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Evolution of ciprofloxacin resistance in Pseudomonas aeruginosa
Pseudomonas aeruginosa causes a wide range of infections. Ciprofloxacin is one of the most widely used antibiotics for the treatment of these infections. Antibiotic resistance in P. aeruginosa has made its eradication complicated and commonly leads to treatment failures. The genetic basis of ciprofloxacin resistance in P. aeruginosa is partially understood and a more complete understanding may improve chemotherapeutic regimens for treatment of this pathogen.
The overall aim of this thesis was to identify genes associated with ciprofloxacin resistance. Ciprofloxacin-resistant mutants were obtained from an antibiotic sensitive reference strain, P. aeruginosa PAO1, through experimental evolution, and genomic analysis of mutants was carried out. Mutations were found in gyrA, parC, parE, and nfxB, which are genes previously associated with ciprofloxacin resistance, and in genes not previously known to be associated with resistance such as PA3491, and pil genes. The mutation in gyrA was a key determinant of ciprofloxacin resistance. Mutation in the PA3491 gene was shown to be involved in increasing the ciprofloxacin resistance for the first time and was shown to influence the expression of the mexCD efflux pump genes. To quantify the contribution of mutations to ciprofloxacin resistance, mutations were engineered into the PAO1 genome individually and in multiple combinations, and Minimum Inhibitory Concentration (MIC) testing was carried out. Combinations of multiple mutations led to the high level of resistance. MICs of engineered mutants showed that gene-gene interactions were involved in the development of a high level of ciprofloxacin resistance. This information was used to predict the resistance of 237 clinical isolates through analysis of their genome sequences. 71%, 24%, and 7% clinical isolates had actual MICs equal, greater, and less than the predicted MICs, respectively.
Overall, this study enhanced our understanding of the genetic basis of ciprofloxacin resistance evolution in P. aeruginosa. This study has also shown that gene-gene interactions can play an important role in antibiotic resistance and can be successfully incorporated into models predicting resistance phenotype
Essays on retirement wellbeing in New Zealand
The thesis is motivated by the unique retirement provision system in New Zealand (NZ). NZ has a low replacement rate from its public pension provision, New Zealand Superannuation (OECD, 2015), lack of a public mandatory contributory retirement savings scheme, a voluntary retirement savings system with limited power to accumulate wealth and lacking annuitisation options (KiwiSaver) and a taxation system that favours investment in housing. The nature of the system limits retirees’ capacity to accumulate wealth for retirement and puts considerable pressure on them to manage their wealth but not outlive their wealth. Despite the concerns, there is limited research on the investigation of the financial wellbeing of New Zealand retirees.
This thesis consists of three essays which contribute to closing this gap in the literature. The first essay reports on the impact of housing on the financial adequacy of NZ retirees using panel data from the Survey of Family, Income and Employment (SoFIE) for the period 2002–2009. The essay examines the differential effect of housing liquidation options, rent imputation and asset liquidity on financial adequacy. The essay finds that Māori, renters and individuals living in multi-dwelling occupancies have much lower levels of financial adequacy. Individuals of Pākehā or Asian ethnicity, homeowners and those living alone benefit more from imputed rent derived through home ownership.
The second essay examines the effects of holding asset class liquidity, specifically housing and liquid wealth on optimal consumption and housing options. By using an analytic tool of the Life-Cycle model, the essay presents findings for optimal consumption and housing that incorporate uncertainty over a person’s health, income and their time of death, and the probability of health, income and house price shocks. By applying two sets of probability matrices, the study reports that housing liquidation options change when there is persistent bad health probability. Persistent health probability causes a divergence of utility between Renting, Sell/Buy and Stay scenarios. Renting is the most flexible option when it comes to dealing with health shocks, although it may not be the optimal choice. Sell/Buy is an optimal choice for many different scenarios, but is also the most prone to utility drops in the event of a bad health shock.
The third essay investigates the financial literacy of older New Zealanders and the relationship between financial literacy and decision-making. The study finds that the level of financial literacy in New Zealand is high. Subjects who are younger, of Māori or Pacific Islands ethnicity, female, have lower educational attainment, lower incomes and high family responsibility have significantly lower levels of financial literacy, and this potentially leaves them more vulnerable to financial mistakes (Calvet et al., 2009; Stolper and Walter, 2017). The study also finds that higher financial literacy has a significant correlation with better debt position and higher risk tolerance. The results show that higher financial literacy has a strong positive effect on choosing KiwiSaver and that having more worrying levels of debt is the main driving factor behind choosing to pay off debt, regardless of financial literacy levels.
