THE MUSIC PERFORMED FOR THE SACRIFICIAL RITE AT THE ROYAL ANCESTRAL SHRINE OF THE CHOSŎN DYNASTY (1392–1910): INDIVIDUAL AGENCY AND DISCOURSE ON MUSIC EXPRESSED IN THE EIGHTEENTH-CENTURY KOREAN ENCYCLOPEDIA _TONGGUK MUNHŎN PIGO_ (1770)

In 1964, the South Korean government designated the music for the sacrificial rite at the Royal Ancestral Shrine (Chongmyo) as Intangible Cultural Property No. 1, and in 2001 UNESCO awarded the rite and music a place in the Intangible Cultural Heritage of Humanity. The Royal Ancestral Shine sacrificial rite and music together have long been an admired symbol of Korean cultural history, and they are currently performed annually and publicly in an abridged form. While the significance of the modern version of the music mainly rests on the claimed authenticity and continuity of the tradition since the fifteenth century, scholarly inquiry sheds further light on contextual issues such as nationalism, identity, and modernity in the post-colonial era (after 1945), as well as providing additional insights into the music. This dissertation focuses on the Royal Ancestral Shrine’s musical past as reflected in documentary sources, especially those compiled in the eighteenth century during the Chosŏn dynasty (1392–1910). In particular, the substantial music section of an encyclopedic work, Tongguk Munhŏn pigo (Encyclopedia of Documents and Institutions of the East Kingdom, 1770), mainly compiled by a government official, Sŏ Myŏngŭng (1716–1787), provides a considerable amount of information on not only the music and sacrificial rite program, but also on eighteenth-century and earlier concerns about them, as discussed by the kings and ministers at the Chosŏn royal court. After detailed examination of various relevant documentary sources on the historical, social and political contexts, I investigate the various discourses on music and ritual practices. I then focus on Sŏ Myŏngŭng’s familial background, his writings on music prior to the compilation of the encyclopedia, and the corresponding content in the encyclopedia. I argue that Sŏ successfully converted the music section of the encyclopedia from a straightforward scholarly reference work to a space for publishing his own research on and interpretation of the musical past, illustrating what he considered to be the inappropriateness of the existing music for the sacrificial rite at the Royal Ancestral Shrine in the later eighteenth century.

Influence of Nitrogen and Sink Competition on Shoot Growth of Poplar

Terrestrial and oceanic biomass carbon sinks help reduce anthropogenic CO2 emissions and mitigate the long-term effect of increasing atmospheric CO2. Woody plants have large carbon pools because of their long residence time, however N availability can negatively impact tree responses to elevated CO2. Seasonal cycling of internal N in trees is a component that contributes to fitness especially in N limited environments. It involves resorption from senescing leaves of deciduous trees and storage as vegetative storage proteins (VSP) in perennial organs. Populus is a model organism for tree biology that efficiently recycles N. Bark storage proteins (BSP) are the most abundant VSP that serves as seasonal N reserves. Here I show how poplar growth is influenced by N availability and how growth is influenced by shoot competition for stored N reserves. I also provide data that indicates that auxin mediates BSP catabolism during renewed shoot growth. Understanding the components of N accumulation, remobilization and utilization can provide insights leading to increasing N use efficiency (NUE) of perennial plants.

Universities and Welfare States Coping with Permanent Financial Austerity: Pressures on (Competing) Public Institutions

