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.

Academic career development workshop for research students and early career academics

For research students and early career academics, universities offer resources that help develop their research skills – for example, critical theory development, literature reviews, research methods, data analysis, writing skills, etc. However, building a successful career in academia poses a wide range of new challenges in addition to the pure academic craft of research. The resources and resilience one needs in order to shape an academic career path often appear ambiguous, particularly in the innately transformative field of Internet research. In response to feedback from AoIR members, this full-day workshop seeks to address this concern by offering a supportive and constructive environment to discuss career development related issues that are of specific interest to research students and early career academics.

An integrated information management model for ecologically sustainable development

Ecologically sustainable development has become a major feature of legal systems at the international, national and local levels throughout the world. In Australia, governments have responded to environmental crises by enacting legislation imposing obligations and restrictions over privately-owned land. Whilst these obligations and restrictions may well be necessary to achieve sustainability, the approach to management of information concerning these instruments is problematic. For example, management of information concerning obligations and restrictions in Queensland is fragmented, with some instruments registered or recorded on the land title register, some on external registers, and some information only available in the legislation itself. This approach is used in most Australian jurisdictions. This fragmented approach has led to two separate but interconnected problems. First, the Torrens system is no longer meeting its goal of providing a complete and accurate picture of title. Second, this uncoordinated approach to the management of land titles, and obligations and restrictions on land use, has created a barrier to sustainable management of natural resources. This is because compliance with environmental laws is impaired in the absence of easily accessible and accurate information. These problems demonstrate a clear need for reform in this area. To determine how information concerning these obligations and restrictions may be most effectively managed, this thesis will apply a comparative methodology and consider three case studies, which each utilise different models for management of this information. These jurisdictions will be assessed according to a set of guidelines for comparison to identify which features of their systems provide for effective management of information concerning obligations and restrictions on title and use. Based on this comparison, this thesis will devise a series of recommendations for an effective system for the management of information concerning obligations and restrictions on land title and use, taking into account any potential legal issues and barriers to implementation. This series of recommendations for reform will be supplemented by suggested draft legislative provisions.

The Development of a Critical Thinking Conceptual Model to Enhance Critical Thinking Skills in Middle-Eastern Nurses: A Middle-Eastern Experience

This paper aims to describe the development of a critical thinking conceptual model which was constructed to guide the teaching and evaluation of critical thinking skills to Middle-Eastern nurses.

The development of a "Good Practice Guide" for first year curriculum development, revision and evaluation : a moving feast

Since 2002 QUT has sponsored a range of first year-focussed initiatives, most recently the Transitions In Project (TIP) which was designed to complement the First Year Experience Program and be a capacity building initiative. A primary focus of TIP was The First Year Curriculum Project: the review, development, implementation and evaluation of first year curriculum which has culminated in the development of a “Good Practice Guide” for the management of large first year units. First year curriculum initiates staff-student relationships and provides the scaffolding for the learning experience and engagement. Good practice in first year curriculum is within the control of the institution and can be redesigned and reviewed to improve outcomes. This session will provide a context for the First Year Curriculum Project and a concise overview of the suite of resources developed that have culminated in the Good Practice Guide.

The development of an on-line module for students on “Working in Inter-cultural Teams”

Since 2005 QUT through a number of large Teaching and Learning Grants has sponsored a range of teamwork learning initiatives to assist students to develop the teamwork skills demanded by industry. After a suite of six online team learning modules was developed, first year unit coordinators requested an additional module to address the challenges of working with the diverse range of social, cultural and personal values that students from different backgrounds bring to student teams. The Intercultural Teams module asks students to map themselves against a Cultural Orientations Framework so they can understand their own cultural beliefs. By learning about other cultural orientations and comparing and analysing their effects, team members can develop communication and team process management strategies to leverage their differences to realise effective and creative outcomes. The interactive session will demonstrate the elements of the Intercultural Teams module and ask participants to consider ways the module can be integrated into classroom learning to support the development of students’ intercultural competencies.

