussion showed promise, and indicated that iCon has a potential role to play as an adjunct to traditional management strategies for concussion. The pilot study of iCon demonstrated that the use of Facebook in this manner showed acceptability within this cohort, and suggests that a larger trial of iCon is warranted.

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