Investigation of highly regulated promoters for the production of recombinant proteins in plants

Plants have been identified as promising expression systems for the commercial production of recombinant proteins. Plant-based protein production or “biofarming” offers a number of advantages over traditional expression systems in terms of scale of production, the capacity for post-translation processing, providing a product free of contaminants and cost effectiveness. A number of pharmaceutically important and commercially valuable proteins, such as antibodies, biopharmaceuticals and industrial enzymes are currently being produced in plant expression systems. However, several challenges still remain to improve recombinant protein yield with no ill effect on the host plant. The ability for transgenic plants to produce foreign proteins at commercially viable levels can be directly related to the level and cell specificity of the selected promoter driving the transgene. The accumulation of recombinant proteins may be controlled by a tissue-specific, developmentally-regulated or chemically-inducible promoter such that expression of recombinant proteins can be spatially- or temporally- controlled. The strict control of gene expression is particularly useful for proteins that are considered toxic and whose expression is likely to have a detrimental effect on plant growth. To date, the most commonly used promoter in plant biotechnology is the cauliflower mosaic virus (CaMV) 35S promoter which is used to drive strong, constitutive transgene expression in most organs of transgenic plants. Of particular interest to researchers in the Centre for Tropical Crops and Biocommodities at QUT are tissue-specific promoters for the accumulation of foreign proteins in the roots, seeds and fruit of various plant species, including tobacco, banana and sugarcane. Therefore this Masters project aimed to isolate and characterise root- and seed-specific promoters for the control of genes encoding recombinant proteins in plant-based expression systems. Additionally, the effects of matching cognate terminators with their respective gene promoters were assessed. The Arabidopsis root promoters ARSK1 and EIR1 were selected from the literature based on their reported limited root expression profiles. Both promoters were analysed using the PlantCARE database to identify putative motifs or cis-acting elements that may be associated with this activity. A number of motifs were identified in the ARSK1 promoter region including, WUN (wound-inducible), MBS (MYB binding site), Skn-1, and a RY core element (seed-specific) and in the EIR1 promoter region including, Skn-1 (seed-specific), Box-W1 (fungal elicitor), Aux-RR core (auxin response) and ABRE (ABA response). However, no previously reported root-specific cis-acting elements were observed in either promoter region. To confirm root specificity, both promoters, and truncated versions, were fused to the GUS reporter gene and the expression cassette introduced into Arabidopsis via Agrobacterium-mediated transformation. Despite the reported tissue-specific nature of these promoters, both upstream regulatory regions directed constitutive GUS expression in all transgenic plants. Further, similar levels of GUS expression from the ARSK1 promoter were directed by the control CaMV 35S promoter. The truncated version of the EIR1 promoter (1.2 Kb) showed some differences in the level of GUS expression compared to the 2.2 Kb promoter. Therefore, this suggests an enhancer element is contained in the 2.2 Kb upstream region that increases transgene expression. The Arabidopsis seed-specific genes ATS1 and ATS3 were selected from the literature based on their seed-specific expression profiles and gene expression confirmed in this study as seed-specific by RT-PCR analysis. The selected promoter regions were analysed using the PlantCARE database in order to identify any putative cis elements. The seed-specific motifs GCN4 and Skn-1 were identified in both promoter regions that are associated with elevated expression levels in the endosperm. Additionaly, the seed-specific RY element and the ABRE were located in the ATS1 promoter. Both promoters were fused to the GUS reporter gene and used to transform Arabidopsis plants. GUS expression from the putative promoters was consitutive in all transgenic Arabidopsis tissue tested. Importantly, the positive control FAE1 seed-specific promoter also directed constitutive GUS expression throughout transgenic Arabidopsis plants. The constitutive nature seen in all of the promoters used in this study was not anticipated. While variations in promoter activity can be caused by a number of influencing factors, the variation in promoter activity observed here would imply a major contributing factor common to all plant expression cassettes tested. All promoter constructs generated in this study were based on the binary vector pCAMBIA2300. This vector contains the plant selection gene (NPTII) under the transcriptional control of the duplicated CaMV 35S promoter. This CaMV 35S promoter contains two enhancer domains that confer strong, constitutive expression of the selection gene and is located immediately upstream of the promoter-GUS fusion. During the course of this project, Yoo et al. (2005) reported that transgene expression is significantly affected when the expression cassette is located on the same T-DNA as the 35S enhancer. It was concluded, the trans-acting effects of the enhancer activate and control transgene expression causing irregular expression patterns. This phenomenon seems the most plausible reason for the constitutive expression profiles observed with the root- and seed-specific promoters assessed in this study. The expression from some promoters can be influenced by their cognate terminator sequences. Therefore, the Arabidopsis ARSK1, EIR1, ATS1 and ATS3 terminator sequences were isolated and incorporated into expression cassettes containing the GUS reporter gene under the control of their cognate promoters. Again, unrestricted GUS activity was displayed throughout transgenic plants transformed with these reporter gene fusions. As previously discussed constitutive GUS expression was most likely due to the trans-acting effect of the upstream CaMV 35S promoter in the selection cassette located on the same T-DNA. The results obtained in this study make it impossible to assess the influence matching terminators with their cognate promoters have on transgene expression profiles. The obvious future direction of research continuing from this study would be to transform pBIN-based promoter-GUS fusions (ie. constructs containing no CaMV 35S promoter driving the plant selection gene) into Arabidopsis in order to determine the true tissue specificity of these promoters and evaluate the effects of their cognate 3’ terminator sequences. Further, promoter truncations based around the cis-elements identified here may assist in determining whether these motifs are in fact involved in the overall activity of the promoter.

