Within-host evolution of Staphylococcus aureus during asymptomatic carriage

Background Staphylococcus aureus is a major cause of healthcare associated mortality, but like many important bacterial pathogens, it is a common constituent of the normal human body flora. Around a third of healthy adults are carriers. Recent evidence suggests that evolution of S. aureus during nasal carriage may be associated with progression to invasive disease. However, a more detailed understanding of within-host evolution under natural conditions is required to appreciate the evolutionary and mechanistic reasons why commensal bacteria such as S. aureus cause disease. Therefore we examined in detail the evolutionary dynamics of normal, asymptomatic carriage. Sequencing a total of 131 genomes across 13 singly colonized hosts using the Illumina platform, we investigated diversity, selection, population dynamics and transmission during the short-term evolution of S. aureus. Principal Findings We characterized the processes by which the raw material for evolution is generated: micro-mutation (point mutation and small insertions/deletions), macro-mutation (large insertions/deletions) and the loss or acquisition of mobile elements (plasmids and bacteriophages). Through an analysis of synonymous, non-synonymous and intergenic mutations we discovered a fitness landscape dominated by purifying selection, with rare examples of adaptive change in genes encoding surface-anchored proteins and an enterotoxin. We found evidence for dramatic, hundred-fold fluctuations in the size of the within-host population over time, which we related to the cycle of colonization and clearance. Using a newly-developed population genetics approach to detect recent transmission among hosts, we revealed evidence for recent transmission between some of our subjects, including a husband and wife both carrying populations of methicillin-resistant S. aureus (MRSA). Significance This investigation begins to paint a picture of the within-host evolution of an important bacterial pathogen during its prevailing natural state, asymptomatic carriage. These results also have wider significance as a benchmark for future systematic studies of evolution during invasive S. aureus disease.

Regulation of early steps of GPVI signal transduction by phosphatases: a systems biology approach

We present a data-driven mathematical model of a key initiating step in platelet activation, a central process in the prevention of bleeding following Injury. In vascular disease, this process is activated inappropriately and causes thrombosis, heart attacks and stroke. The collagen receptor GPVI is the primary trigger for platelet activation at sites of injury. Understanding the complex molecular mechanisms initiated by this receptor is important for development of more effective antithrombotic medicines. In this work we developed a series of nonlinear ordinary differential equation models that are direct representations of biological hypotheses surrounding the initial steps in GPVI-stimulated signal transduction. At each stage model simulations were compared to our own quantitative, high-temporal experimental data that guides further experimental design, data collection and model refinement. Much is known about the linear forward reactions within platelet signalling pathways but knowledge of the roles of putative reverse reactions are poorly understood. An initial model, that includes a simple constitutively active phosphatase, was unable to explain experimental data. Model revisions, incorporating a complex pathway of interactions (and specifically the phosphatase TULA-2), provided a good description of the experimental data both based on observations of phosphorylation in samples from one donor and in those of a wider population. Our model was used to investigate the levels of proteins involved in regulating the pathway and the effect of low GPVI levels that have been associated with disease. Results indicate a clear separation in healthy and GPVI deficient states in respect of the signalling cascade dynamics associated with Syk tyrosine phosphorylation and activation. Our approach reveals the central importance of this negative feedback pathway that results in the temporal regulation of a specific class of protein tyrosine phosphatases in controlling the rate, and therefore extent, of GPVI-stimulated platelet activation.

A low mortality, high morbidity reduced intensity status epilepticus (RISE) model of epilepsy and epileptogenesis in the rat

Animal models of acquired epilepsies aim to provide researchers with tools for use in understanding the processes underlying the acquisition, development and establishment of the disorder. Typically, following a systemic or local insult, vulnerable brain regions undergo a process leading to the development, over time, of spontaneous recurrent seizures. Many such models make use of a period of intense seizure activity or status epilepticus, and this may be associated with high mortality and/or global damage to large areas of the brain. These undesirable elements have driven improvements in the design of chronic epilepsy models, for example the lithium-pilocarpine epileptogenesis model. Here, we present an optimised model of chronic epilepsy that reduces mortality to 1% whilst retaining features of high epileptogenicity and development of spontaneous seizures. Using local field potential recordings from hippocampus in vitro as a probe, we show that the model does not result in significant loss of neuronal network function in area CA3 and, instead, subtle alterations in network dynamics appear during a process of epileptogenesis, which eventually leads to a chronic seizure state. The model’s features of very low mortality and high morbidity in the absence of global neuronal damage offer the chance to explore the processes underlying epileptogenesis in detail, in a population of animals not defined by their resistance to seizures, whilst acknowledging and being driven by the 3Rs (Replacement, Refinement and Reduction of animal use in scientific procedures) principles.