Development of a Systematic Approach to Assessing Quality within Australian Residential Aged Care Facilities: The Clinical Care Indicators Tool

Recent years have seen the introduction of formalised accreditation processes in both community and residential aged care, but these only partially address quality assessment within this sector. Residential aged care in Australia does not yet have a standardised system of resident assessment related to clinical, rather than administrative, outcomes. This paper describes the development of a quality assessment tool aimed at addressing this gap. Utilising previous research and the results of nominal groups with experts in the field, the 21-item Clinical Care Indicators (CCI) Tool for residential aged care was developed and trialled nationally. The CCI Tool was found to be simple to use and an effective means of collecting data on the state of resident health and care, with potential benefits for resident care planning and continuous quality improvement within facilities and organisations. The CCI Tool was further refined through a small intervention study to assess its utility as a quality improvement instrument and to investigate its relationship with resident quality of life. The current version covers 23 clinical indicators, takes about 30 minutes to complete and is viewed favourably by nursing staff who use it. Current work focuses on psychometric analysis and benchmarking, which should enable the CCI Tool to make a positive contribution to the measurement of quality in aged care in Australia.

Development of a Resource for Parents with Advanced Cancer: What do Parents Want?

OBJECTIVE: Parents coping with a diagnosis of advanced cancer experience distress and guilt about the impact of the disease on their children but report that there are few resources specific to advanced disease to guide and support them in discussions with their children. Although some resources have been developed to assist parents with advanced cancer, it appears that these are not widely disseminated. METHODS: To determine the need for a brief resource that could be given to parents at the point of diagnosis of advanced cancer, including its content, in-depth interviews were conducted with eight women with advanced breast cancer. RESULTS: Women confirmed that they had received minimal assistance from health professionals in discussing the diagnosis with their children, and even when professional counselors were accessed they were not always attuned to the specific needs of parents with advanced cancer. Women felt frustrated that information they did access focused on early disease and lacked the details women felt they needed in coping with advanced cancer. Women felt that there was a need for a brief resource that reassured parents about the impact of the cancer on their children, including practical strategies to help them cope and examples of the ways other parents had responded to difficult questions such as about parental death. A draft resource was developed, critically reviewed by the participants, and their comments incorporated into a final version. SIGNIFICANCE OF RESULTS: This article expands on the themes highlighted by women as important to assist parents with advanced cancer, including the final resource that was developed.

The contribution of physical activity and sedentary behaviours to the growth and development of children and adolescents : implications for overweight and obesity

The obesity epidemic is a global trend and is of particular concern in children. Recent reports have highlighted the severity of obesity in children by suggesting: “today's generation of children will be the first for over a century for whom life expectancy falls.” This review assesses the evidence that identifies the important role of physical activity in the growth, development and physical health of young people, owing to its numerous physical and psychological health benefits. Key issues, such as “does a sedentary lifestyle automatically lead to obesity” and “are levels of physical activity in today's children less than physical activity levels in children from previous generations?”, are also discussed. Today's environment enforces an inactive lifestyle that is likely to contribute to a positive energy balance and childhood obesity. Whether a child or adolescent, the evidence is conclusive that physical activity is conducive to a healthy lifestyle and prevention of disease. Habitual physical activity established during the early years may provide the greatest likelihood of impact on mortality and longevity. It is evident that environmental factors need to change if physical activity strategies are to have a significant impact on increasing habitual physical activity levels in children and adolescents. There is also a need for more evidence-based physical activity guidelines for children of all ages. Efforts should be concentrated on facilitating an active lifestyle for children in an attempt to put a stop to the increasing prevalence of obese children

Dragline automation - a decade of development : shared autonomy for improving mining equipment productivity

Draglines are massive machines commonly used in surface mining to strip overburden, revealing the targeted minerals for extraction. Automating some or all of the phases of operation of these machines offers the potential for significant productivity and maintenance benefits. The mining industry has a history of slow uptake of automation systems due to the challenges contained in the harsh, complex, three-dimensional (3D), dynamically changing mine operating environment. Robotics as a discipline is finally starting to gain acceptance as a technology with the potential to assist mining operations. This article examines the evolution of robotic technologies applied to draglines in the form of machine embedded intelligent systems. Results from this work include a production trial in which 250,000 tons of material was moved autonomously, experiments demonstrating steps towards full autonomy, and teleexcavation experiments in which a dragline in Australia was tasked by an operator in the United States.

