Otago University Research Archive
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The History of New Zealand/ Aotearoa Dolphins Cephalorhynchus hectori: Abundance and Distribution
No full textHector’s and Māui dolphins (Cephalorhynchus hectori) are endemic dolphins of Aotearoa New Zealand. This thesis documents how C. hectori have changed from being the most common dolphin species seen in New Zealand waters to one of the rarest. The decline of C. hectori has been almost entirely due to bycatch in inshore net fisheries.
This collection and analysis of historical information documents and examines observations and the earliest scientific information of C. hectori from the 1800s onwards. Peer reviewed publications, old books and historical media have been accessed, providing general descriptions, information about distribution, habitat use, sightings, strandings, bycatch and pod sizes. Creative components produced as part fulfilment of the MSciComm and documented in this thesis include a music CD, a public awareness campaign and a museum exhibition.
Convincing evidence is presented that C. hectori were previously abundant in many places around New Zealand including the wider Cook Strait, Tasman Bay and much of the North Island. Many small subpopulations (hapū) have been removed or reduced to very small population fragments from the Hauraki Gulf, Bay of Islands, Hawkes Bay, Wairarapa, Palliser Bay, Kapiti, Whanganui and Taranaki. Some of these hapū began to be impacted in large numbers from the 1960s onwards.
Estuaries, lagoons and rivers were historically much more important foraging areas than they are now. Group sizes used to range in the hundreds and have reduced over time.
This important, historical information is critical to a comprehensive analysis of the conservation status of these dolphins. By understanding the patterns of decline, we can know what to expect to see when Hector’s and Māui dolphin hapū are on the path to true recovery. This will require adequate protection from the fishing impacts responsible for their demise
Predicting the past: Mathematical models and numerical methods in molecular phylogenetics
No full textMolecular phylogenetics is the study of phylogenies and processes of evolution by the analyses of DNA or amino acid sequence data. In this thesis we describe a computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. The new diffusion approach coupled with state-of-the-art numerical algorithms allow for analyses of datasets containing hundreds or even thousands of individuals. We demonstrate the scale of analyses possible using a SNP data sampled from 399 fresh water turtles in 41 populations. The method, which we call Snapper, is the successor of the coalescent based method Snapp. A reanalysis of soybean SNP data demonstrates that the two methods are hard to distinguish in practice. We also describe a Bayesian methodology for inferring niches of present and ancestral species of plants from environmental measurements and estimated phylogenies. Fitting the phylogenetic niche model to three conifer species endemic to New Zealand confirms that viable ancestral niches can be inferred. Lastly, in anticipation of even larger genomic datasets we look into graphical processing units as computational tools for efficient model fitting. We introduce a new graphical processing unit based algorithm designed to fit long chain Hidden Markov models, applying this approach to an Hidden Markov model for nonvolcanic tremor events. Our implementation resulted in a 1000-fold increase in speed over the standard single processing algorithm, allowing for a full Bayesian inference of model parameters
Investigating Cultural Dimensions via Developers Artefacts: The Utility of Repository Mining
No full textA growing body of research is using artefacts from online development communities to explore the impact of developers’ behaviours on the software development process. Although this research has produced many insights, researchers have yet to fully explore the impact of developers’ cultural backgrounds on their behaviours in an online community, although such understandings could be useful for helping the community to understand and plan for team dynamics. This study utilised a pragmatic case study to explore the relationship between culture and online behaviour among developers from the United States (U.S.), China, and Russia—three countries that differ in their orientations as individualistic or collectivist cultures. The data for the study comprised artefacts supplied over an 11-year period by users of Stack Overflow1, a popular online programming community that addresses questions from members by providing them with rapid access to the knowledge and expertise of their peers. Artefacts