Development of a Rep-inducible, BBTV-based expression system in banana

Banana bunchy top is regarded as the most important viral disease of banana, causing significant yield losses worldwide. The disease is caused by Banana bunchy top virus (BBTV), which is a circular ssDNA virus belonging to the genus Babuvirus in the family Nanoviridae. There are currently few effective control strategies for this and other ssDNA viruses. “In Plant Activation” (InPAct) is a novel technology being developed at QUT for ssDNA virus-activated suicide gene expression. The technology exploits the rolling circle replication mechanism of ssDNA viruses and is based on a unique “split” gene design such that suicide gene expression is only activated in the presence of the viral Rep. This PhD project aimed to develop a BBTV-based InPAct system as a suicide gene strategy to control BBTV. The BBTV-based InPAct vector design requires a BBTV intergenic region (IR) to be embedded within an intron in the gene expression cassette. To ensure that the BBTV IR would not interfere with intron splicing, a TEST vector was initially generated that contained the entire BBTV IR embedded within an intron in a β-glucuronidase (GUS) expression vector. Transient GUS assays in banana embryogenic cell suspensions indicated that cryptic intron splice sites were present within the IR. Transcript analysis revealed two cryptic intron splice sites in the Domain III sequence of the CR-M within the IR. Removal of the CR-M from the TEST vector resulted in an enhancement of GUS expression suggesting that the cryptic intron splice sites had been removed. An InPAct GUS vector was subsequently generated that contained the modified BBTV IR, with the CR-M (minus Domain III) repositioned within the InPAct cassette. Using transient histochemical and fluorometric GUS assays in banana embryogenic cells, the InPAct GUS vector was shown to be activated in the presence of the BBTV Rep. However, the presence of both BBTV Rep and Clink was shown to have a deleterious effect on GUS expression suggesting that these proteins were cytotoxic at the levels expressed. Analysis of replication of the InPAct vectors by Southern hybridisation revealed low levels of InPAct cassette-based episomal DNA released from the vector through the nicking/ligation activity of BBTV Rep. However, Rep-mediated episomal replicons, indicative of rolling circle replication of the released circularised cassettes, were not observed. The inability of the InPAct cassette to be replicated was further investigated. To examine whether the absence of Domain III of the CR-M was responsible, a suite of modified BBTV-based InPAct GUS vectors was constructed that contained the CR-M with the inclusion of Domain III, the CR-M with the inclusion of Domain III and additional upstream IR sequence, or no CR-M. Analysis of replication by Southern hybridisation revealed that neither the presence of Domain III, nor the entire CR-M, had an effect on replication levels. Since the InPAct cassette was significantly larger than the native BBTV genomic components (approximately 1 kb), the effect of InPAct cassette size on replication was also investigated. A suite of size variant BBTV-based vectors was constructed that increased the size of a replication competent cassette to 1.1 kbp through to 2.1 kbp.. Analysis of replication by Southern hybridisation revealed that an increase in vector size above approximately 1.5 - 1.7 kbp resulted in a decrease in replication. Following the demonstration of Rep-mediated release, circularisation and expression from the InPAct GUS vector, an InPAct vector was generated in which the uidA reporter gene was replaced with the ribonuclease-encoding suicide gene, barnase. Initially, a TEST vector was generated to assess the cytotoxicity of Barnase on banana cells. Although transient assays revealed a Barnase-induced cytotoxic effect in banana cells, the expression levels were sub-optimal. An InPAct BARNASE vector was generated and tested for BBTV Rep-activated Barnase expression using transient assays in banana embryogenic cells. High levels of background expression from the InPAct BARNASE vector made it difficult to accurately assess Rep-activated Barnase expression. Analysis of replication by Southern hybridisation revealed low levels of InPAct cassette-based episomal DNA released from the vector but no Rep-mediated episomal replicons indicative of rolling circle replication of the released circularised cassettes were again observed. Despite the inability of the InPAct vectors to replicate to enable high level gene expression, the InPAct BARNASE vector was assessed in planta for BBTV Rep-mediated activation of Barnase expression. Eleven lines of transgenic InPAct BARNASE banana plants were generated by Agrobacterium-mediated transformation and were challenged with viruliferous Pentalonia nigronervosa. At least one clonal plant in each line developed bunchy top symptoms and infection was confirmed by PCR. No localised lesions were observed on any plants, nor was there any localised GUS expression in the one InPAct GUS line challenged with viruliferous aphids. The results presented in this thesis are the first study towards the development of a BBTV-based InPAct system as a Rep-activatable suicide gene expression system to control BBTV. Although further optimisation of the vectors is necessary, the preliminary results suggest that this approach has the potential to be an effective control strategy for BBTV. The use of iterons within the InPAct vectors that are recognised by Reps from different ssDNA plant viruses may provide a broad-spectrum resistance strategy against multiple ssDNA plant viruses. Further, this technology holds great promise as a platform technology for the molecular farming of high-value proteins in vitro or in vivo through expression of the ssDNA virus Rep protein.

Work integrated learning for design : a scholarship of integration

Within an action research framework, this paper describes the conceptual basis for developing a crossdisciplinary pedagogical model of higher education/industry engagement for the built environment design disciplines including architecture, interior design, industrial design and landscape architecture. Aiming to holistically acknowledge and capitalize on the work environment as a place of authentic learning, problems arising in practice are understood as the impetus, focus and ‘space’ for a process of inquiry and discovery that, in the spirit of Boyer’s ‘Scholarship of Integration’, provides for generic as well as discipline-specific learning.