This thesis contributes to the literature on retirement wellbeing, in general, and particularly in New Zealand. The findings on financial adequacy, optimal consumption and housing choices, financial literacy and role of financial literacy in spending decisions can better inform retirement decision-making. The essays in the thesis provide motivation for future research in the relevant area of wellbeing in retirement
Application of PEF technology and new smart ageing techniques to dry ageing venison and lean bull beef
Dry ageing of red meat is a re-emerging technique and product demand has increased considerably in recent years. Dry ageing of meat generates unique flavours and adds value. Most dry ageing is done on premium, highly marbled beef. With all its popularity, minimal research has been done on dry ageing of lean, low fat content animal models. In this research, the main focus was to study dry ageing in two lean red meat models, venison and bull beef with fast and slow oxidation, respectively. The two studies investigated the application of novel technology to enhance and add value to some low value cuts from lean bull beef.
The first research project applied pulsed electric field (PEF), a standalone non-thermal technology, with the aim of improving meat quality attributes and enhanced moisture transfer in the dry ageing process. The results across the two trials showed that High PEF (HPEF-10 kV, 50 Hz, 20 µs) treatment had sufficient pulsed electrical field strength to cause cell electroporation; this was confirmed by the transmission electron microscopy (TEM) images that showed reduced myofibril organisation and deformation and rupture of z-lines. Application of HPEF improved drying rates during the dry ageing process by up to 6% in the two trials run at 65 and 80% relative humidity (RH). Ultrastructural modifications induced by HPEF treatment also caused improved meat tenderness by up to 9%. This is of considerable interest to meat processors as it would positively impact on consumer repurchase of the product. HPEF decreased the polyunsaturated fatty acids (PUFAs) throughout dry ageing but it did not affect cis 9, trans 11 conjugated linoleic acid (CLA) across both venison trials. The preference for CLA to be esterified on the sn-2 position of the triacylglycerol strongly reflects their oxidative stability regardless of the chosen ageing method of venison. The development of secondary oxidation by-products as assayed by thiobarbituric acid reactive substances (TBARS) was not influenced by PEF treatment. The PEF treatment groups had no effect on mineral content (including pro-oxidant transition elements) of meat samples. This was critically important as it showed that at the treatment level, little to no mineral leakage from the electrodes to the meat product was occurring. The derived changes in mineral content were due to the concentration effect between the dry ageing and wet ageing processes.
The investigation into protein oxidative modifications showed similar trends to lipid oxidation with both PEF treatment groups not increasing total carbonyl content. Oxidative carbonylation increased in the dry ageing regime compared to the wet ageing process. To gather more information on specific protein oxidative modifications in the study, the protein oxidation biomarkers γ-glutamic semialdehyde (GGS) and α-aminoadipic semialdehyde (AAS) resulting from the oxidative deamination of proline, arginine and lysine residues, respectively, were investigated. No influence by PEF treatment was observed, but the AAS and GGS by-products were higher in dry aged venison compared to wet.
The second part of this study was done in collaboration with AgResearch Ltd, and explored the use of novel smart ageing techniques by using stepwise in-bag dry ageing on lean bull beef. The study established lipid oxidation, protein oxidation and metabolite profile changes during ageing under standard operating conditions for in-bag dry ageing (stored at 2°C, 75% RH, with air velocity in chiller set at 0.5 m/s for 21 d). This was compared to treatment groups where air velocities were set at 0.5 m/s (T2), 1.5 m/s (T3) and 2.5 m/s (T4) all for 7 d and then the samples were vacuum packed for another 14 d. PUFA levels declined with exposure to the high air velocity treatment group (T4). These changes indicated that the increased chiller air velocity exposed the longer chain unsaturated fatty such as linoleic acid (C18:2tω-6 and C18:2cω-6) and linolenic acid (C18:3ω-3 and C18:3ω-6) were readily modified compared to lower air velocity (T2 = 0.5 m/s), although the changes were comparable with the control treatment group which was in-bag dry aged for 21 d. Other NMR-based lipid oxidation analyses on aliphatic to diallylmethylene proton ratios also confirmed these identified changes. Once again the CLAs showed high oxidative stability as they were not impacted by the treatment groups and the product across all treatments retained high antioxidant content in the form of α-tocopherols. The influence of the treatment groups and ageing time on the metabolomics of lean bull beef were investigated. The high velocity treatments did not affect metabolite profiles; however, the metabolite profiles were affected by ageing time (p < 0.05). As for protein oxidative modifications, treatments with high air velocity reported higher total carbonyl content. The oxidative biomarkers showed the same trend but their quantities indicate low accumulation levels.