Children's preconceptions of science: how these can be used in teaching

This paper focuses on young children’s initial ideas about science prior to any teaching and discusses teachers’ identification of these ‘preconceptions’ when teaching science in the early years. The research focuses on early years teaching in public and private kindergartens with children from three to five. The area of the children’s preconceptions has been extensively investigated by other researchers in the past. However, research focusing on children’s preconceptions and how teachers work with these in the early years is still limited in comparison, especially within Cypriot context. A case study was employed which facilitated in-depth investigation employing different methods of data collection including interviews and observations. The results indicate that teachers tend to avoid identification of the children’s preconceptions when planning and teaching science. This suggests a lack of appreciation of the children’s preconceptions and the consequences when they are not acknowledged. To help teachers respond to the children’s preconceptions, this paper provides a number of suggestion on how to identify children’s preconceptions.

From Rational Design of Drug Crystals to Understanding of Nucleic Acid Structures: Lamivudine Duplex

A DNA-like duplex of nucleosides is probable to exist even without the 5`-phosphate groups needed to assemble the chain backbone. However, double-stranded helical structures of nucleosides are unknown. Here, we report a duplex of nucleoside analogs that is spontaneously assembled due to stacking of the neutral and protonated molecules of lamivudine, a nucleoside reverse transcriptase inhibitor (NTRI) widely used in anti-HIV drug combinatory medication. The left-handed lamivudine duplex has features similar to those of i-motif DNA, as the face-to-face base stacking and the helix rise per base pair. Furthermore, the protonation pattern on alternate bases expected for it DNA-like duplex stabilized by pairing of neutral and protonated cytosine fragments was observed for the first time in the lamivudine double-stranded helix. This structure demonstrates that hydrogen bonds can substitute for covalent phosphodiester linkage in the stabilization of the duplex backbone. This interesting example of spontaneous molecular self-organization indicates that the 5`-phosphate group could not be a requirement for duplex assembly.

Teaching for understanding in science: constructivist / conceptual change teaching approaches

This two-paper set has arisen from a concern within the Victorian Science in Schools Research Project, to help teachers support student learning of science content. In the first paper, the research on student learning of science conceptions was reviewed, and the major findings presented. It traced the changing ways we have viewed science teaching and learning, over the last two decades. This second paper looks at a variety of teaching schemes that aim to support meaningful learning in science, some based on the metaphor of conceptual change, and draws out principles from these for how we might best support student learning of major science ideas.

Public views of the benefits and barriers to the consumption of a plant-based diet

Objective: The aim of this study was to examine consumers' perceived benefits and barriers to the consumption of a plant-based diet. Design: Mail survey that included questions on perceived benefits and barriers to the consumption of a plant-based diet. Setting: Victoria, Australia. Subjects: Four hundred and fifteen randomly selected Victorian adults. Results: The main perceived barrier to adoption of a plant-based diet was a lack of information about plant-based diets (42% agreement). Sex, age and education differences were present in over a quarter of the barrier items. For example, non-university-educated respondents and older people were less willing to change their current eating pattern than were university educated and younger respondents. The main benefits associated with plant-based diets were health benefits, particularly decreased saturated fat intake (79% agreement), increased fibre intake (76%), and disease prevention (70%). Age, sex and education differences with regard to benefits were apparent, although sex differences were more important than age or education differences. Conclusions: The majority of respondents perceived there to be health benefits associated with the consumption of a plant-based diet. Compared with the proportion of respondents who agreed that there were particular benefits of eating a plant-based diet, perceived barriers were relatively low. An understanding of the perceived benefits and barriers of consuming a plant-based diet will help formulate strategies that aim to influence beliefs about plant foods, plant food consumption, and, ultimately, public health.

Year 8 students' understanding of astronomy as a representational issue : insights from a classroom video study

The research described in this paper argues that difficulties of leaming science concepts such as those associated with processes involving the Sun, Moon and Earth, such as day and night, the seasons and phases of the moon, are fundamentally representational in nature. There is a need for learners to use their own representational, cultural and cognitive resources to engage with the subject-specific representational practices of science. From this perspective students need to understand and conceptually integrate different representational modalities or forms in learning science and reasoning in science. The researchers worked with two experienced teachers in planning a teaching sequence in astronomy using a teaching approach that highlight representational issues and options in helping students explore and develop key conceptual understandings. Classroom sequences involving the two teachers were videotaped using a combined focus on the teacher and groups of students. Video analysis software was used to capture the variety of representations used, and sequences of representational negotiation. From a pedagogical perspective the representational approach placed a significant agency in the hands of students which resulted in structured discussions around conceptual problems. Representations were used as tools for reasoning and communication to drive classroom discussions and develop higher levels of understanding in the students. The pre- and post-testing showed significant gains in students thinking from naive to more scientific understandings of astronomy.

Applications and fundamental understanding of selected analytically important chemiluminescence reactions

This thesis encompasses a series of investigations into the fundamental chemistry and spectroscopy of chemiluminescence (chemical reactions that produce light). This new knowledge enabled the development of innovative analytical methodologies for rapid chemical measurements in forensic science, industrial process monitoring and clinical diagnostics.

