Factors affecting reproductive performance of the prawn, Penaeus monodon

The growth of the Penaeus monodon prawn aquaculture industry in Australia is hampered by a reliance on wild-caught broodstock. This species has proven difficult to breed from if broodstock are reared in captivity. Studies were therefore carried out to investigate factors controlling reproduction and influencing egg quality. Results of the studies revealed that patterns of nutrient accumulation during early ovary development are altered by captive conditions, possibly contributing to reduce larval quality. The sinus gland hormones were shown, together with the environment, to regulate two stages of ovary development. In a separate study it was further revealed that the hormone methyl farnesoate (MF) could negatively regulate the final stages of ovary development. Lastly it was shown that broodstock reared in captivity are less likely to mate and that this is due to inherent problems in both the male and the female prawns.

Complementarity and the uncertainty principle as aesthetic principles : the practice and performance of The Physics Project

Using the generative processes developed over two stages of creative development and the performance of The Physics Project at the Loft at the Creative Industries Precinct at the Queensland University of Technology (QUT) from 5th – 8th April 2006 as a case study, this exegesis considers how the principles of contemporary physics can be reframed as aesthetic principles in the creation of contemporary performance. The Physics Project is an original performance work that melds live performance, video and web-casting and overlaps an exploration of personal identity with the physics of space, time, light and complementarity. It considers the acts of translation between the language of physics and the language of contemporary performance that occur via process and form. This exegesis also examines the devices in contemporary performance making and contemporary performance that extend the reach of the performance, including the integration of the live and the mediated and the use of metanarratives.

The nature and extent of policing alcohol related crime and reducing violence in and around late night entertainment areas