A chapter linking universities and welfare states to permanent financial austerity can take a shorter or a longer historical perspective. This chapter looks further back (to the postwar expansion of European welfare states) to better understand future transformations of both public institutions. Their long-term sustainability problems did not start with the financial crisis of 2008 but have been growing since the 1970s (Schäfer and Streeck 2013; Bonoli and Natali 2012; Hay and Wincott 2012). Financial austerity is not a post-crisis phenomenon. As a concept, it was used in welfare state research at least a decade earlier, although it does not seem to have been used in higher education studies until recently. Two quotations bring us to the heart of the matter: welfare states and universities are currently changing under adverse financial conditions caused by an array of interrelating and mutually reinforcing forces and their long-term financial sustainability is at stake across Europe. The welfare state is a “particular trademark of the European social model” (Svallfors 2012: 1), “the jewel in the crown” and a “fundamental part of what Europe stands for” (Giddens 2006: 14), as are tuition-free universities, the cornerstone of intergenerational social mobility in Continental Europe. The past trajectories of major types of welfare states and of universities in Europe tend to go hand in hand: first vastly expanding following the Second World War, and especially in the 1960s and 1970s, and then being in the state of permanent resource-driven and legitimacy-based “crisis” in the last two decades. Welfare states and universities, two critically important public institutions, seem to be under heavy attacks from the public, the media and politicians. Their long-term sustainability is being questioned, and solutions to their (real and perceived) problems are being sought at global, European, and national levels.

Long-term Success of Family Firms: Investigating Specific Aspects of Firm-level Entrepreneurship and Individual-level Antecedents

Long-term success of family firms is of utmost social and economic importance. Three of its determinants are in the center of this Dissertation: firmlevel entrepreneurial orientation (EO), managers' entrepreneurial behavior, and value-creating attitudes of non-family employees. Each determinant and respective research gaps are addressed by one paper of this cumulative dissertation. Referring to firm-level EO, scholars claim that EO is a main antecedent to firms' both short- and long-term success. However, family firms seem to be successful across generations despite rather low levels of EO. The first paper addresses this paradox by investigating EO patterns of long-lived family firms in three Swiss case studies. The main finding is that the key to success is not to be as entrepreneurially as possible all the time, but to continuously adapt the EO profile depending on internal and external factors. Moreover, the paper suggest new subcategories to different EO dimensions. With regard to entrepreneurial behavior of managers, there is a lack of knowledge how individual-level and organizational level factors affect its evolvement. The second paper addresses this gap by investigating a sample of 403 middle-level managers from both family and non-family firms. It introduces psychological ownership of managers as individual-level antecedent and investigates the interaction with organizational factors. As a central insight, management support is found to strengthen the psychological ownership-entrepreneurial behavior relationship. The third paper is based on the fact that employees' justice perceptions are established antecedents of value-creating employee attitudes such as affective commitment and job satisfaction. Even though family firms are susceptible to nonfamily employees´ perceptions of injustice, corresponding research is scarce. Moreover, the mechanism connecting justice perceptions and positive outcomes is still unclear. Addressing these gaps, the analysis of a sample of 310 non-family employees reveals that psychological ownership is a mediator in the relationships between distributive justice perceptions and both affective commitment and job satisfaction. Altogether, the three papers offer valuable contributions to family business literature with respect to EO, entrepreneurial behavior, and value-creating employee attitudes. Thus, they increase current understanding about important determinants of family firms' long-term success, while opening up numerous ways of future research.

Healing wounds institutional strength, peacebuilding, and productive entrepreneurship – exploratory analysis on 23 departments of Colombia

Este estudio presenta un análisis exploratorio sobre la correlación entre la fortaleza institucional, las condiciones de paz, y el emprendimiento en una muestra de 23 departamentos en Colombia usando datos de 2014. Para llevar a cabo este objetivo se propusieron y construyeron tres índices siguiendo definiciones conceptuales seminales o estándares de evaluación internacional, a saber: 1) El Índice de Fortaleza Institucional, 2) El Índice de Construcción de Paz (construido a partir del índice de paz negativa y el índice de paz positiva) y 3) El Índice de Emprendimiento Productivo. Los resultados no muestran una correlación significativa entre todos los tres índices. Por un lado, existe una correlación significativa (p<0.05) entre los índices de fortaleza institucional y emprendimiento productivo. Por otro lado, existen correlaciones negativas no significativas entre los índices de paz positiva y fortaleza institucional, emprendimiento productivo y paz positiva y emprendimiento productivo y construcción de paz. En un segundo acercamiento, la población de los departamentos fue la variable con mayor número de correlaciones significativas (p<0.01) entre variables relacionadas con emprendimiento productivo, empleo, producto interno bruto, sofisticación industrial, innovación (patentes) y crimen. Finalmente, se discuten las conclusiones y las futuras investigaciones.