Students’ conceptual knowledge about workplace pedagogies and applications to learning in the workplace

The development of effective workplace pedagogies is integral to work-integrated and work-based learning. The workplace pedagogies that facilitate and support learning include: activities in which individuals engage such as daily work practices, questioning; observing, and listening; interactions with more experienced workers through coaching and modelling; and referencing documented procedures. Each of these dimensions is significant in enhancing processes of workplace learning. Learning can be optimised when these pedagogies are appropriately embedded in the context of and process of participating in normal work activities. Yet learners need to understand the nature of these pedagogies, and how and for what purposes to use these to achieve a range of learning outcomes. This is because it is the worker-learners who play the key roles in the process and outcomes of learning through work. A pilot study was conducted on students’ conceptions of how each of these dimensions of workplace pedagogy help their learning, by providing examples of learning from these sources; and stating their preferences for learning in the workplace. A sample of seventeen students, enrolled in the second year of a Diploma in Nursing course at a Technical and Further Education institution, participated in a survey intended to capture these conceptions and the importance attached to each of them. The findings indicate that these students have basic understanding of how each of seven workplace pedagogic practices can contribute to their learning. They reported relying mostly on daily practices, observing and listening to others, modelling, coaching, and other workers. Their selection of these contributions emphasise significant opportunities for guided learning by others, yet suggest fewer student-initiated interactions, less intensity in interactions, and likelihood that learning is more passive. The data also suggests that these students rely mostly on using academic learning skill, and limited workplace learning skills. It is proposed, therefore, that the knowledge and understandings about workplace learning and pedagogies might be best embedded in the full curriculum and not become add-on shortly before students go on work placement. This approach will allow students to appreciate the significance and use of workplace pedagogies for learning.