consisted of developers’ questions and answers, personal profiles, Up and Down voting records, online reputations, and earned badges. Data mining techniques, as well as statistical, linguistic, and content analysis were used to compare artefacts from the three groups of developers based on their cultural orientation as individualistic or collectivistic, attitudes, and interaction and knowledge sharing patterns. The findings revealed differences among the three groups that were consistent with their cultural backgrounds. U.S. developers, who are from an individualistic culture, asked and responded to more questions, had higher average reputations, used the pronoun “I” more frequently, and were more task- focused. Conversely, Chinese developers, who are from a collectivistic culture, provided more extensive commenting and editing of posts, used the pronouns “we” and “you” more frequently, and were more likely to engage in information exchange. Russian developers had been using Stack Overflow the longest and were the most reflective. The cultural patterns identified in this study have numerous implications for enhancing in- group interactions and behaviour management among software development communities
Investigating the invasion biology of Plasmodium vivax using its sister species, Plasmodium cynomolgi
No full textThe erythrocytic stages of the relapsing human malaria parasite, Plasmodium vivax (P. vivax), preferentially invades immature CD71+ reticulocytes. This strict tropism for nascent reticulocytes is the primary reason for the absence of P. vivax long term in vitro culture. Plasmodium cynomolgi (P. cynomolgi), a closely related simian malaria parasite, also preferentially invades human CD71+ reticulocytes, however it can be cultured continuously using mature monkey erythrocytes. In this thesis, I investigated the invasion biology of P. vivax using a recently re-established P. cynomolgi strain, P. cynomolgi Berok, which is sustained in Macaca fascicularis erythrocytes for long term in vitro culture.
The first aim of this research was to re-establish and optimise the long term in vitro culture of erythrocytic P. cynomolgi at the University of Otago. Here we not only succeeded in establishing a robust continuous culture of P. cynomolgi in New Zealand, but also developed methods to replace expensive monkey serum with cost effective human serum. We also optimised the enrichment and cryopreservation of cultured P. cynomolgi.
Secondly, the research compared the functional invasion characteristics between P. vivax and P. cynomolgi Berok erythrocytic merozoites. We observed both P. vivax and P. cynomolgi Berok to preferentially invade immature CD71+ human reticulocytes. Furthermore, as P. vivax is duffy-dependent, we incorporated the use of Fy6 2c3 and FyB antibodies to block the extracellular domain of the Duffy receptor (DARC, Fy or CD234) and observed a decrease in percentage of invasion in both P. vivax and P. cynomolgi Berok respectively. Our data shows that P. cynomolgi Berok is a representative model species navigating further exploration of the interaction between the P. vivax Duffy Binding Protein (PvDBP) and the host red cell DARC.
The next section of this study aimed to further characterize P. cynomolgi Berok ligand-receptor interactions with the human reticulocyte surface receptors based on solved P. vivax protein binding complexes to their cognate human host surface proteins. In addition to further investigating the PvDBP-DARC relationship using an in-situ protein binding assay we also endeavoured to study the less known relationship between P. vivax Reticulocyte Binding Protein 2b (PvRBP2b) and the Transferrin receptor 1 (TfR1 or CD71) by co-immunoprecipitation assay. The study explored the binding of these recombinant proteins and their respective homologs in P. cynomolgi Berok to human and macaque recombinant proteins. Interestingly, no interaction was observed between paralog PcyDBP2 and DARC, and ortholog PcyRBP2b and TfR1.
We briefly explored the genotype underlying the expression of Vel blood group using cord blood donors collected at Shoklo Malaria Research Unit, Mae Sod, and Thailand. This newly identified blood group is highly expressed on the surface of immature reticulocytes. We have observed that in the majority of the donors, the intron 2 region of the underlying gene, Small integral membrane protein 1 (SMIM1), harbours the rs143702418C and rs1175550A genotypes.
Following the functional and recombinant protein studies, we compiled a series of transmission electron micrographs (TEMs) to show merozoite invasion with and without Cytochalasin D, trophozoite maturation, asexual multiplication, and cytoadherence to neighboring erythrocytes using the in vitro P. cynomolgi Berok culture.
