Morphologic and genomic characterisation of the koala Chlamydia pneumoniae strain

Chlamydia pneumoniae is a common human and animal pathogen associated with a wide range of upper and lower respiratory tract infections. In more recent years there has been increasing evidence to suggest a link between C. pneumoniae and chronic diseases in humans, including atherosclerosis, stroke and Alzheimer’s disease. C. pneumoniae human strains show little genetic variation, indicating that the human-derived strain originated from a common ancestor in the recent past. Despite extensive information on the genetics and morphology processes of the human strain, knowledge concerning many other hosts (including marsupials, amphibians, reptiles and equines) remains virtually unexplored. The koala (Phascolarctos cinereus) is a native Australian marsupial under threat due to habitat loss, predation and disease. Koalas are very susceptible to chlamydial infections, most commonly affecting the conjunctiva, urogenital tract and/or respiratory tract. To address this gap in the literature, the present study (i) provides a detailed description of the morphologic and genomic architecture of the C. pneumoniae koala (and human) strain, and shows that the koala strain is microscopically, developmentally and genetically distinct from the C. pneumoniae human strain, and (ii) examines the genetic relationship of geographically diverse C. pneumoniae isolates from human, marsupial, amphibian, reptilian and equine hosts, and identifies two distinct lineages that have arisen from animal-to-human cross species transmissions. Chapter One of this thesis explores the scientific problem and aims of this study, while Chapter Two provides a detailed literature review of the background in this field of work. Chapter Three, the first results chapter, describes the morphology and developmental stages of C. pneumoniae koala isolate LPCoLN, as revealed by fluorescence and transmission electron microscopy. The profile of this isolate, when cultured in HEp-2 human epithelial cells, was quite different to the human AR39 isolate. Koala LPCoLN inclusions were larger; the elementary bodies did not have the characteristic pear-shaped appearance, and the developmental cycle was completed within a shorter period of time (as confirmed by quantitative real-time PCR). These in vitro findings might reflect biological differences between koala LPCoLN and human AR39 in vivo. Chapter Four describes the complete genome sequence of the koala respiratory pathogen, C. pneumoniae LPCoLN. This is the first animal isolate of C. pneumoniae to be fully-sequenced. The genome sequence provides new insights into genomic ‘plasticity’ (organisation), evolution and biology of koala LPCoLN, relative to four complete C. pneumoniae human genomes (AR39, CWL029, J138 and TW183). Koala LPCoLN contains a plasmid that is not shared with any of the human isolates, there is evidence of gene loss in nucleotide salvage pathways, and there are 10 hot spot genomic regions of variation that were previously not identified in the C. pneumoniae human genomes. Sequence (partial-length) from a second, independent, wild koala isolate (EBB) at several gene loci confirmed that the koala LPCoLN isolate was representative of a koala C. pneumoniae strain. The combined sequence data provides evidence that the C. pneumoniae animal (koala LPCoLN) genome is ancestral to the C. pneumoniae human genomes and that human infections may have originated from zoonotic infections. Chapter Five examines key genome components of the five C. pneumoniae genomes in more detail. This analysis reveals genomic features that are shared by and/or contribute to the broad ecological adaptability and evolution of C. pneumoniae. This analysis resulted in the identification of 65 gene sequences for further analysis of intraspecific variation, and revealed some interesting differences, including fragmentation, truncation and gene decay (loss of redundant ancestral traits). This study provides valuable insights into metabolic diversity, adaptation and evolution of C. pneumoniae. Chapter Six utilises a subset of 23 target genes identified from the previous genomic comparisons and makes a significant contribution to our understanding of genetic variability among C. pneumoniae human (11) and animal (6 amphibian, 5 reptilian, 1 equine and 7 marsupial hosts) isolates. It has been shown that the animal isolates are genetically diverse, unlike the human isolates that are virtually clonal. More convincing evidence that C. pneumoniae originated in animals and recently (in the last few hundred thousand years) crossed host species to infect humans is provided in this study. It is proposed that two animal-to-human cross species events have occurred in the context of the results, one evident by the nearly clonal human genotype circulating in the world today, and the other by a more animal-like genotype apparent in Indigenous Australians. Taken together, these data indicate that the C. pneumoniae koala LPCoLN isolate has morphologic and genomic characteristics that are distinct from the human isolates. These differences may affect the survival and activity of the C. pneumoniae koala pathogen in its natural host, in vivo. This study, by utilising the genetic diversity of C. pneumoniae, identified new genetic markers for distinguishing human and animal isolates. However, not all C. pneumoniae isolates were genetically diverse; in fact, several isolates were highly conserved, if not identical in sequence (i.e. Australian marsupials) emphasising that at some stage in the evolution of this pathogen, there has been an adaptation/s to a particular host, providing some stability in the genome. The outcomes of this study by experimental and bioinformatic approaches have significantly enhanced our knowledge of the biology of this pathogen and will advance opportunities for the investigation of novel vaccine targets, antimicrobial therapy, or blocking of pathogenic pathways.

