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.

Use of IP addresses for high rate flooding attack detection

High-rate flooding attacks (aka Distributed Denial of Service or DDoS attacks) continue to constitute a pernicious threat within the Internet domain. In this work we demonstrate how using packet source IP addresses coupled with a change-point analysis of the rate of arrival of new IP addresses may be sufficient to detect the onset of a high-rate flooding attack. Importantly, minimizing the number of features to be examined, directly addresses the issue of scalability of the detection process to higher network speeds. Using a proof of concept implementation we have shown how pre-onset IP addresses can be efficiently represented using a bit vector and used to modify a “white list” filter in a firewall as part of the mitigation strategy.

Towards a game theoretic authorisation model

Authorised users (insiders) are behind the majority of security incidents with high financial impacts. Because authorisation is the process of controlling users’ access to resources, improving authorisation techniques may mitigate the insider threat. Current approaches to authorisation suffer from the assumption that users will (can) not depart from the expected behaviour implicit in the authorisation policy. In reality however, users can and do depart from the canonical behaviour. This paper argues that the conflict of interest between insiders and authorisation mechanisms is analogous to the subset of problems formally studied in the field of game theory. It proposes a game theoretic authorisation model that can ensure users’ potential misuse of a resource is explicitly considered while making an authorisation decision. The resulting authorisation model is dynamic in the sense that its access decisions vary according to the changes in explicit factors that influence the cost of misuse for both the authorisation mechanism and the insider.

The peer-to-patent initiative : revitalizing patent examination with peer review

Every day we hear someone complain that this or that patent should not have been granted. People complain that the patent system is now a threat to existing business and innovation be- cause the patent office grants with alarming regularity patents for inventions that are neither novel nor non-obvious. People argue that the patent office cannot keep up with the job of examining the backlog of hundreds of thousands of patents and that, even if it could, the large volumes of prior art literature that need to be considered each time a patent application is received make the decision as to whether a patent should be granted or not a treacherous one.

Ramifications of development projects deemed “state significant”

Purpose, Design/methodology / approach The acknowledgement of state significance in relation to development projects can result in special treatment by regulatory authorities, particularly in terms of environmental compliance and certain economic and other government support measures. However, defining just what constitutes a “significant project”, or a project of “state significance”, varies considerably between Australian states. In terms of establishing threshold levels, in Queensland there is even less clarity. Despite this lack of definition, the implications of “state significance” can nevertheless be considerable. For example, in Queensland if the Coordinator-General declares a project to be a “significant project” under the State Development and Public Works Organisation Act 1971, the environmental impact assessment process may become more streamlined – potentially circumventing certain provisions under The Integrated Planning Act 1997. If the project is not large enough to be so deemed, an extractive resource under the State Planning Policy 2/07 - Protection of Extractive Resources 2007 may be considered to be of State or regional significance and subsequently designated as a “Key Resource Area”. As a consequence, such a project is afforded some measure of resource protection but remains subject to the normal assessment process under the Integrated Development Assessment System, as well as the usual requirements of the vegetation management codes, and other regulations. Findings (Originality/value) & Research limitations / implications This paper explores the various meanings of “state significance” in Queensland and the ramifications for development projects in that state. It argues for a streamlining of the assessment process in order to avoid or minimise constraints acting on the state’s development. In so doing, it questions the existence of a strategic threat to the delivery of an already over-stretched infrastructure program.

Information sharing in the 21st century : progress and challenges

With the increasing threat of cyber and other attacks on critical infrastructure, governments throughout the world have been organizing industry to share information on possible threats. In Australia the Office of the Attorney General has formed Trusted Information Sharing Networks (TISN) for the various critical industries such as banking and electricity. Currently the majority of information for a TISN is shared at physical meetings. To meet cyber threats there are clearly limitations to physical meetings. Many of these limitations can be overcome by the creation of a virtual information sharing network (VISN). However there are many challenges to overcome in the design of a VISN both from a policy and technical viewpoint. We shall discuss some of these challenges in this talk.