In summary, our findings emphasized the role for in vitro P. cynomolgi Berok as a laboratory surrogate for erythrocytic P. vivax. The re-established in vitro P. cynomolgi Berok culture has widened our perspective to current P. vivax vaccine candidates (PvDBP and PvRBP2b), and strengthens our ability to develop effective treatments and vaccines to control vivax malaria in the future
Experiences of the use of an iPad application (ADOC-E) for shared decision making around goal setting in rehabilitation: a qualitative descriptive study
No full textInvestigation of the Genes sll1354, sll1165, and sll1520 in Genomic Instability in Cyanobacterium Synechocystis sp. PCC 6803
No full textThe model cyanobacterium Synechocystis sp. PCC 6803 is used extensively in the studies of oxygenic photosynthesis as well as genetic engineering. The ability to incorporate exogenous DNA into its genome through homologous recombination makes it a potential biosystem that can be manipulated to produce valuable compounds. Synechocystis sp. PCC 6803 possesses an advanced DNA recombination and repair mechanism that enables the survival of the bacterium in various environments. This mechanism serves as a double edge sword as it improves the plasticity of the cyanobacterium; on the other hand, it also promotes genomic instability. This study investigated the role of the genes sll1354 (recJ), sll1165 (mutS1), and sll1520 (recN) in genomic instability. A PS II mutant strain showed signs of genomic instability where it grew photoautotrophically in pH 7.5 medium, which it is incapable of growing initially. When the constructs of interrupted genes of interest were introduced into the strain, the mutants' ability to grow photoautotrophically in pH 7.5 medium was compared to the control. The interruption of sll1354 and sll1520 was found to show a minimal effect on the growth rate reversion, whereas disruption on sll1165 was found to restored photoautotrophic growth in pH7.5 medium. This preliminary data in this study suggested that the gene sll1165 may be one of the genes that is involved in the DNA recombination and repair mechanism in Synechocystis sp. PCC 6803, which, in turn, may plays a role in cyanobacterial genomic instability
‘Bring me a shrubbery’: Assessing the habitat preference of mammalian predators in the urban green spaces of New Zealand cities
No full textWithin cities, areas of green space, such as patches of forest, play a vital role as habitat for wildlife, and can be especially important for supporting native biodiversity. As such, urban restoration efforts often aim to enhance the quality of existing green spaces to provide better habitat for native wildlife and increase biodiversity as a whole. In New Zealand, the number of urban restoration efforts have been steadily growing in recent years, with emphasis often placed on supporting bringing native bird species back to the city. One of the greatest threats to these conservation efforts are introduced mammalian predators (IMPs). IMPs have substantially impacted native biodiversity throughout NZ, causing the extinction of many endemic species. While the impacts and ecology IMPs have been thoroughly studied outside of urban areas in NZ, their urban ecology is not well understood. Such information is essential if successful restoration and reintegration of native wildlife is to be successful. The research undertaken in this thesis aimed to identify what IMPs are present in the urban green spaces of NZ cities, and what habitat characteristics influence their distributions, for the purpose of improving the effectiveness and efficiency of urban predator management. To investigate these aspects of IMP ecology, transects of predator detection devices were deployed during spring and autumn in three types of prominent urban green space: forest fragments, amenity parks, and residential gardens, and within three NZ cities: Dunedin, Hamilton, and Wellington.