Teachers’ understanding of school connectedness : implications for the development and implementation of school based injury prevention strategies

Aim: Worldwide, injury is the leading cause of death and disability for young people. Injuries among young people are commonly associated with risk taking behaviour, including violence and transport risks, which often occur in the context of alcohol use. The school environment has been identified as having a significant role in shaping adolescent behaviour. In particular, school connectedness, the degree to which adolescents feel that they belong and are accepted at school, has been shown to be an important protective factor. Strategies for increasing school connectedness may therefore be effective in reducing risk taking and associated injury. Prior to developing connectedness strategies, it is important to understand the perspectives of those in the school regarding the construct and how it is realised in the school context. The aim of this research was to understand teachers’ perspectives of school connectedness, the strategies they employ to connect with students, and their perceptions of school connectedness as a strategy for risk taking and injury prevention. Method: In depth interviews of approximately 45 minutes duration were conducted with 13 Health and PE teachers and support staff from 2 high schools in Southeast Queensland, Australia. Additionally, 6 focus group workshop discussions were held with 35 Education department employees (5-6 per group), including teachers from 15 Southeast Queensland high schools. Results: Participants were found to place strong importance on the development of connectedness among students, including those at risk for problem behaviour. Strategies used to promote connectedness included building trust, taking an interest in each student and being available to talk to, and finding something positive for students to succeed at. Teachers identified strategies as being related to decreased risk taking behavior. Teacher training on school connectedness was perceived as an important and useful inclusion in a school based injury prevention program. Conclusions: The established link between increased school connectedness and decreased problem behaviour has implications for school based strategies designed to decrease adolescent risk taking behaviour and associated injury. Targeting school connectedness as a point of intervention, in conjunction with individual attitude and behaviour change programs, may be an effective injury prevention strategy.

A decision support system for sustainable urban development : the integrated land use and transportation indexing model

Broad, early definitions of sustainable development have caused confusion and hesitation among local authorities and planning professionals. This confusion has arisen because loosely defined principles of sustainable development have been employed when setting policies and planning projects, and when gauging the efficiencies of these policies in the light of designated sustainability goals. The question of how this theory-rhetoric-practice gap can be filled is the main focus of this chapter. It examines the triple bottom line approach–one of the sustainability accounting approaches widely employed by governmental organisations–and the applicability of this approach to sustainable urban development. The chapter introduces the ‘Integrated Land Use and Transportation Indexing Model’ that incorporates triple bottom line considerations with environmental impact assessment techniques via a geographic, information systems-based decision support system. This model helps decision-makers in selecting policy options according to their economic, environmental and social impacts. Its main purpose is to provide valuable knowledge about the spatial dimensions of sustainable development, and to provide fine detail outputs on the possible impacts of urban development proposals on sustainability levels. In order to embrace sustainable urban development policy considerations, the model is sensitive to the relationship between urban form, travel patterns and socio-economic attributes. Finally, the model is useful in picturing the holistic state of urban settings in terms of their sustainability levels, and in assessing the degree of compatibility of selected scenarios with the desired sustainable urban future.

A planning support system for airport city development

Many airports around the world are diversifying their land use strategies to integrate non-aeronautical development. These airports embrace the “airport city” concept to develop a wide range of commercial and light industrial land uses to support airport revenues. The consequences of this changing urban form are profound for both airport and municipal planners alike and present numerous challenges with regard to integration of airport and regional planning. While several tools exist for regional planning and airport operational planning, no holistic airport landside and regional planning tool exist. What is required is a planning support system that can integrate the sometimes conflicting stakeholder interests into one common goal for the airport and the surrounding region. This paper presents a planning support system and evaluates its application to a case study involving Brisbane Airport and the South East Queensland region in Australia.

Development of descriptor tools for the characterization of Australian sugar mill evaporator scale

Cleaning of sugar mill evaporators is an expensive exercise. Identifying the scale components assists in determining which chemical cleaning agents would result in effective evaporator cleaning. The current methods (based on x-ray diffraction techniques, ion exchange/high performance liquid chromatography and thermogravimetry/differential thermal analysis) used for scale characterisation are difficult, time consuming and expensive, and cannot be performed in a conventional analytical laboratory or by mill staff. The present study has examined the use of simple descriptor tests for the characterisation of Australian sugar mill evaporator scales. Scale samples were obtained from seven Australian sugar mill evaporators by mechanical means. The appearance, texture and colour of the scale were noted before the samples were characterised using x-ray fluorescence and x-ray powder diffraction to determine the compounds present. A number of commercial analytical test kits were used to determine the phosphate and calcium contents of scale samples. Dissolution experiments were carried out on the scale samples with selected cleaning agents to provide relevant information about the effect the cleaning agents have on different evaporator scales. Results have shown that by simply identifying the colour and the appearance of the scale, the elemental composition and knowing from which effect the scale originates, a prediction of the scale composition can be made. These descriptors and dissolution experiments on scale samples can be used to provide factory staff with an on-site rapid process to predict the most effective chemicals for chemical cleaning of the evaporators.