DNI Measurements in the South of Portugal: Long Term Results through Direct Comparison with Global and Diffuse Radiation Measurements and Existing Time Series

The present work describes the measurement effort for direct normal irradiance (DNI) evaluation in the sunny south of Portugal, with a network of eight radiation measurement stations in several locations (including Évora) providing a good coverage of the region. This new initiative for DNI measurement will still need many years (typically 10 or more) to produce a time series which can claim having long term statistical value. This problem can, however, be temporarily mitigated by measuring DNI at the same time as GHI and DHI, in a place where long term series dating back, already exist for those two. It so happens that a long term series (20 years) of global and diffuse solar irradiation exists for the location Évora. So the expectation is to establish correlations with the goal of attributing at least some long term statistical significance to the short and recent DNI series. The paper describes the setup of the measuring stations and presents the preliminary measurements obtained. It further presents the first correlations of monthly averages between normal beam (DNI), global and diffuse radiation. It then uses these correlations, admittedly without acceptable statistical significance (short series of less than one year of measured data), to exemplify how to get a prediction of long term DNI for Évora. This preliminary obtained value is compared to that predicted by the commercial data from Meteonorm.

Health Problems of Institutionalized Elderly

Introduction: human aging is marked by a decrease in the performance of some daily tasks, some even considered banal and imperceptibly when this limitation is followed by chronic diseases, the elderly becomes a source of concern for the family. Objective: identifying the health problems of the elderly living in long-stay institutions from self-reported diseases. This is a descriptive and quantitative study, conducted in northeastern Brazil capital, involving 138 elderly. For data collection we used a questionnaire containing demographic variables, institutional and related to self-reported health problems. Data were evaluated using bivariate analysis and association chi-square. Results: predominance of women was found (61.6%), aged 60-69 years old (39.1%), coming from the state capital (51.4%), and institutional permanence time between 1-5 years (77.5%). The most frequent diseases were related to the cardiovascular system (15.9%) and endocrine, nutritional and metabolic diseases (9.4%). It showed a significant association between self-reported diseases and the age of the elderly (p=0.047). Conclusion: it is expected to raise awareness among health professionals to provide a better assistance to the institutionalized elderly focusing on the real needs of these persons.

Error, Bias, and Long-Branch Attraction in Data for Two Chloroplast Photosystem Genes in Seed Plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brady

Predatory police : the roles of ethics and networks as mediating factors

The institution the police force has been established to protect citizens and their property from harm and predatory opportunism. However, there have been occasions when the very people assigned to protect become part of the predatory force against society. Predatory policing occurs when the police use their powers to extort money in the form of bribes. While, the concept is receiving attention in Europe but there have not been any direct studies in Australia. To overcome this research deficit and determine the extent, if any, of predatory policing in Australia data is interrogated from four police corruption inquiries in the Australian states of Queensland, New South Wales, Victoria and Western Australia. In addition, it examines the role of the type of networks used by corrupt police officers. The synthesis and application of public corruption and network literatures to the predatory policing domain provides new and relevant insights to assist those responsible for the administration of our institutions of justice. The paper concludes with a framework, drawn from the first stage of the project, to assist in the conceptualisation and monitoring of this public problem.

Views of general practitioners and benzodiazepine users on benzodiazepines : a qualitative analysis

Effectively assisting benzodiazepine users to cease use requires a greater understanding of general practitioners’ (GPs)and benzodiazepine users’ views on using and ceasing benzodiazepines. This paper reports the findings from a qualitative study that examined the views of 28 GPs and 23 benzodiazepine users (BUs) in Cairns, Australia. A semistructured interview was conducted with all participants and the information gained was analysed using the Consensual Qualitative Research Approach, which allowed comparisons to be made between the views of the two groups of interviewees. There was commonality between GPs and BUs on reasons for commencing benzodiazepines, the role of dependence in continued use, and the importance of lifestyle change in its cessation. However, several differences emerged regarding commencement of use and processes of cessation. In particular, users felt there was greater need for GPs to routinely advise patients about non-pharmacological management of their problems and potential adverse consequences of long-term use before commencing benzodiazepines. Cessation could be discussed with all patients who use benzodiazepines for longer than 3 months, strategies offered to assist in management of withdrawal and anxiety, and referral to other health service providers for additional support. Lifestyle change could receive greater focus at all stages of treatment.