‘Keep telling until someone listens’ : understanding prevention concepts in children’s picture books dealing with child sexual abuse

Children’s picture books dealing with the topic of child sexual abuse appeared in the 1980s with the aim of addressing the need for age-appropriate texts to teach sexual abuse prevention concepts and to provide support for young children who may be at risk of or have already experienced sexual abuse. Despite the apparent potential of children’s picture books to convey child sexual abuse prevention concepts, very few studies have addressed the topic of child sexual abuse in children’s literature. This article critically examines a selection of 15 picture books (published in the US, Canada and Australia) for children aged 3–8 years dealing with this theme. It makes use of an established set of evaluative criteria to conduct an audit of the books’ content and applies techniques of literary discourse analysis to explain how these picture books satisfy criteria for child sexual abuse prevention. The analysis is used as a way to understand the discourses available to readers, both adults and children, on the topic of child sexual abuse. Key themes in the books include children’s empowerment and agency, and the need for persistence and hope.

Data-driven background dataset selection for SVM-based speaker verification

The recently proposed data-driven background dataset refinement technique provides a means of selecting an informative background for support vector machine (SVM)-based speaker verification systems. This paper investigates the characteristics of the impostor examples in such highly-informative background datasets. Data-driven dataset refinement individually evaluates the suitability of candidate impostor examples for the SVM background prior to selecting the highest-ranking examples as a refined background dataset. Further, the characteristics of the refined dataset were analysed to investigate the desired traits of an informative SVM background. The most informative examples of the refined dataset were found to consist of large amounts of active speech and distinctive language characteristics. The data-driven refinement technique was shown to filter the set of candidate impostor examples to produce a more disperse representation of the impostor population in the SVM kernel space, thereby reducing the number of redundant and less-informative examples in the background dataset. Furthermore, data-driven refinement was shown to provide performance gains when applied to the difficult task of refining a small candidate dataset that was mis-matched to the evaluation conditions.

Exploiting multiple feature sets in data-driven impostor dataset selection for speaker verification

This study assesses the recently proposed data-driven background dataset refinement technique for speaker verification using alternate SVM feature sets to the GMM supervector features for which it was originally designed. The performance improvements brought about in each trialled SVM configuration demonstrate the versatility of background dataset refinement. This work also extends on the originally proposed technique to exploit support vector coefficients as an impostor suitability metric in the data-driven selection process. Using support vector coefficients improved the performance of the refined datasets in the evaluation of unseen data. Further, attempts are made to exploit the differences in impostor example suitability measures from varying features spaces to provide added robustness.

The home stigma : adverse selection in ADRs and the home capital market environment

We investigate whether characteristics of the home country capital environment, such as information disclosure and investor rights protection continue to affect ADRs cross-listed in the U.S. Using microstructure measures as proxies for adverse selection, we find that characteristics of the home markets continue to be relevant, especially for emerging market firms. Less transparent disclosure, poorer protection of investor rights and weaker legal institutions are associated with higher levels of information asymmetry. Developed market firms appear to be affected by whether or not home business laws are common law or civil law legal origin. Our finding contributes to the bonding literature. It suggests that cross-listing in the U.S. should not be viewed as a substitute for improvement in the quality of local institutions, and attention must be paid to improve investor protection in order to achieve the full benefits of improved disclosure. Improvement in the domestic capital market environment can attract more investors even for U.S. cross-listed firms.

Persistent navigation and mapping using a biologically inspired SLAM system

The challenge of persistent navigation and mapping is to develop an autonomous robot system that can simultaneously localize, map and navigate over the lifetime of the robot with little or no human intervention. Most solutions to the simultaneous localization and mapping (SLAM) problem aim to produce highly accurate maps of areas that are assumed to be static. In contrast, solutions for persistent navigation and mapping must produce reliable goal-directed navigation outcomes in an environment that is assumed to be in constant flux. We investigate the persistent navigation and mapping problem in the context of an autonomous robot that performs mock deliveries in a working office environment over a two-week period. The solution was based on the biologically inspired visual SLAM system, RatSLAM. RatSLAM performed SLAM continuously while interacting with global and local navigation systems, and a task selection module that selected between exploration, delivery, and recharging modes. The robot performed 1,143 delivery tasks to 11 different locations with only one delivery failure (from which it recovered), traveled a total distance of more than 40 km over 37 hours of active operation, and recharged autonomously a total of 23 times.