The misuse of alcohol is well documented in Australia and has been associated with disorders and harms that often require police attention. The extent of alcohol-related incidents requiring police attention has been recorded as substantial in some Australian cities (Arro, Crook, & Fenton, 1992; Davey & French, 1995; Ireland & Thommeny, 1993). A significant proportion of harmful drinking occurs in and around licensed premises (Jochelson, 1997; Stockwell, Masters, Phillips, Daly, Gahegan, Midford, & Philp, 1998; Borges, Cherpitel, & Rosovsky, 1998) and most of these incidents are not reported to police (Bryant & Williams, 2000; Lister, Hobbs, Hall, & Winlow, 2000). Alcohol-related incidents have also been found to be concentrated in certain places at certain times (Jochelson, 1997) and therefore manipulating the context in which these incidents occur may provide a means to prevent and reduce the harm associated with alcohol misuse. One of the major objectives of the present program of research was to investigate the occurrence and resource impact of alcohol-related incidents on operational (general duties) policing across a large geographical area. A second objective of the thesis was to examine the characteristics and temporal/spatial dynamics of police attended alcohol incidents in the context of Place Based theories of crime. It was envisaged that this approach would reveal the patterns of the most prevalent offences and demonstrate the relevance of Place Based theories of crime to understanding these patterns. In addition, the role of alcohol, time and place were also explored in order to examine the association between non criminal traffic offences and other types of criminal offences. A final objective of the thesis was to examine the impact of a situational crime prevention strategy that had been initiated to reduce the violence and disorder associated with late-night liquor trading premises. The program of research in this doctorate thesis has been undertaken through the presentation of published papers. The research was conducted in three stages which produced six manuscripts, five of which were submitted to peer reviewed journals and one that was published in a peer reviewed conference proceedings. Stage One included two studies (Studies 1 & 2) both of which involved a cross sectional approach to examine the prevalence and characteristics of alcohol-related incidents requiring police attendance across three large geographical areas that included metropolitan cities, provincial regions and rural areas. Stage Two of the program of research also comprised two cross sectional quantitative studies (Studies 3 & 4) that investigated the temporal and spatial dynamics of the major offence categories attended by operational police in a specific Police District (Gold Coast). Stage Three of the program of research involved two studies (Studies 5 & 6) that assessed the effectiveness of a situational crime prevention strategy. The studies employed a pre-post design to assess the impact on crime, disorder and violence by preventing patrons from entering late-night liquor trading premises between 3 a.m. and 5 a.m. (lockout policy). Although Study Five was solely quantitative in nature, Study Six included both quantitative and qualitative aspects. The approach adopted in Study Six, therefore facilitated not only a quantative comparison of the impact of the lockout policy on different policing areas, but also enabled the processes related to the implementation of the lockout policy to be examined. The thesis reports a program of research involving a common data collection method which then involved a series of studies being conducted to explore different aspects of the data. The data was collected from three sources. Firstly a pilot phase was undertaken to provide participants with training. Secondly a main study period was undertaken immediately following the pilot phase. The first and second sources of data were collected between 29th March 2004 and 2nd May 2004. Thirdly, additional data was collected between the 1st April 2005 and 31st May 2005. Participants in the current program of research were first response operational police officers who completed a modified activity log over a 9 week period (4 week pilot phase & 5 week survey study phase), identifying the type, prevalence and characteristics of alcohol-related incidents that were attended. During the study period police officers attended 31,090 alcohol-related incidents. Studies One and Two revealed that a substantial proportion of current police work involves attendance at alcohol-related incidents (i.e., 25% largely involving young males aged between 17 and 24 years). The most common incidents police attended were vehicle and/or traffic matters, disturbances and offences against property. The major category of offences most likely to involve alcohol included vehicle/traffic matters, disturbances and offences against the person (e.g., common & serious assaults). These events were most likely to occur in the late evenings and early hours of the morning on the weekends, and importantly, usually took longer for police to complete than non alcohol-related incidents. The findings in Studies Three and Four suggest that serious traffic offences, disturbances and offences against the person share similar characteristics and occur in concentrated places at similar times. In addition, it was found that time, place and incident type all have an influence on whether an incident attended by a police officer is alcohol-related. Alcohol-related incidents are more likely to occur in particular locations in the late evenings and early mornings on the weekends. In particular, there was a strong association between the occurrence of alcohol-related disturbances and alcohol-related serious traffic offences in regards to place and time. In general, stealing and property offences were not alcohol-related and occurred in daylight hours during weekdays. The results of Studies Five and Six were mixed. A number of alcohol-related offences requiring police attention were significantly reduced for some policing areas and for some types of offences following the implementation of the lockout policy. However, in some locations the lockout policy appeared to have a negative or minimal impact. Interviews with licensees revealed that although all were initially opposed to the lockout policy as they believed it would have a negative impact on business, most perceived some benefits from its introduction. Some of the benefits included, improved patron safety and the development of better business strategies to increase patron numbers. In conclusion, the overall findings of the six studies highlight the pervasive nature of alcohol across a range of criminal incidents, demonstrating the tremendous impact alcohol-related incidents have on police. The findings also demonstrate the importance of time and place in predicting the occurrence of alcohol-related offences. Although this program of research did not set out to test Place Based theories of crime, these theories were used to inform the interpretation of findings. The findings in the current research program provide evidence for the relevance of Place Based theories of crime to understanding the factors contributing to violence and disorder, and designing relevant crime prevention strategies. For instance, the results in Studies Five and Six provide supportive evidence that this novel lockout initiative can be beneficial for public safety by reducing some types of offences in particular areas in and around late-night liquor trading premises. Finally, intelligent-led policing initiatives based on problem oriented policing, such as the lockout policy examined in this thesis, have potential as a major crime prevention technique to reduce specific types of alcohol-related offences.

The impact of usability on clinician acceptance of a health information system

The two longitudinal case studies that make up this dissertation sought to explain and predict the relationship between usability and clinician acceptance of a health information system. The overall aim of the research study was to determine what role usability plays in the acceptance or rejection of systems used by clinicians in a healthcare context. The focus was on the end users (the clinicians) rather than the views of the system designers and managers responsible for implementation and the clients of the clinicians. A mixed methods approach was adopted that drew on both qualitative and quantitative research methods. This study followed the implementation of a community health information system from early beginnings to its established practice. Users were drawn from different health service departments with distinctly different organisational cultures and attitudes to information and communication technology used in this context. This study provided evidence that a usability analysis in this context would not necessarily be valid when the users have prior reservations on acceptance. Investigation was made on the initial training and post-implementation support together with a study on the nature of the clinicians to determine factors that may influence their attitude. This research identified that acceptance of a system is not necessarily a measure of its quality, capability and usability, is influenced by the user’s attitude which is determined by outside factors, and the nature and quality of training. The need to recognise the limitations of the current methodologies for analysing usability and acceptance was explored to lay the foundations for further research.