secFleck: A Public Key Technology Platform for Wireless Sensor Networks

We describe the design and implementation of a public-key platform, secFleck, based on a commodity Trusted Platform Module (TPM) chip that extends the capability of a standard node. Unlike previous software public-key implementations this approach provides E- Commerce grade security; is computationally fast, energy efficient; and has low financial cost — all essential attributes for secure large-scale sen- sor networks. We describe the secFleck message security services such as confidentiality, authenticity and integrity, and present performance re- sults including computation time, energy consumption and cost. This is followed by examples, built on secFleck, of symmetric key management, secure RPC and secure software update.

Poster Abstract : A public key technology platform for wireless sensor networks

Communication security for wireless sensor networks (WSN) is a challenge due to the limited computation and energy resources available at nodes. We describe the design and implementation of a public-key (PK) platform based on a standard Trusted Platform Module (TPM) chip that extends the capability of a standard node. The result facilitates message security services such as confidentiality, authenticity and integrity. We present results including computation time, energy consumption and cost.

Advancing the meaning of nursing and technology

Technology and Nursing Practice explains and critically engages with the practice implications of technology for nursing. It takes a broad view of technology, covering not only health informatics, but also 'tele-nursing' and the use of equipment in clinical practice.

Access to public sector information : law, technology and policy

On the back of the growing capacity of networked digital information technologies to process and visualise large amounts of information in a timely, efficient and user-driven manner we have seen an increasing demand for better access to and re-use of public sector information (PSI). The story is not a new one. Share knowledge and together we can do great things; limit access and we reduce the potential for opportunity. The two volumes of this book seek to explain and analyse this global shift in the way we manage public sector information. In doing so they collect and present papers, reports and submissions on the topic by leading authors and institutions from across the world. These in turn provide people tasked with mapping out and implementing information policy with reference material and practical guidance. Volume 1 draws together papers on the topic by policymakers, academics and practitioners while Volume 2 presents a selection of the key reports and submissions that have been published over the last few years.

Use of advanced technology videotapes in the delivery of structual engineering courses

A teaching and learning development project is currently under way at Queensland 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.

An initial technology roadmap for home automation : home and personal life management

Home Automation (HA) has emerged as a prominent ¯eld for researchers and in- vestors confronting the challenge of penetrating the average home user market with products and services emerging from technology based vision. In spite of many technology contri- butions, there is a latent demand for a®ordable and pragmatic assistive technologies for pro-active handling of complex lifestyle related problems faced by home users. This study has pioneered to develop an Initial Technology Roadmap for HA (ITRHA) that formulates a need based vision of 10-15 years, identifying market, product and technology investment opportunities, focusing on those aspects of HA contributing to e±cient management of home and personal life. The concept of Family Life Cycle is developed to understand the temporal needs of family. In order to formally describe a coherent set of family processes, their relationships, and interaction with external elements, a reference model named Fam- ily System is established that identi¯es External Entities, 7 major Family Processes, and 7 subsystems-Finance, Meals, Health, Education, Career, Housing, and Socialisation. Anal- ysis of these subsystems reveals Soft, Hard and Hybrid processes. Rectifying the lack of formal methods for eliciting future user requirements and reassessing evolving market needs, this study has developed a novel method called Requirement Elicitation of Future Users by Systems Scenario (REFUSS), integrating process modelling, and scenario technique within the framework of roadmapping. The REFUSS is used to systematically derive process au- tomation needs relating the process knowledge to future user characteristics identi¯ed from scenarios created to visualise di®erent futures with richly detailed information on lifestyle trends thus enabling learning about the future requirements. Revealing an addressable market size estimate of billions of dollars per annum this research has developed innovative ideas on software based products including Document Management Systems facilitating automated collection, easy retrieval of all documents, In- formation Management System automating information services and Ubiquitous Intelligent System empowering the highly mobile home users with ambient intelligence. Other product ideas include robotic devices of versatile Kitchen Hand and Cleaner Arm that can be time saving. Materialisation of these products require technology investment initiating further research in areas of data extraction, and information integration as well as manipulation and perception, sensor actuator system, tactile sensing, odour detection, and robotic controller. This study recommends new policies on electronic data delivery from service providers as well as new standards on XML based document structure and format.