In conclusion, the represented studies reported in this thesis demonstrate the improvement in meat tenderness as a result of the PEF treatment application. The improved, regulated mass and solute transfer via PEF treatment and smart packaging technology has potential industrial application to increase product turnover and shorter processing time of this niche product. The stepwise ageing process offers the meat processor an opportunity to design the level of oxidative modification they would prefer as the air velocity has been shown to play a role in protein carbonylation
Causative alternation licensing in Urdu: An event structure account
Given the central role of the verb in clause structure, it is vital to understand the properties of the SEMANTIC ROOT and the EVENT SCHEMA, two constituent aspects of verb meaning, in order to understand how lexical semantic categories relate to syntactic categories. The nature of the interface between these components can, in turn, reveal the overall design of language. However, the main challenge is to make precise the nature of the semantic root and event schema, and their interactive role in argument realization options. To address this challenge, empirical evidence from diverse languages is required to determine how argument realization can be universally accounted for in terms of semantic root and event schema-based lexical semantic representation. The primary purpose of this study is to explicate the roles of semantic root and event schema in Urdu change-of-state (COS) verbs’ causative alternation, formulating licensing conditions on the lexical semantics-syntax interface involved in the phenomenon. On the semantic side of the interface, the argumentation is framed within Rappaport-Hovav and Levin’s (1998a) event structure account, and on the syntactic side, the study assumes Culicover and Jackendoff’s (2005) Simpler Syntax which accounts for an alternation in terms of constraint-based interface principles.
Given that the adequacy of theory is bound up with the reliability of empirical evidence, this study is based on data from multiple sources (lexical translation, Urdu WordNet, Urdu Lughat, individual and dialogical introspection, and speaker survey), conducts extensive analysis of morphosemantic as well as morphosyntactic aspects of 112 Urdu COS verbs, and shows that the causative alternation results from an interaction of multiple licensing factors.
The study reaches the following conclusions: (a) The anticausative form of a COS verb is basic and causative forms are derived. (b) The causative derivation shows gradient and dynamic productivity, and an interaction between lexical schemas and morphological operations, marking the CAUSE relation which reflects causal responsibility between the event participants. (c) An anticausative lexicalizes both manner and result, with a [BECOME [Y ]] event structure. (d) An anticausative’s event schema and root license only the patient argument; any additional argument is licensed by the root. The cause arguments in causatives are introduced by causative operations, and are obligatorily event schema participants. The syntactic realization of semantic arguments is sensitive to the causal responsibility relation which is reflected in the predicate’s event structure through the primitive predicate CAUSE and its relation with ACT and BECOME. (e) The various aspects of Urdu COS verbs’ causative alternation lead us to the linking rules which show that the argument structure reflects the semantics it inherits from its semantic sources of roots and event schema.
Overall the study shows that the event structure account of Urdu COS verbs’ causative alternation supports the decomposition of the grammar into independent generative components that interact through interface rules. The bottom line is that such a syntax-semantics interface formulation of alternation avoids syntactic complexity
Keep Calm and Belong to be Strong: Social identity developed through an Adventure Education Programme foster resilience in Māori and New Zealand European youth.