Employee engagement : the development of a three dimensional model of engagement; and an exploration of its relationship with affective leader behaviours

This study was designed to examine affective leader behaviours, and their impact on cognitive, affective and behavioural engagement. Researchers (e.g., Cropanzano & Mitchell, 2005; Moorman et al., 1998) have called for more research to be directed toward modelling and testing sets of relationships which better approximate the complexity associated with contemporary organisational experience. This research has attempted to do this by clarifying and defining the construct of engagement, and then by examining how each of the engagement dimensions are impacted by affective leader behaviours. Specifically, a model was tested that identifies leader behaviour antecedents of cognitive, affective and behavioural engagement. Data was collected from five public-sector organisations. Structural equation modelling was used to identify the relationships between the engagement dimensions and leader behaviours. The results suggested that affective leader behaviours had a substantial direct impact on cognitive engagement, which in turn influenced affective engagement, which then influenced intent to stay and extra-role performance. The results indicated a directional process for engagement, but particularly highlighted the significant impact of affective leader behaviours as an antecedent to engagement. In general terms, the findings will provide a platform from which to develop a robust measure of engagement, and will be helpful to human resource practitioners interested in understanding the directional process of engagement and the importance of affective leadership as an antecedent to engagement.

Book Review: Larissa Behrendt, Chris Cuneen and Terri Libesman, Indigenous Legal Relations in Australia (Oxford University Press, Melbourne 2009) 376pp

Indigenous Legal Relations in Australia is a welcome and refreshing addition to the current literature on Indigenous legal issues. Written by a team of highly qualified Indigenous and non-Indigenous academics who share a long term commitment to Indigenous legal and social justice issues, this book provides a clearly written and accessible introductory text for tertiary students and general readers alike who are seeking to gain a deeper understanding of the relationship between Indigenous Australians and the Anglo-Australian legal system.

Intentional first year curriculum design as a means of facilitating student engagement: some exemplars

The importance of student engagement to higher education quality, making deep learning outcomes possible for students, and achieving student retention, is increasingly being understood. The issue of student engagement in the first year of tertiary study is of particular significance. This paper takes the position that the first year curriculum, and the pedagogical principles that inform its design, are critical influencers of student engagement in the first year learning environment. We use an analysis of case studies prepared for Kift’s ALTC Senior Fellowship to demonstrate ways in which student engagement in the first year of tertiary study can be successfully supported through intentional curriculum design that motivates students to learn, provides a positive learning climate, and encourages students to be active in their learning.

Characterisation of soluble components and PAH in PM10 atmospheric particulate matter in Brisbane

