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.

A hybrid genetic algorithm for the optimal constrained web service selection problem in web service composition

Web service composition is an important problem in web service based systems. It is about how to build a new value-added web service using existing web services. A web service may have many implementations, all of which have the same functionality, but may have different QoS values. Thus, a significant research problem in web service composition is how to select a web service implementation for each of the web services such that the composite web service gives the best overall performance. This is so-called optimal web service selection problem. There may be mutual constraints between some web service implementations. Sometimes when an implementation is selected for one web service, a particular implementation for another web service must be selected. This is so called dependency constraint. Sometimes when an implementation for one web service is selected, a set of implementations for another web service must be excluded in the web service composition. This is so called conflict constraint. Thus, the optimal web service selection is a typical constrained ombinatorial optimization problem from the computational point of view. This paper proposes a new hybrid genetic algorithm for the optimal web service selection problem. The hybrid genetic algorithm has been implemented and evaluated. The evaluation results have shown that the hybrid genetic algorithm outperforms other two existing genetic algorithms when the number of web services and the number of constraints are large.

Use of advanced computer graphics and data visualisation technologies in teaching and learning of steel structural design

A teaching and learning development project is currently under way at Queens-land University of Technology to develop advanced technology videotapes for use with the delivery of structural engineering courses. These tapes consist of integrated computer and laboratory simulations of important concepts, and behaviour of structures and their components for a number of structural engineering subjects. They will be used as part of the regular lectures and thus will not only improve the quality of lectures and learning environment, but also will be able to replace the ever-dwindling laboratory teaching in these subjects. The use of these videotapes, developed using advanced computer graphics, data visualization and video technologies, will enrich the learning process of the current diverse engineering student body. This paper presents the details of this new method, the methodology used, the results and evaluation in relation to one of the structural engineering subjects, steel structures.

Green energy : sustainable energy sources and alternative technologies

Despite the general evolution and broadening of the scope of the concept of infrastructure in many other sectors, the energy sector has maintained the same narrow boundaries for over 80 years. Energy infrastructure is still generally restricted in meaning to the transmission and distribution networks of electricity and, to some extent, gas. This is especially true in the urban development context. This early 20th century system is struggling to meet community expectations that the industry itself created and fostered for many decades. The relentless growth in demand and changing political, economic and environmental challenges require a shift from the traditional ‘predict and provide’ approach to infrastructure which is no longer economically or environmentally viable. Market deregulation and a raft of demand and supply side management strategies have failed to curb society’s addiction to the commodity of electricity. None of these responses has addressed the fundamental problem. This chapter presents an argument for the need for a new paradigm. Going beyond peripheral energy efficiency measures and the substitution of fossil fuels with renewables, it outlines a new approach to the provision of energy services in the context of 21st century urban environments.

The contemporary librarian : skills, knowledge and attributes required in a world of emerging technologies

Seventy-six librarians participated in a series of focus groups in support of research exploring the skills, knowledge and attributes required by the contemporary library and information professional in a world of every changing technology. The project was funded by the Australian Learning and Teaching Council. Text data mining analysis revealed three main thematic clusters (libraries, people, jobs) and one minor thematic cluster (community). Library 2.0 was broadly viewed by participants as being about change whilst librarian 2.0 was perceived by participants as not a new creation but just about good librarian practices. Participants expressed the general belief that personality traits, not just qualifications, were critical to be a successful librarian or information worker in the future.

Information and communication technologies : catalysts for sustainable development

The concept of sustainable urban development has been pushed to the forefront of policy-making and politics as the world wakes up to the impacts of climate change and the effects of modern urban lifestyles. Today, sustainable development has become a very prominent element in the day-to-day debate on urban policy and the expression of that policy in urban planning and development decisions. As a result of this, during the last few years, sustainable development automation applications such as sustainable urban development decision support systems have become popular tools as they offer new opportunities for local governments to realise their sustainable development agendas. This chapter explores a range of issues associated with the application of information and communication technologies and decision support systems in the process of underpinning sustainable urban development. The chapter considers how information and communication technologies can be applied to enhance urban planning, raise environmental awareness, share decisions and improve public participation. It introduces and explores three web-based geographical information systems projects as best practice. These systems are developed as support tools to include public opinion in the urban planning and development processes, and to provide planners with comprehensive tools for the analysis of sustainable urban development variants in order to prepare the best plans for constructing sustainable urban communities and futures.

Sustainable urban and regional infrastructure development : technologies, applications and management

Sustainable Urban and Regional Infrastructure Development: Technologies, Applications and Management, bridges the gap in the current literature by addressing the overall problems present in society's major infrastructures, and the technologies that may be applied to overcome these problems. It focuses on ways in which energy intensive but 'invisible' (to the general public) facilities can become green or greener. The studies presented re lessons to be learnt from our neighbors and from our own backyard, and provide an excellent general overview of the issues facing us all.

Preface : sustainable urban and regional infrastructure development : technologies, applications and management

The concept of ‘sustainability’ has been pushed to the forefront of policy-making and politics as the world wakes up to the impacts of climate change and the effects of the modern urban lifestyle. Climate change has emerged to be one of the biggest challenges faced by our planet today, threatening both built and natural systems with long term consequences which may be irreversible. While there is a vast literature in the market on sustainable cities and urban development, there is currently none that bring together the vital issues of urban and regional development, and the planning, management and implementation of sustainable infrastructure. Large scale infrastructure plays an important part in modern society by not only promoting economic growth, but also by acting as a key indicator for it. More importantly, it supplies municipal/local amenity and services: water, electricity, social and communication facilities, waste removal, transport of people and goods, as well as numerous other services. For the most part, infrastructure has been built by teams lead by engineers who are more concerned about functionality than the concept of sustainability. However, it has been widely stated that current practices and lifestyle cannot continue if we are to leave a healthy living planet to not only the next generation, but also to the generations beyond. Therefore, in order to be sustainable, there are drastic measures that need to be taken. Current single purpose and design infrastructures that are open looped are not sustainable; they are too resource intensive, consume too much energy and support the consumption of natural resources at a rate that will exhaust their supply. Because of this, it is vital that modern society, policy-makers, developers, engineers and planners become pioneers in introducing and incorporating sustainable features into urban and regional infrastructure.