Research on the Social Cure has demonstrated the undeniable importance of belonging to social groups and the impact that this has on one’s functioning, quality of life, health and well-being. Here, we extend this research into the realm of psychological resilience. Psychological resilience is defined as positive growth or adaptation following an adverse event. For youth, psychological resilience is extremely important and there is growing interest in the development of interventions that foster/develop resilience. The current study used sail training as a method to promote psychological resilience in New Zealand European and Māori youth. Specifically, 54 Māori and 37 New Zealand European adolescents completed the 7-day youth-development voyage on-board the gaffed rigged schooner, R. Tucker Thompson. The R. Tucker Thompson encourages a social and supportive atmosphere that provides participants with skills to overcome adversity and challenges. For both New Zealand European and Māori, there was a significant increase in resilience from the first day of the voyage to the final day. Furthermore, it was found that the social identity participants established through the development of the new group contributed to the increases in resilience observed over the course of the voyage
Reproductive cycle and settlement of Evechinus chloroticus in the SUR 5 fishery
Evechinus chloroticus (Kina) are an important commercial species in New Zealand waters, being harvested for their gonads or roe. In southern New Zealand the commercial fishery area (SUR 5) for urchins extends from Slope Point to Ararua Bay with a TACC of 455 tons. Information regarding the reproductive cycle of two sizes (>140mm and 80-100mm) of urchin and larval settlement were gathered from two sea urchin populations (Green Islets and Chalky Sound) in southern Fiordland between May 2006 and March 2007, while working on board a commercial vessel harvesting sea urchins. Urchin reproduction was annual at both sites with gametogenesis beginning in June followed by gamete proliferation and differentiation between July and September. Mature gametes were first observed in October. Gametogenesis was typically asynchronous between sexes with spawning activity varying considerably both between urchin sizes and between sites. There were statistically significant differences in the gonad index (GI) of large and small urchins at each site, with much higher GI present at Green Islets overall. Lantern indices were higher in smaller urchins at each site while gut indices were significantly different between size classes at Green Islets but not at Chalky Sound. Settlement was measured using samplers covered with artificial turf, deployed at 8-10 metres depth. A large pulse of settlement was recorded at Green Islets between September and December 2006, no other settlement was found at other times of the year.
This thesis is a combination of scientific investigation by a student in marine science but also includes my anecdotal observations as a commercial urchin diver in the SUR 5 fishery
Investigation into the mechanism of action and chemical enhancement of transdermal iontophoreses of LHRH
Recent developments in drug design and advances in mapping of the human genome have quickened the pace of development of peptide and protein drugs. Unfortunately, this class of compound often has specialised delivery requirements that preclude administration via traditional routes due to biological barriers, physicochemical drug properties, and issues of pharmacokinetics and pharmacodynamics. Transdermal drug delivery has advantages over other routes of administration. Also, the use of an external driving force, such as iontophoresis, is a technique that is well suited for delivery of these compounds. However, the large molecular size of peptides may limit the amounts of drug that can be delivered across the skin barrier. In this study the potential to enhance transdermal iontophoretic delivery of peptides was investigated. Two approaches to this were used: manipulating electrical field strengths to induce structural changes in the skin; and combining a chemical permeation enhancer with iontophoresis to determine if peptide delivery could be synergistically enhanced. In vitro permeability investigations were performed through human epidermal membrane (HEM) using the model peptide, luteinizing hormone releasing hormone (LHRH). Increasing the electrical field strength across the HEM resulted in marked porosity changes above 1 V. This was accompanied by dramatic increases in permeability enhancement of a small ionic solute, tetraethylammonium bromide (TEAB). However, the increases that were observed in LHRH permeability enhancement was several orders of magnitude less. The modified Nernst-Planck model, after correction for porosity changes, predicted results that matched the observed TEAB enhancement. However, LHRH enhancement predictions were markedly different from observed values indicating that the electrically-induced pathways were largely unavailable for LHRH transport, a finding that is consistent with recent reports characterising these pores. The influence of the voltage-induced pores on electroosmosis was also studied, since this transport mechanism is more important as molecular size increases. Sucrose, a small non-ionic polar solute, was used as an electroosmotic flow marker during these investigations. The enhancement of sucrose closely mirrored porosity increases in the membrane indicating considerable electroosmosis occurs within electrically-induced pores. These two parallel investigations showed moderate voltage iontophoresis (> 1 V) causes the induction of pores in the HEM, however, transport through these pores, despite significant electroosmosis, is limited to small solutes. The potential for