Fours sets of PM10 samples were collected in three sites in SEQ from December 2002 to August 2004. Three of these sets of samples were collected by QLD EPA as a part of their regular air monitoring program at Woolloongabba, Rocklea and Eagle Farm. Half of the samples were used in this study for the analysis of water-soluble ions, which are Na+, K+, Mg2+, Ca2+, NH4 +, Cl-, NO3 -, SO4 2-, F-, Br-, NO2 -, PO4 -3 and the other half was retained by QLD EPA. The fourth set of samples was collected at Rocklea, specifically for this study. A quarter of the samples obtained from this set of samples were used to analyse water-soluble ions; a quarter of the sample was used to analyse Pb, Cu, Al, Fe, Mn and Zn; and the rests were used to analyse US EPA 16 priority PAHs. The water-soluble ions were extracted ultrasonically with water and the major watersoluble anions as well as NH4 + were analysed using IC. Na+, K+, Mg2+, Ca2+ Pb, Cu, Al, Fe, Mn and Zn were analysed using ICP-AES while PAHs were extracted by acetonitrile and analysed using HPLC. Of the analysed water-soluble ions, Cl-, NO3 -, SO4 2-, Na+, K+, Mg2+ and Ca2+ were high in concentration and determined in all the samples. F-, Br-, NO2 -, PO4 -3 and NH4 + ions were lower in concentration and determined only in some samples. Na+ and Cl- were high in all samples indicating the importance of a marine source. Principal Component Analysis (PCA) was used to examine the temporal variations of the water-soluble ions at the three sites. The results indicated that there was no major difference between the three sites. However, comparing the average concentrations of ions and Cl-/Na+ it was concluded that Woolloongabba had more marine influence than the other sites. Al, Fe and Zn were detected in all samples. Al and Fe were high in all samples indicating the significance of a source of crustal matter. Cu, Mn and Pb were in low concentrations and were determined only in some samples. The lower Pb concentrations observed in the study than in previous studies indicate that the phasing-out of leaded petrol had an appreciable impact on Pb levels in SEQ. This study reports for the first time, simultaneous data on the water-soluble, metal ion and PAH levels of PM10 aerosols in Brisbane, and provides information on the most likely sources of these chemical species. Such information can be used alongside those that already exist to formulate PM10 pollution reduction strategies for SEQ in order to protect the community from the adverse effects of PM pollution.

Does the summative assessment of real world learning using criterion-referenced assessment need to be discipline specific?

This paper synthesises the existing literature on the contemporary conception of ‘real world’ and compares it with similar notions such as ‘authentic’ and ‘work integrated learning’. While the term ‘real world’ may be partly dependent on the discipline, it does not necessarily follow that the criterion-referenced assessment of ‘real world’ assessment must involve criteria and performance descriptors that are discipline specific. Two examples of summative assessment (court report and trial process exercise) from a final year core subject at the Queensland University of Technology, LWB432 Evidence, emphasise real world learning, are authentic, innovative and better prepare students for the transition into the workplace than more generic forms of assessment such as tutorial participation or oral presentations. The court report requires students to attend a criminal trial in a Queensland Court and complete a two page report on what they saw in practice compared with what they learned in the classroom. The trial process exercise is a 50 minute written closed book activity conducted in tutorials, where students plan questions that they would ask their witness in examination-in-chief, plan questions that they would ask their opponent’s witness in cross-examination, plan questions that they would ask in reexamination given what their opponent asked in cross-examination, and prepare written objections to their opponent’s questions. The trial process exercise simulates the real world, whereas the court report involves observing the real world, and both assessment items are important to the role of counsel. The design of the criterion-referenced assessment rubrics for the court report and trial process exercise is justified by the literature. Notably, the criteria and performance descriptors are not necessarily law specific and this paper highlights the parts that may be easily transferred to other disciplines.

A phenomenological study of contemplative experiences : implications for interior design

This research reports on a project concerned with the relationship between the person and the environment in the context of achieving a contemplative or existential state – a state which can be experienced either consciously or subconsciously. The need for such a study originated with the desire to contribute to the design of multicultural spaces which could be used for a range of activities within the public and the personal arena, activities including contemplation, meditation and prayer. The concept of ‘sacred’ is explored in the literature review and in primary interviews with the participants of this study. Given that the word ‘sacred’ is highly value-laden and potentially alienating for some people, it was decided to use the more accessible term ‘contemplative’. The outcomes of the study inform the practice of interior design and architecture which tends currently to neglect the potential for all spaces to be existentially meaningful. Informed by phenomenological methodology, data were collected from a diverse group of people, using photo-elicitation and interviews. The technique of photo-elicitation proved to be highly effective in helping people reveal their everyday lived experience of contemplative spaces. Reflective analysis (Van Manen 2000) was used to explore the data collected. The initial stage of analysis produced three categories of data: varying conceptions of contemplation, aspects of the person involved in the contemplation, and aspects of environment involved in contemplation. From this, it was found that achieving a state of contemplation involves both the person and the environment in a dialectic process of unfolding. The unfolding has various physical, psycho-social, and existential dimensions or qualities which operate sequentially and simultaneously. Two concepts emerged as being central to unfolding: ‘Cleansing’ and ‘Nothingness’. Unfolding is found to comprise the Core; Distinction; Manifestation; Cleansing; Creation; and Sharing. This has a parallel with Mircea Eliade’s (1959) definition of sacred as something that manifests itself as different from the profane. The power of design, re-contextualization through utility and purpose, and the existential engagements between the person and environment are used as a basis for establishing the potential contribution of the study to interior design. In this way, the study makes a contribution to our understanding of how space and its elements inspire, support and sustain person environment interaction – particularly at the existential level – as well as to our understanding of the multi-dimensional and holistic nature of this interaction. In addition, it points to the need for a phenomenological re-conceptualisation of the design/client relationship. In summary, the contributions of this research are: the exploration of contemplative experience as sacred experience; an understanding of the design of space as creating engagement between person and environment; a rationale for the introduction of a phenomenological approach to the relationship between designer and clients; and raising awareness of the spiritual in a holistic approach to design.