Age-related differences in exercise and quality of life among breast cancer survivors

Purpose: Physical activity has become a focus of cancer recovery research as it has the potential to reduce treatment-related burden and optimize health-related quality of life (HRQoL). However, the potential for physical activity to influence recovery may be age-dependent. This paper describes physical activity levels and HRQoL among younger and older women after surgery for breast cancer and explores the correlates of physical inactivity. Methods: A population-based sample of breast cancer patients diagnosed in South-East Queensland, Australia, (n=287) were assessed once every three months, from 6 to 18 months post-surgery. The Functional Assessment of Cancer Therapy-Breast questionnaire (FACTB+4) and items from the Behavioral Risk Factor Surveillance System (BRFSS) questionnaire were used to measure HRQoL and physical activity, respectively. Physical activity was assigned metabolic equivalent task (MET) values, and categorized as < 3, 3 to 17.9 and 18+ MET-hours/weeks. Descriptive statistics, generalized linear models with age stratification (<50 years versus 50+ years), and logistic regression were used for analyses (p=0.05, two-tailed). Results: Younger women who engaged in 3 or more MET-hours/week of physical activity reported a higher HRQoL at 18 months compared to their more sedentary counterparts (p<0.05). Older women reported similar HRQoL irrespective of activity level and consistently reported clinically higher HRQoL than younger women. Increasing age, being overweight or obese, and restricting use of the treated side at six months post-surgery increased the likelihood of sedentary behavior (OR>3, p<0.05). Conclusions: Age influences the potential to observe HRQoL benefits related to physical activity participation. These results also provide relevant information for the design of exercise interventions for breast cancer survivors and highlights that some groups of women are at greater risk of long-term sedentary behavior.

Stochastic modelling of financial time series with memory and multifractal scaling