Selection and optimization of piezoelectric polyvinylidene fluoride polymers for adaptive optics in space environments

Various piezoelectric polymers based on polyvinylidene fluoride (PVDF) are of interest for large aperture space-based telescopes. Dimensional adjustments of adaptive polymer films depend on charge deposition and require a detailed understanding of the piezoelectric material responses which are expected to deteriorate owing to strong vacuum UV, � -, X-ray, energetic particles and atomic oxygen exposure. We have investigated the degradation of PVDF and its copolymers under various stress environments detrimental to reliable operation in space. Initial radiation aging studies have shown complex material changes with lowered Curie temperatures, complex material changes with lowered melting points, morphological transformations and significant crosslinking, but little influence on piezoelectric d33 constants. Complex aging processes have also been observed in accelerated temperature environments inducing annealing phenomena and cyclic stresses. The results suggest that poling and chain orientation are negatively affected by radiation and temperature exposure. A framework for dealing with these complex material qualification issues and overall system survivability predictions in low earth orbit conditions has been established. It allows for improved material selection, feedback for manufacturing and processing, material optimization/stabilization strategies and provides guidance on any alternative materials.

From the cathedral to the classroom : the emergence of new discourses on religious education

In 2009, Religious Education is a designated key learning area in Catholic schools in the Archdiocese of Brisbane and, indeed, across Australia. Over the years, though, different conceptualisations of the nature and purpose of religious education have led to the construction of different approaches to the classroom teaching of religion. By investigating the development of religious education policy in the Archdiocese of Brisbane from 1984 to 2003, the study seeks to trace the emergence of new discourses on religious education. The study understands religious education to refer to a lifelong process that occurs through a variety of forms (Moran, 1989). In Catholic schools, it refers both to co-curricula activities, such as retreats and school liturgies, and the classroom teaching of religion. It is the policy framework for the classroom teaching of religion that this study explores. The research was undertaken using a policy case study approach to gain a detailed understanding of how new conceptualisations of religious education emerged at a particular site of policy production, in this case, the Archdiocese of Brisbane. The study draws upon Yeatman’s (1998) description of policy as occurring “when social actors think about what they are doing and why in relation to different and alternative possible futures” (p. 19) and views policy as consisting of more than texts themselves. Policy texts result from struggles over meaning (Taylor, 2004) in which specific discourses are mobilised to support particular views. The study has a particular interest in the analysis of Brisbane religious education policy texts, the discursive practices that surrounded them, and the contexts in which they arose. Policy texts are conceptualised in the study as representing “temporary settlements” (Gale, 1999). Such settlements are asymmetrical, temporary and dependent on context: asymmetrical in that dominant actors are favoured; temporary because dominant actors are always under challenge by other actors in the policy arena; and context - dependent because new situations require new settlements. To investigate the official policy documents, the study used Critical Discourse Analysis (hereafter referred to as CDA) as a research tool that affords the opportunity for researchers to map and chart the emergence of new discourses within the policy arena. As developed by Fairclough (2001), CDA is a three-dimensional application of critical analysis to language. In the Brisbane religious education arena, policy texts formed a genre chain (Fairclough, 2004; Taylor, 2004) which was a focus of the study. There are two features of texts that form genre chains: texts are systematically linked to one another; and, systematic relations of recontextualisation exist between the texts. Fairclough’s (2005) concepts of “imaginary space” and “frameworks for action” (p. 65) within the policy arena were applied to the Brisbane policy arena to investigate the relationship between policy statements and subsequent guidelines documents. Five key findings emerged from the study. First, application of CDA to policy documents revealed that a fundamental reconceptualisation of the nature and purpose of classroom religious education in Catholic schools occurred in the Brisbane policy arena over the last twenty-five years. Second, a disjuncture existed between catechetical discourses that continued to shape religious education policy statements, and educational discourses that increasingly shaped guidelines documents. Third, recontextualisation between policy documents was evident and dependent on the particular context in which religious education occurred. Fourth, at subsequent links in the chain, actors created their own “imaginary space”, thereby altering orders of discourse within the policy arena, with different actors being either foregrounded or marginalised. Fifth, intertextuality was more evident in the later links in the genre chain (i.e. 1994 policy statement and 1997 guidelines document) than in earlier documents. On the basis of the findings of the study, six recommendations are made. First, the institutional Church should carefully consider the contribution that the Catholic school can make to the overall pastoral mission of the diocese in twenty-first century Australia. Second, policymakers should articulate a nuanced understanding of the relationship between catechesis and education with regard to the religion classroom. Third, there should be greater awareness of the connections among policies relating to Catholic schools – especially the connection between enrolment policy and religious education policy. Fourth, there should be greater consistency between policy documents. Fifth, policy documents should be helpful for those to whom they are directed (i.e. Catholic schools, teachers). Sixth, “imaginary space” (Fairclough, 2005) in policy documents needs to be constructed in a way that allows for multiple “frameworks for action” (Fairclough, 2005) through recontextualisation. The findings of this study are significant in a number of ways. For religious educators, the study highlights the need to develop a shared understanding of the nature and purpose of classroom religious education. It argues that this understanding must take into account the multifaith nature of Australian society and the changing social composition of Catholic schools themselves. Greater recognition should be given to the contribution that religious studies courses such as Study of Religion make to the overall religious development of a person. In view of the social composition of Catholic schools, there is also an issue of ecclesiological significance concerning the conceptualisation of the relationship between the institutional Catholic Church and Catholic schools. Finally, the study is of significance because of its application of CDA to religious education policy documents. Use of CDA reveals the foregrounding, marginalising, or excluding of various actors in the policy arena.