The phenomenology of utopia : reimagining the political

This thesis argues that the end of Soviet Marxism and a bipolar global political imaginary at the dissolution of the short Twentieth Century poses an obstacle for anti-systemic political action. Such a blockage of alternate political imaginaries can be discerned by reading the work of Francis Fukuyama and "Endism" as performative invocations of the closure of political alternatives, and thus as an ideological proclamation which enables and constrains forms of social action. It is contended that the search through dialectical thought for a competing universal to posit against "liberal democracy" is a fruitless one, because it reinscribes the terms of teleological theories of history which work to effect closure. Rather, constructing a phenomenological analytic of the political conjuncture, the thesis suggests that the figure of messianism without a Messiah is central to a deconstructive reframing of the possibilities of political action - a reframing attentive to the rhetorical tone of texts. The project of recovering the political is viewed through a phenomenological lens. An agonistic political distinction must be made so as to memorialise the remainders and ghosts of progress, and thus to gesture towards an indeconstructible justice which would serve as a horizon for the articulation of an empty universal. This project is furthered by a return to a certain phenomenology inspired by Cornelius Castoriadis, Claude Lefort, Maurice Merleau-Ponty and Ernesto Laclau. The thesis provides a reading of Jacques Derrida and Walter Benjamin as thinkers of a minor universalism, a non-prescriptive utopia, and places their work in the context of new understandings of religion and the political as quasi-transcendentals which can be utilised to think through the aporias of political time in order to grasp shards of meaning. Derrida and Chantal Mouffe's deconstructive critique and supplement to Carl Schmitt's concept of the political is read as suggestive of a reframing of political thought which would leave the political question open and thus enable the articulation of social imaginary significations able to inscribe meaning in the field of political action. Thus, the thesis gestures towards a form of thought which enables rather than constrains action under the sign of justice.

Utilisation of seed resources by small mammals : a two-way interaction

Within the Australian wet tropics bioregion, only 900 000 hectares of once continuous rainforest habitat between Townsville and Cooktown now remains. While on the Atherton Tableland, only 4% of the rainforest that once occurred there remains today with remnant vegetation now forming a matrix of rainforest dispersed within agricultural land (sugarcane, banana, orchard crops, townships and pastoral land). Some biologists have suggested that remnants often support both faunal and floral communities that differ significantly from remaining continuous forest. Australian tropical forests possess a relatively high diversity of native small mammal species particularly rodents, which unlike larger mammalian and avian frugivores elsewhere, have been shown to be resilient to the effects of fragmentation, patch isolation and reduction in patch size. While small mammals often become the dominant mammalian frugivores, in terms of their relative abundance, the relationship that exists between habitat diversity and structure, and the impacts of small mammal foraging within fragmented habitat patches in Australia, is still poorly understood. The relationship between foraging behaviour and demography of two small mammal species, Rattus fuscipes and Melomys cervinipes, and food resources in fragmented rainforest sites, were investigated in the current study. Population densities of both species were strongly related with overall density of seed resources in all rainforest fragments. The distribution of both mammal species however, was found to be independent of the distribution of seed resources. Seed utilisation trials indicated that M.cervinipes and R.fuscipes had less impact on seed resources (extent of seed harvesting) than did other rainforest frugivores. Experimental feeding trials demonstrated that in 85% of fruit species tested, rodent feeding increased seed germination by a factor of 3.5 suggesting that in Australian tropical rainforest remnants, small mammals may play a significant role in enhancing germination of large seeded fruits. This study has emphasised the role of small mammals in tropical rainforest systems in north eastern Australia, in particular, the role that they play within isolated forest fragments where larger frugivorous species may be absent.