First a broad assessment of predator detection rates across season, city and habitat type was conducted, followed by a comparison of detection methods. Lastly, detection data was paired with complex microhabitat information to generate models used to assess small scale and broadscale habitat preferences. There were five predator species/groups that were regularly detected: mice (Mus musculus), rats (Rattus spp.), hedgehogs (Erinaceus europaeus), possums (Trichosurus vulpecula), and domestic cats (Felis catus), while detection of mustelids (Mustela spp.) were very rare. Possums exhibited a clear affinity for forest patches, with distance to nearest forest patch a strong determinant of detection probability, and were very abundant in Dunedin. Possums were rarely detected in residential areas and were almost absent in Wellington due to a history of robust possum control. Rodent detections were substantially higher in autumn than in spring and were generally detected least in residential areas. Rats and mice were significantly associated with abundant low vegetation cover. Detection probability of rats were also significantly higher in residential properties with compost bins. Rats were more abundant in Wellington, likely in part because of the low possum abundance. Hedgehogs displayed a strong seasonal pattern, displaying much higher detections in spring than in autumn. Hedgehogs had no clear preference for any broad habitat but were linked with forest patch proximity and were very abundant in Dunedin. Detection rate of cats generally increased in autumn, especially in residential areas. This may have resulted in behavioural changes by residential rodents.
Comparison of predator detection methods (chew cards, tracking tunnels, and cameras) found that while some methods are better for specific species, using a multidevice approach is beneficial. Although, cameras were the most effective at detecting all species.
The body of work within this thesis will help towards the effective and efficient control of urban IMPs, which is essential if restoration and biodiversity goals are to be successful in New Zealand cities
Investigating RNF43 Mutations as Biomarkers for ctDNA Surveillance of Colorectal Cancer
No full textThis project aimed to investigate the utility of RNF43 mutations for circulating tumour DNA (ctDNA) surveillance of colorectal cancer (CRC). CRC is the second deadliest cancer in New Zealand. CRC patients currently under-go 5 years of follow-up surveillance post-resection of primary tumours, requiring CT scans, colonoscopies, and CEA-tests to detect disease recurrences. These methods can be invasive, difficult to access, and inaccurate. Surveillance with ctDNA during and after treatment is a promising alternative to these current methods.
ctDNA is DNA released into the bloodstream by dying tumour cells. It carries tumour-specific information such as somatic mutations and methylation changes that distinguish it from normal cell-free DNA in the bloodstream. ctDNA can be detected and quantified in patient plasma samples via assays for these tumour-specific alterations. ctDNA levels have been shown to correlate with tumour burden, disease progression, risk of recurrence, and real-time response to treatment.
RNF43 is a tumour suppressor that plays an important role in regulating the Wnt signalling pathway that is frequently dysregulated in CRC. We investigated RNF43 mutations in a New Zealand CRC patient cohort to determine if they occur at a high enough frequency to justify their inclusion on custom targeted tumour sequencing panels being developed for the detection of personalised mutation markers for ctDNA surveillance of CRC.
In this project, we designed a novel protocol for sequencing RNF43 that optimises time and cost efficiencies and yields highly accurate exome sequence data to identify true pathogenic mutations. Using this protocol, we identified pathogenic mutations in RNF43 in 3 of 24 (~13%) primary tumour samples. This fairly high mutation rate and the likely founder status of the pathogenic RNF43 mutations justifies the inclusion of the RNF43 gene in targeted sequencing panels for the routine detection and quantification of ctDNA markers in CRC
Managing older adults requiring endodontic treatment. A New Zealand practice-based research network study
No full textNew Zealand (NZ) has an ageing population and like most countries, this is expected to increase. Many older adults (65+ years), including those with comorbidities, are retaining their teeth into old age, meaning treatment planning and management of these patients is often complex. The scope of endodontics encompasses the prevention or treatment of apical periodontitis and enables preservation of the natural dentition. There is a limited understanding of the preparedness of the NZ general dental workforce to manage the endodontic needs of older adults.
The last national survey of endodontics among NZ dentists was reported over 17 years ago and it indicated that general dental practitioners (GDPs) provided endodontic treatment but technology, management philosophies and health in older adults has changed over time. Further, there is no recent information about NZ practice to guide clinical decision making.
This Practice-Based Research Network study used a mixed-methods approach to better understand the endodontic needs of older adults and the challenges faced by GDPs in NZ. An online national survey was followed by focus group interviews with dentists who had varying experience levels and resided in main centres and regional areas of NZ.