Financial processes may possess long memory and their probability densities may display heavy tails. Many models have been developed to deal with this tail behaviour, which reflects the jumps in the sample paths. On the other hand, the presence of long memory, which contradicts the efficient market hypothesis, is still an issue for further debates. These difficulties present challenges with the problems of memory detection and modelling the co-presence of long memory and heavy tails. This PhD project aims to respond to these challenges. The first part aims to detect memory in a large number of financial time series on stock prices and exchange rates using their scaling properties. Since financial time series often exhibit stochastic trends, a common form of nonstationarity, strong trends in the data can lead to false detection of memory. We will take advantage of a technique known as multifractal detrended fluctuation analysis (MF-DFA) that can systematically eliminate trends of different orders. This method is based on the identification of scaling of the q-th-order moments and is a generalisation of the standard detrended fluctuation analysis (DFA) which uses only the second moment; that is, q = 2. We also consider the rescaled range R/S analysis and the periodogram method to detect memory in financial time series and compare their results with the MF-DFA. An interesting finding is that short memory is detected for stock prices of the American Stock Exchange (AMEX) and long memory is found present in the time series of two exchange rates, namely the French franc and the Deutsche mark. Electricity price series of the five states of Australia are also found to possess long memory. For these electricity price series, heavy tails are also pronounced in their probability densities. The second part of the thesis develops models to represent short-memory and longmemory financial processes as detected in Part I. These models take the form of continuous-time AR(∞) -type equations whose kernel is the Laplace transform of a finite Borel measure. By imposing appropriate conditions on this measure, short memory or long memory in the dynamics of the solution will result. A specific form of the models, which has a good MA(∞) -type representation, is presented for the short memory case. Parameter estimation of this type of models is performed via least squares, and the models are applied to the stock prices in the AMEX, which have been established in Part I to possess short memory. By selecting the kernel in the continuous-time AR(∞) -type equations to have the form of Riemann-Liouville fractional derivative, we obtain a fractional stochastic differential equation driven by Brownian motion. This type of equations is used to represent financial processes with long memory, whose dynamics is described by the fractional derivative in the equation. These models are estimated via quasi-likelihood, namely via a continuoustime version of the Gauss-Whittle method. The models are applied to the exchange rates and the electricity prices of Part I with the aim of confirming their possible long-range dependence established by MF-DFA. The third part of the thesis provides an application of the results established in Parts I and II to characterise and classify financial markets. We will pay attention to the New York Stock Exchange (NYSE), the American Stock Exchange (AMEX), the NASDAQ Stock Exchange (NASDAQ) and the Toronto Stock Exchange (TSX). The parameters from MF-DFA and those of the short-memory AR(∞) -type models will be employed in this classification. We propose the Fisher discriminant algorithm to find a classifier in the two and three-dimensional spaces of data sets and then provide cross-validation to verify discriminant accuracies. This classification is useful for understanding and predicting the behaviour of different processes within the same market. The fourth part of the thesis investigates the heavy-tailed behaviour of financial processes which may also possess long memory. We consider fractional stochastic differential equations driven by stable noise to model financial processes such as electricity prices. The long memory of electricity prices is represented by a fractional derivative, while the stable noise input models their non-Gaussianity via the tails of their probability density. A method using the empirical densities and MF-DFA will be provided to estimate all the parameters of the model and simulate sample paths of the equation. The method is then applied to analyse daily spot prices for five states of Australia. Comparison with the results obtained from the R/S analysis, periodogram method and MF-DFA are provided. The results from fractional SDEs agree with those from MF-DFA, which are based on multifractal scaling, while those from the periodograms, which are based on the second order, seem to underestimate the long memory dynamics of the process. This highlights the need and usefulness of fractal methods in modelling non-Gaussian financial processes with long memory.

Improved image contrast of the bone-muscle interface with 3T MRI compared to 1.5T MRI [Abstract]

Virtual 3D models of long bones are increasingly being used for implant design and research applications. The current gold standard for the acquisition of such data is Computed Tomography (CT) scanning. Due to radiation exposure, CT is generally limited to the imaging of clinical cases and cadaver specimens. Magnetic Resonance Imaging (MRI) does not involve ionising radiation and therefore can be used to image selected healthy human volunteers for research purposes. The feasibility of MRI as alternative to CT for the acquisition of morphological bone data of the lower extremity has been demonstrated in recent studies [1, 2]. Some of the current limitations of MRI are long scanning times and difficulties with image segmentation in certain anatomical regions due to poor contrast between bone and surrounding muscle tissues. Higher field strength scanners promise to offer faster imaging times or better image quality. In this study image quality at 1.5T is quantitatively compared to images acquired at 3T. --------- The femora of five human volunteers were scanned using 1.5T and 3T MRI scanners from the same manufacturer (Siemens) with similar imaging protocols. A 3D flash sequence was used with TE = 4.66 ms, flip angle = 15° and voxel size = 0.5 × 0.5 × 1 mm. PA-Matrix and body matrix coils were used to cover the lower limb and pelvis respectively. Signal to noise ratio (SNR) [3] and contrast to noise ratio (CNR) [3] of the axial images from the proximal, shaft and distal regions were used to assess the quality of images from the 1.5T and 3T scanners. The SNR was calculated for the muscle and bone-marrow in the axial images. The CNR was calculated for the muscle to cortex and cortex to bone marrow interfaces, respectively. --------- Preliminary results (one volunteer) show that the SNR of muscle for the shaft and distal regions was higher in 3T images (11.65 and 17.60) than 1.5T images (8.12 and 8.11). For the proximal region the SNR of muscles was higher in 1.5T images (7.52) than 3T images (6.78). The SNR of bone marrow was slightly higher in 1.5T images for both proximal and shaft regions, while it was lower in the distal region compared to 3T images. The CNR between muscle and bone of all three regions was higher in 3T images (4.14, 6.55 and 12.99) than in 1.5T images (2.49, 3.25 and 9.89). The CNR between bone-marrow and bone was slightly higher in 1.5T images (4.87, 12.89 and 10.07) compared to 3T images (3.74, 10.83 and 10.15). These results show that the 3T images generated higher contrast between bone and the muscle tissue than the 1.5T images. It is expected that this improvement of image contrast will significantly reduce the time required for the mainly manual segmentation of the MR images. Future work will focus on optimizing the 3T imaging protocol for reducing chemical shift and susceptibility artifacts.