Stochastic modelling of financial time series with memory and multifractal scaling

Financial processes may possess long memory and their probability densities may display heavy tails. Many models have been developed to deal with this tail behaviour, which reflects the jumps in the sample paths. On the other hand, the presence of long memory, which contradicts the efficient market hypothesis, is still an issue for further debates. These difficulties present challenges with the problems of memory detection and modelling the co-presence of long memory and heavy tails. This PhD project aims to respond to these challenges. The first part aims to detect memory in a large number of financial time series on stock prices and exchange rates using their scaling properties. Since financial time series often exhibit stochastic trends, a common form of nonstationarity, strong trends in the data can lead to false detection of memory. We will take advantage of a technique known as multifractal detrended fluctuation analysis (MF-DFA) that can systematically eliminate trends of different orders. This method is based on the identification of scaling of the q-th-order moments and is a generalisation of the standard detrended fluctuation analysis (DFA) which uses only the second moment; that is, q = 2. We also consider the rescaled range R/S analysis and the periodogram method to detect memory in financial time series and compare their results with the MF-DFA. An interesting finding is that short memory is detected for stock prices of the American Stock Exchange (AMEX) and long memory is found present in the time series of two exchange rates, namely the French franc and the Deutsche mark. Electricity price series of the five states of Australia are also found to possess long memory. For these electricity price series, heavy tails are also pronounced in their probability densities. The second part of the thesis develops models to represent short-memory and longmemory financial processes as detected in Part I. These models take the form of continuous-time AR(∞) -type equations whose kernel is the Laplace transform of a finite Borel measure. By imposing appropriate conditions on this measure, short memory or long memory in the dynamics of the solution will result. A specific form of the models, which has a good MA(∞) -type representation, is presented for the short memory case. Parameter estimation of this type of models is performed via least squares, and the models are applied to the stock prices in the AMEX, which have been established in Part I to possess short memory. By selecting the kernel in the continuous-time AR(∞) -type equations to have the form of Riemann-Liouville fractional derivative, we obtain a fractional stochastic differential equation driven by Brownian motion. This type of equations is used to represent financial processes with long memory, whose dynamics is described by the fractional derivative in the equation. These models are estimated via quasi-likelihood, namely via a continuoustime version of the Gauss-Whittle method. The models are applied to the exchange rates and the electricity prices of Part I with the aim of confirming their possible long-range dependence established by MF-DFA. The third part of the thesis provides an application of the results established in Parts I and II to characterise and classify financial markets. We will pay attention to the New York Stock Exchange (NYSE), the American Stock Exchange (AMEX), the NASDAQ Stock Exchange (NASDAQ) and the Toronto Stock Exchange (TSX). The parameters from MF-DFA and those of the short-memory AR(∞) -type models will be employed in this classification. We propose the Fisher discriminant algorithm to find a classifier in the two and three-dimensional spaces of data sets and then provide cross-validation to verify discriminant accuracies. This classification is useful for understanding and predicting the behaviour of different processes within the same market. The fourth part of the thesis investigates the heavy-tailed behaviour of financial processes which may also possess long memory. We consider fractional stochastic differential equations driven by stable noise to model financial processes such as electricity prices. The long memory of electricity prices is represented by a fractional derivative, while the stable noise input models their non-Gaussianity via the tails of their probability density. A method using the empirical densities and MF-DFA will be provided to estimate all the parameters of the model and simulate sample paths of the equation. The method is then applied to analyse daily spot prices for five states of Australia. Comparison with the results obtained from the R/S analysis, periodogram method and MF-DFA are provided. The results from fractional SDEs agree with those from MF-DFA, which are based on multifractal scaling, while those from the periodograms, which are based on the second order, seem to underestimate the long memory dynamics of the process. This highlights the need and usefulness of fractal methods in modelling non-Gaussian financial processes with long memory.