synergism between iontophoresis and chemical enhancers to improve peptide delivery was investigated. It was hypothesised that oleic acid (OA) may cause synergistic enhancement of LHRH during iontophoresis by increasing the pore sizes of the HEM. Synergistic enhancement of LHRH was observed. Permeability and conductance changes, in addition to structural investigations (differential scanning calorimetry (DSC) and infrared spectroscopy (IR)) were also performed. OA treatment of the skin promoted the permeability of LHRH, sucrose, and TEAB during passive conditions. This suggests that pre-existing pores in the membrane increased in size. However when the enhancer was used in combination with iontophoresis, LHRH was the only solute to be co-enhanced. This finding was consistent with increases in pore size of the pre-existing pores in the stratum corneum as modelled using the hindered pore theory. Co-enhancement of LHRH may also be due to an effect of the enhancer on the accumulation of peptide in the stratum corneum. Interestingly, disruption of the fixed negative charges on the skin by the enhancer may have negatively influenced transport via decreases in electroosmosis. The disordered effect caused by the action of oleic acid on the stratum corneum was confirmed using DSC and IR investigations. In summary, the transport of peptides across the skin during iontophoresis may become less restricted following the pre-treatment of the barrier with suitable chemical permeation enhancers
Investigating the Direct Role of Promoter DNA Methylation in Gene Expression using a Targeted TET1CD-dCas9 Demethylase Tool
DNA hypermethylation of gene promoter regions has long been associated with transcriptional repression. Furthermore, the establishment of dense promoter methylation within tumour- suppressor genes has been widely-characterised as a prominent hallmark of oncogenesis. The presence of dense DNA methylation, concentrated to promoter region CpG islands, is known to recruit methyl-CpG binding domain proteins (MBDs) and transcriptional repressors which manipulate the local chromatin environment to downregulate transcriptional activity.
However, there is an accumulating body of evidence which now suggests, in some specific contexts, that promoter hypermethylation is also associated with high or increased levels of active gene expression. Recent research has uncovered this phenomenon in the context of cutaneous melanoma. Early B-cell factor 3 (EBF3) has been identified as a putative ‘epigenetic driver’ of metastasis in melanoma, associated with an increase in aggressive phenotypic behaviour. Interestingly, EBF3 acquires substantial promoter DNA methylation during the transition to metastasis, which is associated with a corresponding increase in gene expression. Moreover, when treated with a global demethylating agent, EBF3 expression was subsequently reduced.
Unfortunately, investigations using global demethylation inhibitors do not conclusively demonstrate that promoter-specific methylation gain is responsible for a change in gene expression. However, with the recent emergence of Clustered, Regularly Interspaced Short Palindromic Repeats (CRISPR)-based epigenetic editing technologies, there is now scope for more targeted investigation into this relationship.
Here, I have constructed a CRISPR-based targeting system to investigate the EBF3 promoter region in more detail. The CRISPR construct is fused to the SUperNova Tagging (SunTag) protein scaffold, which allows for the recruitment of effector proteins to induce active demethylation at the target locus. In this case, the effector protein is a catalytic domain derived from the human ten-eleven translocation 1 (TET1) dioxygenase.
Directed by locus-specific guide-RNA (gRNA) molecules, this system was used to induce site- specific active demethylation within the target promoter region of EBF3, in human melanoma cell lines. Methylation changes across this target locus have been evaluated using Combined Bisulfite Restriction Assay (CoBRA) and methylation-specific Illumina MiSeq sequencing.
Variable levels of targeted demethylation have been observed, of up to 58.8% absolute methylation difference between edited and control samples.
In generating a modifiable, RNA-guided construct for site-specific DNA methylation editing, this work has laid a strong platform for further investigation into the direct relationship between DNA methylation and gene expression with regards to both EBF3, and a limitless range of additional contexts in future
Leisure activities and well-being in residential care: Voices of older Adults in New Zealand.
This doctoral thesis contributes to gerontology research by investigating the leisure experiences of older adults living in residential care in New Zealand. There is a need to understand how frail residents experience their leisure in their everyday world. The New Zealand strategies for active and successful ageing focus on community-dwelling seniors rather than on those in residential care. These policy initiatives ignore the leisure practices of the increasing numbers of older adults who require long-term residential care. A few international studies have attempted to highlight the importance of leisure participation among older adults living in residential care, but the information on the New Zealand context is scant. Through a phenomenological approach, this thesis provides clarity to poorly understood leisure experiences. This thesis, which was informed by an integrated theoretical approach (constructs adapted from six major ageing theories), provides insight into leisure experiences and sources of satisfaction for older adults living in residential care. In a supplementary finding, it also sheds light on their adaptation to the conditions they encounter in residential care.