Development of rapid and highly resolving combinatorial genotyping schemes for Campylobacter jejuni and Campylobacter coli

Campylobacter jejuni followed by Campylobacter coli contribute substantially to the economic and public health burden attributed to food-borne infections in Australia. Genotypic characterisation of isolates has provided new insights into the epidemiology and pathogenesis of C. jejuni and C. coli. However, currently available methods are not conducive to large scale epidemiological investigations that are necessary to elucidate the global epidemiology of these common food-borne pathogens. This research aims to develop high resolution C. jejuni and C. coli genotyping schemes that are convenient for high throughput applications. Real-time PCR and High Resolution Melt (HRM) analysis are fundamental to the genotyping schemes developed in this study and enable rapid, cost effective, interrogation of a range of different polymorphic sites within the Campylobacter genome. While the sources and routes of transmission of campylobacters are unclear, handling and consumption of poultry meat is frequently associated with human campylobacteriosis in Australia. Therefore, chicken derived C. jejuni and C. coli isolates were used to develop and verify the methods described in this study. The first aim of this study describes the application of MLST-SNP (Multi Locus Sequence Typing Single Nucleotide Polymorphisms) + binary typing to 87 chicken C. jejuni isolates using real-time PCR analysis. These typing schemes were developed previously by our research group using isolates from campylobacteriosis patients. This present study showed that SNP + binary typing alone or in combination are effective at detecting epidemiological linkage between chicken derived Campylobacter isolates and enable data comparisons with other MLST based investigations. SNP + binary types obtained from chicken isolates in this study were compared with a previously SNP + binary and MLST typed set of human isolates. Common genotypes between the two collections of isolates were identified and ST-524 represented a clone that could be worth monitoring in the chicken meat industry. In contrast, ST-48, mainly associated with bovine hosts, was abundant in the human isolates. This genotype was, however, absent in the chicken isolates, indicating the role of non-poultry sources in causing human Campylobacter infections. This demonstrates the potential application of SNP + binary typing for epidemiological investigations and source tracing. While MLST SNPs and binary genes comprise the more stable backbone of the Campylobacter genome and are indicative of long term epidemiological linkage of the isolates, the development of a High Resolution Melt (HRM) based curve analysis method to interrogate the hypervariable Campylobacter flagellin encoding gene (flaA) is described in Aim 2 of this study. The flaA gene product appears to be an important pathogenicity determinant of campylobacters and is therefore a popular target for genotyping, especially for short term epidemiological studies such as outbreak investigations. HRM curve analysis based flaA interrogation is a single-step closed-tube method that provides portable data that can be easily shared and accessed. Critical to the development of flaA HRM was the use of flaA specific primers that did not amplify the flaB gene. HRM curve analysis flaA interrogation was successful at discriminating the 47 sequence variants identified within the 87 C. jejuni and 15 C. coli isolates and correlated to the epidemiological background of the isolates. In the combinatorial format, the resolving power of flaA was additive to that of SNP + binary typing and CRISPR (Clustered regularly spaced short Palindromic repeats) HRM and fits the PHRANA (Progressive hierarchical resolving assays using nucleic acids) approach for genotyping. The use of statistical methods to analyse the HRM data enhanced sophistication of the method. Therefore, flaA HRM is a rapid and cost effective alternative to gel- or sequence-based flaA typing schemes. Aim 3 of this study describes the development of a novel bioinformatics driven method to interrogate Campylobacter MLST gene fragments using HRM, and is called ‘SNP Nucleated Minim MLST’ or ‘Minim typing’. The method involves HRM interrogation of MLST fragments that encompass highly informative “Nucleating SNPS” to ensure high resolution. Selection of fragments potentially suited to HRM analysis was conducted in silico using i) “Minimum SNPs” and ii) the new ’HRMtype’ software packages. Species specific sets of six “Nucleating SNPs” and six HRM fragments were identified for both C. jejuni and C. coli to ensure high typeability and resolution relevant to the MLST database. ‘Minim typing’ was tested empirically by typing 15 C. jejuni and five C. coli isolates. The association of clonal complexes (CC) to each isolate by ‘Minim typing’ and SNP + binary typing were used to compare the two MLST interrogation schemes. The CCs linked with each C. jejuni isolate were consistent for both methods. Thus, ‘Minim typing’ is an efficient and cost effective method to interrogate MLST genes. However, it is not expected to be independent, or meet the resolution of, sequence based MLST gene interrogation. ‘Minim typing’ in combination with flaA HRM is envisaged to comprise a highly resolving combinatorial typing scheme developed around the HRM platform and is amenable to automation and multiplexing. The genotyping techniques described in this thesis involve the combinatorial interrogation of differentially evolving genetic markers on the unified real-time PCR and HRM platform. They provide high resolution and are simple, cost effective and ideally suited to rapid and high throughput genotyping for these common food-borne pathogens.