Introducing Mr Perky : subverting the fantasy trope of immortality in contemporary speculative fiction

The Tide Lords series of fantasy novels set out to examine the issue of immortality. Its purpose was to look at the desirability of immortality, specifically why people actively seek it. It was meant to examine the practicality of immortality, specifically — having got there, what does one do to pass the time with eternity to fill? I also wished to examine the notion of true immortality — immortals who could not be killed. What I did not anticipate when embarking upon this series, and what did not become apparent until after the series had been sold to two major publishing houses in Australia and the US, was the strength of the immortality tropes. This series was intended to fly in the face of these tropes, but confronted with the reality of such a work, the Australian publishers baulked at the ideas presented, requesting the series be re-written with the tropes taken into consideration. They wanted immortals who could die, mortals who wanted to be immortal. And a hero with a sense of humour. This exegesis aims to explore where these tropes originated. It will also discuss the ways I negotiated a way around the tropes, and was eventually able to please the publishers by appearing to adhere to the tropes, while still staying true to the story I wanted to tell. As such, this discussion is, in part, an analysis of how an author negotiates the tensions around writing within a genre while trying to innovate within it.

Recombinant protein production using a Tobacco yellow dwarf virus-based episomal expression vector : control of Rep activity

Over the past decade, plants have been used as expression hosts for the production of pharmaceutically important and commercially valuable proteins. Plants offer many advantages over other expression systems such as lower production costs, rapid scale up of production, similar post-translational modification as animals and the low likelihood of contamination with animal pathogens, microbial toxins or oncogenic sequences. However, improving recombinant protein yield remains one of the greatest challenges to molecular farming. In-Plant Activation (InPAct) is a newly developed technology that offers activatable and high-level expression of heterologous proteins in plants. InPAct vectors contain the geminivirus cis elements essential for rolling circle replication (RCR) and are arranged such that the gene of interest is only expressed in the presence of the cognate viral replication-associated protein (Rep). The expression of Rep in planta may be controlled by a tissue-specific, developmentally regulated or chemically inducible promoter such that heterologous protein accumulation can be spatially and temporally controlled. One of the challenges for the successful exploitation of InPAct technology is the control of Rep expression as even very low levels of this protein can reduce transformation efficiency, cause abnormal phenotypes and premature activation of the InPAct vector in regenerated plants. Tight regulation over transgene expression is also essential if expressing cytotoxic products. Unfortunately, many tissue-specific and inducible promoters are unsuitable for controlling expression of Rep due to low basal activity in the absence of inducer or in tissues other than the target tissue. This PhD aimed to control Rep activity through the production of single chain variable fragments (scFvs) specific to the motif III of Tobacco yellow dwarf virus (TbYDV) Rep. Due to the important role played by the conserved motif III in the RCR, it was postulated that such scFvs can be used to neutralise the activity of the low amount of Rep expressed from a “leaky” inducible promoter, thus preventing activation of the TbYDV-based InPAct vector until intentional induction. Such scFvs could also offer the potential to confer partial or complete resistance to TbYDV, and possibly heterologous viruses as motif III is conserved between geminiviruses. Studies were first undertaken to determine the levels of TbYDV Rep and TbYDV replication-associated protein A (RepA) required for optimal transgene expression from a TbYDV-based InPAct vector. Transient assays in a non-regenerable Nicotiana tabacum (NT-1) cell line were undertaken using a TbYDV-based InPAct vector containing the uidA reporter gene (encoding GUS) in combination with TbYDV Rep and RepA under the control of promoters with high (CaMV 35S) or low (Banana bunchy top virus DNA-R, BT1) activity. The replication enhancer protein of Tomato leaf curl begomovirus (ToLCV), REn, was also used in some co-bombardment experiments to examine whether RepA could be substituted by a replication enhancer from another geminivirus genus. GUS expression