Vulnerability factors for disaster-induced child post-traumatic stress disorder : the case for low family resilience and previous mental illness

Objective: The aim of the present study was to investigate whether parent report of family resilience predicted children’s disaster-induced post-traumatic stress disorder (PTSD) and general emotional symptoms, independent of a broad range of variables including event-related factors, previous child mental illness and social connectedness. ---------- Methods: A total of 568 children (mean age = 10.2 years, SD = 1.3) who attended public primary schools, were screened 3 months after Cyclone Larry devastated the Innisfail region of North Queensland. Measures included parent report on the Family Resilience Measure and Strengths and Difficulties Questionnaire (SDQ)–emotional subscale and child report on the PTSD Reaction Index, measures of event exposure and social connectedness. ---------- Results: Sixty-four students (11.3%) were in the severe–very severe PTSD category and 53 families (28.6%) scored in the poor family resilience range. A lower family resilience score was associated with child emotional problems on the SDQ and longer duration of previous child mental health difficulties, but not disaster-induced child PTSD or child threat perception on either bivariate analysis, or as a main or moderator variable on multivariate analysis (main effect: adjusted odds ratio (ORadj) = 0.57, 95% confidence interval (CI) = 0.13–2.44). Similarly, previous mental illness was not a significant predictor of child PTSD in the multivariate model (ORadj = 0.75, 95%CI = 0.16–3.61). ---------- Conclusion: In this post-disaster sample children with existing mental health problems and those of low-resilience families were not at elevated risk of PTSD. The possibility that the aetiological model of disaster-induced child PTSD may differ from usual child and adolescent conceptualizations is discussed.

Metal Contaminants in Leachate from Sanitary Landfills

The uncontrolled disposal of solid wastes poses an immediate threat to public health and a long term threat to the environmental well being of future generations. Solid waste is waste resulting from human activities that is solid and unwanted (Peavy et al., 1985). If unmanaged, dumped solid wastes generate liquid and gaseous emissions that are detrimental to the environment. This can lead to a serious form of contamination known as metal contamination, which poses a risk to human health and ecosystems. For example, some heavy metals (cadmium, chromium compounds, and nickel tetracarbonyl) are known to be highly toxic, and are aggressive at elevated concentrations. Iron, copper, and manganese can cause staining, and aluminium causes depositions and discolorations. In addition, calcium and magnesium cause hardness in water causing scale deposition and scum formation. Though not a metal but a metalloid, arsenic is poisonous at relatively high concentrations and when diluted at low concentrations causes skin cancer. Normally, metal contaminants are found in a dissolved form in the liquid percolating through landfills. Because average metal concentrations from full-scale landfills, test cells, and laboratory studies have tended to be generally low, metal contamination originating from landfills is not generally considered a major concern (Kjeldsen et al., 2002; Christensen et al., 1999). However, a number of factors make it necessary to take a closer look at metal contaminants from landfills. One of these factors relates to variability. Landfill leachate can have different qualities depending on the weather and operating conditions. Therefore, at one moment in time, metal contaminant concentrations may be quite low, but at a later time these concentrations could be quite high. Also, these conditions relate to the amount of leachate that is being generated. Another factor is biodiversity. It cannot be assumed that a particular metal contaminant is harmless to flora and fauna (including micro organisms) just because it is harmless to human health. This has significant implications for ecosystems and the environment. Finally, there is the moral factor. Because uncertainty surrounds the potential effects of metal contamination, it is appropriate to take precautions to prevent it from taking place. Consequently, it is necessary to have good scientific knowledge (empirically supported) to adequately understand the extent of the problem and improve the way waste is being disposed of

A 3D visualisation model applied to a thick, multi-layered alluvial groundwater system under stress : Condamine Valley, QLD