Visitor understanding of museum practices and processes

The study was conducted over 3 years and explored beyond what visitors to museum exhibitions learnt from written labels, to what they learnt and knew about the museum as an institution, its staff and their knowledge and understanding of the subliminal messages of exhibitions. The site used as the Victorian historical mansion, Werribee Park. Visitors to the 1880s Costume Exhibition were surveyed.

Revolt and discovery : towards an understanding of practice as research through Kristevan aesthetics

This paper will examine Kristeva’s conceptions of revolution and revolt to demonstrate the significance of her work for practitioners and researchers working in the emerging field of creative arts practice as research, a field of research that is burgeoning in the UK, Australia, Canada and Scandinavia. I will argue that Kristeva’ thought elaborates the aesthetic underpinnings of discovery and provides a rationale for the methodologies used in artistic research.

In her later work on interpretation, Kristeva places a greater emphasis on the need for analysis or theory, since the art and culture of revolt produce unfamiliar or mutant meanings that are difficult for audiences to grasp in terms of their potency for engendering social change and individual empowerment. However, she places the responsibility for this analysis and interpretation on the art critic. But what if (as is the case with the advent of artistic practice as research), the maker and the “critic” become one and the same? Can this shift in the status of artistic practice within the knowledge economy, be understood in terms of Kristeva account of the sense and nonsense of revolt? I will address these questions by revisiting aspects of Kristeva thinking on experience-in practice and examining her more recent and extended elaboration of revolutionary practice. The paper will explore how her thinking can provide practitioners with a framework for understanding creative arts research as the production of new knowledge. If as Kristeva argues, that art and literature are amongst the few means of revolt and renewal, it seems appropriate to turn to her thinking in order to articulate a rationale and argument for claiming that practice as research can operate as a driver of change and innovation in contemporary culture.

The first part of this task will involve tracing what Kristeva sees as three forms of revolt made possible through aesthetic experience. This will involve a closer examination of the notions of transgression and art as experience. Following on from this discussion, I will discuss how Kristeva’s work constitutes both an implicit and explicit critique of science allowing us to conceive of artistic research as an alternative and performative production of knowledge. Finally in this paper, I will apply and illustrate these ideas through an analysis of a selection of a number of research projects successfully completed by artistic researchers in Australia. I hope to show that artistic practice as a mode of enquiry, reveals the inextricable and necessary relationship between practice and theory, interpretation and making, art and life. I suggest that it is this interrelationship, that underpins what Kristeva describes as creative and revolutionary practice. In the context of creative arts practice as research, Kriteva’s account of experience–in-practice indicates that interpretation and analysis must fall to the practitioner-researcher himself or herself - rather than to another person who has been external to the procedures of making - to trace the significant experiential, subjective and emergent processes involved in the production of the work that allows it to reveal the new. This is necessary if the generative and revolutionary impact of artistic research is to be fully understood in the wider research arena.

Government involvement in entrepreneurship and new business creation in Australia : a quantitative analysis of public perceptions and opinions

In order to determine the range of Australian perceptions on new venture creation at the end of the decade of the 1980s, and in particular attitudes towards government involvement in fostering entrepreneurship, a major quantitative study was conducted. The survey involved more than 1500 Australians in face-to-face interviews (300 in each mainland capital city) chosen on a random basis.

An analysis of the data provides an assessment of the Australian general public&s perceptions in three key areas: their understanding of the word 'entrepreneur' their rating of importance of new venture creation; their belief in government involvement in fostering new venture creation.

It is believed to be the first study attempting to quantify an entire nation&s perceptions in three areas vital to creators of national economic and industry policies.

Conflict between genetic and phenotypic differentiation : the evolutionary history of a ‘lost and rediscovered’ shorebird

Understanding and resolving conflicts between phenotypic and genetic differentiation is central to evolutionary research. While phenotypically monomorphic species may exhibit deep genetic divergences, some morphologically distinct taxa lack notable genetic differentiation. Here we conduct a molecular investigation of an enigmatic shorebird with a convoluted taxonomic history, the White-faced Plover (Charadrius alexandrinus dealbatus), widely regarded as a subspecies of the Kentish Plover (C. alexandrinus). Described as distinct in 1863, its name was consistently misapplied in subsequent decades until taxonomic clarification ensued in 2008. Using a recently proposed test of species delimitation, we reconfirm the phenotypic distinctness of dealbatus. We then compare three mitochondrial and seven nuclear DNA markers among 278 samples of dealbatus and alexandrinus from across their breeding range and four other closely related plovers. We fail to find any population genetic differentiation between dealbatus and alexandrinus, whereas the other species are deeply diverged at the study loci. Kentish Plovers join a small but growing list of species for which low levels of genetic differentiation are accompanied by the presence of strong phenotypic divergence, suggesting that diagnostic phenotypic characters may be encoded by few genes that are difficult to detect. Alternatively, gene expression differences may be crucial in producing different phenotypes whereas neutral differentiation may be lagging behind.