was observed both quantitatively and qualitatively by fluorometric and histochemical assays, respectively. GUS expression from the TbYDV-based InPAct vector was found to be greater when Rep was expected to be expressed at low levels (BT1 promoter) rather than high levels (35S promoter). GUS expression was further enhanced when Rep and RepA were co-bombarded with a low ratio of Rep to RepA. Substituting TbYDV RepA with ToLCV REn also enhanced GUS expression but more importantly highest GUS expression was observed when cells were co-transformed with expression vectors directing low levels of Rep and high levels of RepA irrespective of the level of REn. In this case, GUS expression was approximately 74-fold higher than that from a non-replicating vector. The use of different terminators, namely CaMV 35S and Nos terminators, in InPAct vectors was found to influence GUS expression. In the presence of Rep, GUS expression was greater using pInPActGUS-Nos rather than pInPActGUS-35S. The only instance of GUS expression being greater from vectors containing the 35S terminator was when comparing expression from cells transformed with Rep, RepA and REnexpressing vectors and either non-replicating vectors, p35SGS-Nos or p35SGS-35S. This difference was most likely caused by an interaction of viral replication proteins with each other and the terminators. These results indicated that (i) the level of replication associated proteins is critical to high transgene expression, (ii) the choice of terminator within the InPAct vector may affect expression levels and (iii) very low levels of Rep can activate InPAct vectors hence controlling its activity is critical. Prior to generating recombinant scFvs, a recombinant TbYDV Rep was produced in E. coli to act as a control to enable the screening for Rep-specific antibodies. A bacterial expression vector was constructed to express recombinant TbYDV Rep with an Nterminal His-tag (N-His-Rep). Despite investigating several purification techniques including Ni-NTA, anion exchange, hydrophobic interaction and size exclusion chromatography, N-His-Rep could only be partially purified using a Ni-NTA column under native conditions. Although it was not certain that this recombinant N-His-Rep had the same conformation as the native TbYDV Rep and was functional, results from an electromobility shift assay (EMSA) showed that N-His-Rep was able to interact with the TbYDV LIR and was, therefore, possibly functional. Two hybridoma cell lines from mice, immunised with a synthetic peptide containing the TbYDV Rep motif III amino acid sequence, were generated by GenScript (USA). Monoclonal antibodies secreted by the two hybridoma cell lines were first screened against denatured N-His-Rep in Western analysis. After demonstrating their ability to bind N-His-Rep, two scFvs (scFv1 and scFv2) were generated using a PCR-based approach. Whereas the variable heavy chain (VH) from both cell lines could be amplified, only the variable light chain (VL) from cell line 2 was amplified. As a result, scFv1 contained VH and VL from cell line 1, whereas scFv2 contained VH from cell line 2 and VL from cell line 1. Both scFvs were first expressed in E. coli in order to evaluate their affinity to the recombinant TbYDV N-His-Rep. The preliminary results demonstrated that both scFvs were able to bind to the denatured N-His-Rep. However, EMSAs revealed that only scFv2 was able to bind to native N-His-Rep and prevent it from interacting with the TbYDV LIR. Each scFv was cloned into plant expression vectors and co-bombarded into NT-1 cells with the TbYDV-based InPAct GUS expression vector and pBT1-Rep to examine whether the scFvs could prevent Rep from mediating RCR. Although it was expected that the addition of the scFvs would result in decreased GUS expression, GUS expression was found to slightly increase. This increase was even more pronounced when the scFvs were targeted to the cell nucleus by the inclusion of the Simian virus 40 large T antigen (SV40) nuclear localisation signal (NLS). It was postulated that the scFvs were binding to a proportion of Rep, leaving a small amount available to mediate RCR. The outcomes of this project provide evidence that very high levels of recombinant protein can theoretically be expressed using InPAct vectors with judicious selection and control of viral replication proteins. However, the question of whether the scFvs generated in this project have sufficient affinity for TbYDV Rep to prevent its activity in a stably transformed plant remains unknown. It may be that other scFvs with different combinations of VH and VL may have greater affinity for TbYDV Rep. Such scFvs, when expressed at high levels in planta, might also confer resistance to TbYDV and possibly heterologous geminiviruses.