The upper Condamine River in southern Queensland has formed extensive alluvial deposits which have been used for irrigation of cotton crops for over 40 years. Due to excessive use and long term drought conditions these groundwater resources are under substantial threat. This condition is now recognised by all stakeholders, and Qld Department of Environment and Resource Management (DERM) are currently undertaking a water planning process for the Central Condamine Alluvium with water users and other stakeholders. DERM aims to effectively demonstrate the character of the groundwater system and its current status, and notably the continued long-term drawdown of the watertable. It was agreed that 3D visualisation was an ideal tool to achieve this. The Groundwater Visualisation System (GVS) developed at QUT was utilised and the visualisation model developed in conjunction with DERM to achieve a planning-management tool for this particular application

The urban littoral frontier : land reclamation in the history of human settlements

The urban waterfront may be regarded as the littoral frontier of human settlement. Typically, over the years, it advances, sometimes retreats, where terrestrial and aquatic processes interact and frequently contest this margin of occupation. Because most towns and cities are sited beside water bodies, many of these urban centers on or close to the sea, their physical expansion is constrained by the existence of aquatic areas in one or more directions from the core. It is usually much easier for new urban development to occur along or inland from the waterfront. Where other physical constraints, such as rugged hills or mountains, make expansion difficult or expensive, building at greater densities or construction on steep slopes is a common response. This kind of development, though technically feasible, is usually more expensive than construction on level or gently sloping land, however. Moreover, there are many reasons for developing along the shore or riverfront in preference to using sites further inland. The high cost of developing existing dry land that presents serious construction difficulties is one reason for creating new land from adjacent areas that are permanently or periodically under water. Another reason is the relatively high value of artificially created land close to the urban centre when compared with the value of existing developable space at a greater distance inland. The creation of space for development is not the only motivation for urban expansion into aquatic areas. Commonly, urban places on the margins of the sea, estuaries, rivers or great lakes are, or were once, ports where shipping played an important role in the economy. The demand for deep waterfronts to allow ships to berth and for adjacent space to accommodate various port facilities has encouraged the advance of the urban land area across marginal shallows in ports around the world. The space and locational demands of port related industry and commerce, too, have contributed to this process. Often closely related to these developments is the generation of waste, including domestic refuse, unwanted industrial by-products, site formation and demolition debris and harbor dredgings. From ancient times, the foreshore has been used as a disposal area for waste from nearby settlements, a practice that continues on a huge scale today. Land formed in this way has long been used for urban development, despite problems that can arise from the nature of the dumped material and the way in which it is deposited. Disposal of waste material is a major factor in the creation of new urban land. Pollution of the foreshore and other water margin wetlands in this way encouraged the idea that the reclamation of these areas may be desirable on public health grounds. With reference to examples from various parts of the world, the historical development of the urban littoral frontier and its effects on the morphology and character of towns and cities are illustrated and discussed. The threat of rising sea levels and the heritage value of many waterfront areas are other considerations that are addressed.

Sustainable urban stormwater management : water sensitive urban design perceptions, drivers and barriers

Stormwater has been recognised as one of the main culprits of aquatic ecosystem pollution and as a significant threat to the goal of ecological sustainable development. Water sensitive urban design is one of the key responses to the need to better manage urban stormwater runoff, the objectives of which go beyond rapid and efficient conveyance. Underpinned by the concepts of sustainable urban development, water sensitive urban design has proven to be an efficient and environmentally-friendly approach to urban stormwater management, with the necessary technical know-how and skills already available. However, large-scale implementation of water sensitive urban design is still lacking in Australia due to significant impediments and negative perceptions. Identification of the issues, barriers and drivers that affect sustainability outcomes of urban stormwater management is one of the first steps towards encouraging the wide-scale uptake of water sensitive urban design features which integrate sustainable urban stormwater management. This chapter investigates key water sensitive urban design perceptions, drivers and barriers in order to improve sustainable urban stormwater management efforts.