Data were collected through triangulating participation observation, in-depth interviews, and key informant interviews. This involved six residential care facilities (two large, two medium, and two small). I spent one day of observation in each residential care facility, then conducted semi-structured interviews with a total of twenty-four residents and ten key informants. The data were analysed using thematic analysis. Together the residents and staff provide insights on the importance of leisure activities during adjustment, and the benefits of and barriers to participation, satisfaction, and well-being. The study also revealed the diverse and complex needs of older adults after their transition to residential care.
Given their unique life histories and circumstances, the interests and abilities of residents vary, a fact that seems to be largely ignored in the development of leisure activities in these facilities. Loss of identity and challenges of adaptation were the results of frailty, losses and feeling of institutionalisation. The adjustment processes were influenced by residents’ leisure participation.
The finding elucidates the significant impact of leisure activities in residents’ lives. Lack of leisure opportunities resulted in enforced idleness. From residents’ point of view, barriers to implementing leisure activities include the mismatch between their interests and abilities and the activities on offer, facilities’ lack of resources, and deteriorating health/functional status, which resulted in passivity among the residents. Activities tailored to residents’ abilities and interests are an important part of person-centred care because of the many benefits associated with participation. Older adults with active participation in both self-led and offered activities experienced numerous benefits such as feelings of contribution and achievement, sense of belonging and connection, socialisation, companionship, pleasure, enjoyment, and relaxation. The main barriers to participation reported by both residents and staff were residents’ health condition, lack of budget for activities, shortage of staff, and lack of social network. The key to satisfaction was developing identity through meaningful engagement in the activities of their interest. This study acknowledges the importance of leisure activities and highlights the importance of person-centred care in meeting the diverse needs and enhancing the well-being of older adults in residential care
Towards the synthesis of hydrogen bonded frameworks
Hydrogen-Organic frameworks (HOFs) are supramolecular materials constructed by linking organic molecules through intermolecular hydrogen bonds. HOFs are a lightweight alternative to MOFs and have been shown to be effective in a wide range of applications including gas uptake. HOFs are commonly formed from rigid organic building units as this can promote strongly directional hydrogen bonding and framework stability, creating permanently porous structures. However, the field of flexible HOFs has yet to be thoroughly explored. This thesis will present work towards the synthesis of flexible hydrogen bonded materials.
The origin of HOF materials and an examination of hydrogen bonding interactions is discussed in Chapter 1.
Chapter 2 describes the design, synthesis and characterisation of the flexible organic compound 2,2',5,5'-tetrakis(2''-carboxyethyl)butadiene sulfone (H4L1) and the attempted synthesis of 2,2',5,5'-tetrakis(4-carboxybenzyl)butadiene sulfone (H4L2). H4L1 was synthesised in two steps and was characterised using NMR and IR spectroscopy and microanalysis. H4L1 contained a butadiene sulfone core which undergoes a retro-Diels Alder reaction to produce the corresponding diene. This was supported by thermogravimetric analysis (TGA). The precursor 2,2',5,5'-tetrakis(4-iodobenzyl)butadiene sulfone (7) was synthesised in three steps and a variety of reactions were attempted to add a carboxyl functionality, however, only trace amounts of the desired compound were able to be isolated.
Chapter 3 presents the X-ray crystal structures of ten polymorphic and pseudopolymorphic structures (H4L1 to H4L10) of the compound H4L1. These structures were found to contain different H4L1:solvent ratios and hydrogen bonding motifs which resulted in vastly different assemblies. The structures were further analysed using powder X-ray diffraction and DFT calculations. Exposure experiments to air, vacuum, temperature and solvents were also carried out in attempt to transition from one structure to another. While solvent was unable to be removed from a structure, solvent exchange of MeCN to acetone and acetone to H2O was achieved.
Chapter 4 further explores hydrogen bonding interactions by using charge-assisted hydrogen bonding in an attempt to extend the structures of H4L1. The H4L1 compound was deprotonated and then reacted with amidinium hydrochloride salts to produce the structures L1-1-1, L1-1-2, HL1-1-1 and L1-2-1. These structures were analysed using single crystal and powder X-ray diffraction