Professional development for the integration of biotechnology education

Views on the nature and relevance of science education have changed significantly over recent decades. This has serious implications for the way in which science is taught in secondary schools, particularly with respect to teaching emerging topics such as biotechnology, which have a socio-scientific dimension and also require novel laboratory skills. It is apparent in current literature that there is a lack of adequate teacher professional development opportunities in biotechnology education and that a significant need exists for researchers to develop a carefully crafted and well supported professional development design which will positively impact on the way in which teachers engage with contemporary science. This study used a retrospective case study methodology to document the recent evolution of modern biotechnology education as part of the changing nature of science education; examine the adoption and implementation processes for biotechnology education by three secondary schools; and to propose an evidence based biotechnology professional development model for science educators. Data were gathered from documents, one-on-one interviews and focus group discussions. Analysis of these data has led to the proposal of a biotechnology professional development model which considers all of the key components of science professional development that are outlined in the literature, as well as the additional components which were articulated by the educators studied. This research is timely and pertinent to the needs of contemporary science education because of its recognition of the need for a professional development model in biotechnology education that recognizes and addresses the content knowledge, practical skills, pedagogical knowledge and curriculum management components.

Designing usable ubiquitous computing

This paper demonstrates that in order to design successful ubiquitous computing, designers must consider concurrently both the end user interactions in the context of use and the sustainability of the technology and its underlying infrastructure. We describe methods used to create more useful collaboration and communication between users, designers and engineers in designing ubiquitous computing systems. We tested these methods in a real domain in an attempt to create a system that is affordable, minimally disrupts the end-user's workplace and improves human-computer interaction.

Public-oriented interactive environmental decision support system

With the application of GIS methodologies to spatial data, researchers can now identify patterns of occurrence for many social problems including health-issues and crime. Further more, since this type of data also contains clues as to the underlying causes of social problems, it can be used to make well-educated and consequently, more effective policy decisions.

Moderation as judgement practice: Reconciling system level accountability and local level practice

Internationally, recognition of the role of assessment to inform the learning process has received much attention in recent years. Assessment for learning, not just of learning is being supported by an increasing body of literature providing strategies that teachers and their students can incorporate to support the learning process (Assessment Reform Group, 2002; Broadfoot & Black, 2004; James, 2006). Concurrently there has been an increase internationally in systemic accountability requirements of schools in terms of student results. The convergence of these two movements has resulted in some education systems promoting standards-driven reform involving authentic assessment and a re-examination of the relationship between the teacher and the student in the learning process. In this context standards are intended to be used as the basis for judgements of student achievement; while the results from assessment tasks are meant to both inform the teaching/learning process, and to report and track student progress. In such system, the role and reliability of teacher judgement takes centre stage.

Urban management revolution : intelligent management systems for ubiquitous cities

A successful urban management support system requires an integrated approach. This integration includes bringing together economic, socio-cultural and urban development with a well orchestrated transparent and open decision making mechanism. The paper emphasises the importance of integrated urban management to better tackle the climate change, and to achieve sustainable urban development and sound urban growth management. This paper introduces recent approaches on urban management systems, such as intelligent urban management systems, that are suitable for ubiquitous cities. The paper discusses the essential role of online collaborative decision making in urban and infrastructure planning, development and management, and advocates transparent, fully democratic and participatory mechanisms for an effective urban management system that is particularly suitable for ubiquitous cities. This paper also sheds light on some of the unclear processes of urban management of ubiquitous cities and online collaborative decision making, and reveals the key benefits of integrated and participatory mechanisms in successfully constructing sustainable ubiquitous cities.

An online urban information system initiative for the Shibuya city, Tokyo

The computing tools and technologies with urban information systems are designed to enhance planners’ capability to deal with complex urban environments and to plan for prosperous and liveable communities. This paper examines the role of Online Urban Information Systems or in another words Internet based Geographic Information Systems as spatial decision support systems to aid local planning process. This paper introduces a prototype Internet GIS model that aims to integrate a public oriented interactive decision support system for urban planning process. This model, referred as a ‘Community based Internet GIS’, incorporates advanced information technologies and community involvement in decision making processes on the web environment. This innovative model has been recently applied to a pilot case in Tokyo and this paper concludes with the preliminary results of this project.

A framework for analyzing system intelligence of the building control system : a study of the integrated building management system

The lack of satisfactory consensus for characterizing the system intelligence and structured analytical decision models has inhibited the developers and practitioners to understand and configure optimum intelligent building systems in a fully informed manner. So far, little research has been conducted in this aspect. This research is designed to identify the key intelligent indicators, and develop analytical models for computing the system intelligence score of smart building system in the intelligent building. The integrated building management system (IBMS) was used as an illustrative example to present a framework. The models presented in this study applied the system intelligence theory, and the conceptual analytical framework. A total of 16 key intelligent indicators were first identified from a general survey. Then, two multi-criteria decision making (MCDM) approaches, the analytic hierarchy process (AHP) and analytic network process (ANP), were employed to develop the system intelligence analytical models. Top intelligence indicators of IBMS include: self-diagnostic of operation deviations; adaptive limiting control algorithm; and, year-round time schedule performance. The developed conceptual framework was then transformed to the practical model. The effectiveness of the practical model was evaluated by means of expert validation. The main contribution of this research is to promote understanding of the intelligent indicators, and to set the foundation for a systemic framework that provide developers and building stakeholders a consolidated inclusive tool for the system intelligence evaluation of the proposed components design configurations.