A hybrid genetic algorithm for the optimal constrained web service selection problem in web service composition

Web service composition is an important problem in web service based systems. It is about how to build a new value-added web service using existing web services. A web service may have many implementations, all of which have the same functionality, but may have different QoS values. Thus, a significant research problem in web service composition is how to select a web service implementation for each of the web services such that the composite web service gives the best overall performance. This is so-called optimal web service selection problem. There may be mutual constraints between some web service implementations. Sometimes when an implementation is selected for one web service, a particular implementation for another web service must be selected. This is so called dependency constraint. Sometimes when an implementation for one web service is selected, a set of implementations for another web service must be excluded in the web service composition. This is so called conflict constraint. Thus, the optimal web service selection is a typical constrained ombinatorial optimization problem from the computational point of view. This paper proposes a new hybrid genetic algorithm for the optimal web service selection problem. The hybrid genetic algorithm has been implemented and evaluated. The evaluation results have shown that the hybrid genetic algorithm outperforms other two existing genetic algorithms when the number of web services and the number of constraints are large.

Development of a process for dealing with underutilised Queensland government properties with heritage significance

This thesis addresses the contemporary issue of the control, restoration and potential for reuse of State Government-owned heritage properties with commercial potential. It attempts to reconcile the sometimes competing interests of the range of stakeholders in such properties, particularly those seeking to maximise economic performance and return on one hand and community expectations for heritage preservation and exhibition on the other. The matters are approached principally from the Government's position as asset owner/manager. It includes research into a number of key elements - including statutory, physical and economic parameters and an analysis of the legitimate requirements of all stakeholders. The thesis also recognises the need for innovation in approach and for the careful structuring and pre-planning of proposals on a project-by-project basis. On the matter of innovation, four case studies are included in the thesis to exhibit some approaches and techniques that have already been employed in addressing these issues. From this research base, a series of deductions at both a macro and micro level are established and a model for a rational decision-making process for dealing with such projects is developed as a major outcome of the work. Finally, the general model is applied to a specific project, the currently unused Port Office heritage site in the Brisbane Central Business District.