The influence of habitat heterogeneity on patterns of connectivity among rabbit populations in southern Queensland

Patterns of connectivity among local populations influence the dynamics of regional systems, but most ecological models have concentrated on explaining the effect of connectivity on local population structure using dynamic processes covering short spatial and temporal scales. In this study, a model was developed in an extended spatial system to examine the hypothesis that long term connectivity levels among local populations are influenced by the spatial distribution of resources and other habitat factors. The habitat heterogeneity model was applied to local wild rabbit populations in the semi-arid Mitchell region of southern central Queensland (the Eastern system). Species' specific population parameters which were appropriate for the rabbit in this region were used. The model predicted a wide range of long term connectivity levels among sites, ranging from the extreme isolation of some sites to relatively high interaction probabilities for others. The validity of model assumptions was assessed by regressing model output against independent population genetic data, and explained over 80% of the variation in the highly structured genetic data set. Furthermore, the model was robust, explaining a significant proportion of the variation in the genetic data over a wide range of parameters. The performance of the habitat heterogeneity model was further assessed by simulating the widely reported recent range expansion of the wild rabbit into the Mitchell region from the adjacent, panmictic Western rabbit population system. The model explained well the independently determined genetic characteristics of the Eastern system at different hierarchic levels, from site specific differences (for example, fixation of a single allele in the population at one site), to differences between population systems (absence of an allele in the Eastern system which is present in all Western system sites). The model therefore explained the past and long term processes which have led to the formation and maintenance of the highly structured Eastern rabbit population system. Most animals exhibit sex biased dispersal which may influence long term connectivity levels among local populations, and thus the dynamics of regional systems. When appropriate sex specific dispersal characteristics were used, the habitat heterogeneity model predicted substantially different interaction patterns between female-only and combined male and female dispersal scenarios. In the latter case, model output was validated using data from a bi-parentally inherited genetic marker. Again, the model explained over 80% of the variation in the genetic data. The fact that such a large proportion of variability is explained in two genetic data sets provides very good evidence that habitat heterogeneity influences long term connectivity levels among local rabbit populations in the Mitchell region for both males and females. The habitat heterogeneity model thus provides a powerful approach for understanding the large scale processes that shape regional population systems in general. Therefore the model has the potential to be useful as a tool to aid in the management of those systems, whether it be for pest management or conservation purposes.