The specific objectives included investigating GDP philosophies, knowledge, practices, attitudes (including ageism) when managing older adults requiring endodontic treatment. Alongside this, the role of GDPs in providing domiciliary care and Continuing Professional Development (CPD) activities were also investigated.
The survey collected quantitative and qualitative data from 382 GDPs (response rate 23.3%). Findings were analysed using SPSS and NVivo software. The emerging themes from the survey guided the face-to-face focus group interviews which provided deeper understanding and context to the survey responses.
The results from the survey and focus groups showed that GDPs enjoyed treating older patients, however patients with a reduced cognitive ability rendered dental management ‘more complex’, ‘requiring more skill and patience’. Many GDPs expressed that the dental needs of older adults in residential care is significant, however the ability to provide care is limited. The endodontic requirements of older adults varied, with most patients wanting to retain their teeth, however ‘self-ageism’ was a barrier in many instances. Cost of root canal treatment (RCT) was a significant barrier for many patients with some clinicians electing to carry out vital pulp therapy as an interim means of managing their problem. Most GDPs performed RCT and teeth identified as difficult preoperatively (e.g. calcified canals, retreatment or especially strategically important teeth) were referred to specialist endodontists for management.
The outcomes from this study can be translated to clinical practice, with a desire by most GDPs to undertake further CPD related specifically to the management of older adults with medical problems, and patient centred treatment planning
Clinical handover from the operating theatre nurse to the post anaesthetic care unit nurse: a New Zealand perspective
No full textThe perioperative environment is complex, it encompasses multiple teams of health professionals and numerous transitions of patient care, requiring effective teamwork and communication to avoid negative patient outcomes. Clinical handover provides the critical bridge between professionals; it is an important ritual which, not only provides a sense of professional achievement and personal satisfaction for the nurse, it ensures a safe transition of care for the patient.
Aim of the study
The aim of this research was to identify current practice in handover from the theatre nurse to the post anaesthetic care nurse in the New Zealand perioperative setting.
Research design and method
A quantitative research design was chosen using descriptive statistics, to gain a broad understanding of perioperative handover in New Zealand, about which little is known. Data collection via an online self-completed questionnaire elicited the opinion, observations and experiences of perioperative nurses from a wide a range of surgical hospitals throughout New Zealand. Interest in the study was solicited through communication with the New Zealand Perioperative Nurses College.
Findings and Recommendations
One hundred and thirty survey responses met the study’s criteria and were included in the data analysis. The results illustrate that perioperative nurses in New Zealand are experienced, adaptable in their practice and regularly engage in face-to-face verbal handover. It is also clear that most perioperative nurses are satisfied with nurse-to-nurse handover.
Barriers to effective verbal handover in the perioperative environment were identified, with the receiving post anaesthetic care nurse being required to multitask, and therefore not actively listening highlighted. In addition, collegiality between nurses and a ‘handover pause’ for verbal handover were important to nurses, and factors identified that enabled the safe transfer of information.
International literature has a plethora of suggestions on how to overcome communication barriers and how to mitigate error, with many of those suggestions being integrated into the New Zealand health care system. Indeed, that a culture of patient safety exists to some extent in the New Zealand perioperative environment is the overriding impression from the survey results. There appear to be systems, such as, standardised models to guide verbal handover, and an awareness of appropriate nurse behaviours which results in nurses working together to achieve safe transitions in patient care.
One recommendation to come from this study was for a formal ‘handover pause’ to be instigated in the post anaesthetic care unit, so all the health professionals involved in handover can actively engage in the communication process. Additionally, in the interests of patient safety, face-to-face verbal handover in combination with a written framework of documentation is recommended. Provision of education on how to conduct effective nurse-to-nurse handover also needs to occur.
The results of the current study have identified numerous opportunities for future research, both in New Zealand and internationally. It is clear there is a dearth of literature specifically on nurse handover in the New Zealand perioperative setting, with this study providing the foundation from which future research can occur