Stereotypes of Taiwanese salespeople at the service interface

Stereotypes of salespeople are common currency in US media outlets and research suggests that these stereotypes are uniformly negative. However, there is no reason to expect that stereotypes will be consistent across cultures. The present paper provides the first empirical examination of salesperson stereotypes in an Asian country, specifically Taiwan. Using accepted psychological methods, Taiwanese salesperson stereotypes are found to be twofold, with a negative stereotype being quite congruent with existing US stereotypes, but also a positive stereotype, which may be related to the specific culture of Taiwan.

Anthony Browne and the cultural capital of classic fairy tales

Prolific British author/illustrator Anthony Browne both participates in the classic fairy-tale tradition and appropriates its cultural capital, ultimately undertaking a process of self-canonisation alongside the dissemination of fairy tales. In reading Browne’s Hansel and Gretel (1981), The Tunnel (1989) and Into the Forest (2004), a trajectory emerges that moves from broadly intertextual to more exclusively self-referential modes of representation which reward readers of “Anthony Browne”, rather than readers of “fairy tales”. All three books depict ‘babes in the woods’ stories wherein child characters must negotiate some form of threat outside the home in order to return home safely. Thus, they represent childhood agency. However, these visions of agency are ultimately subordinated to logics of capital, which means that child readers of Browne’s fairy-tale books are overtly invited to identify with children who act, but are interpellated as privileged if they ‘know’. Bourdieu’s model of ‘cultural capital’ offers a lens for considering Browne’s production of ‘value’ for his own works within a broader cultural landscape which privileges literary fairy tales as a register of juvenile cultural competency. If cultural capital can be formulated most simply as the symbolic exchange value of approved modes of knowing and being, it is clearly helpful when trying to unpack logics of meaning within heavily intertextual or citational texts. It is also helpful thinking about what kinds of stories we as a culture choose to disseminate, choose to privilege, or choose to suppress. Zipes notes of fairy tales that, “the genre itself becomes a kind of institute that is involved in the socialization and acculturation of readers” (22). He elaborates that, “We initiate readers and expect them to learn the fairy-tale code as part of our responsibility in the civilizing process” (Zipes 29), so it is little wonder that Tatar describes fairy tales as “a vital part of our cultural capital” (xix). Although Browne is clearly interested in literary fairy tales, the most obvious strategies of self-canonisation take place in Browne’s work not in words but in pictures: hidden in plain sight, as illustration becomes self-reflexive citation.

Legislative proposals to codify directors' liability for insolvent trading in Hong Kong : a 10-year journey

Hong Kong is a modern global city with a reputation for well-regulated financial markets, but for years, the government had been trying to enact laws on corporate rescue procedures with relatively little success. It is under the pretext of the Global Financial Crisis, the threat of a future economic meltdown gave the Hong Kong government the impetus to revisit this issue. This third attempt to codify statutory obligations on directors’ liability for insolvent trading has been criticised for either setting the standards too high or low for directors trading whilst insolvent. There is also some reservation given the beliefs and values of directors in Chinese family-owned and controlled companies. These companies would most likely trade out the difficult times. Nevertheless, this does not negate from the fact that the enactment of corporate rescue procedures in Hong Kong in 2010 is a momentous achievement for the Hong Kong government.

Investigating challenges and opportunities of water sensitive urban design for knowledge based development of Australian cities

A new approach that is slowly replacing neoclassical models of economic growth and commodity based industrial activities, knowledge based urban development (KBUD) aims to provide opportunities for citiesw to foster knowledge creation, exchange and innovation, and is based on the concepts of both sustainable urban development and economic prosperity; sustainable uses and protection of natural resources are therefore integral parts of KBUD. As such, stormwater, which has been recognised as one of the main culprits of aquatic ecosystem pollution and as therefore a significant threat to the goal of sustainable urban development, needs to be managed in a manner that produces ecologically sound outcomes. Water sensitive urban design (WSUD) is one of the key responses to the need to better management urban stormwater runoff and supports KBUD by providing an alternative, innovative and effective strategy to traditional stormwater management.