A generative design system based on evolutionary and mathematical functions

Previous work by Professor John Frazer on Evolutionary Architecture provides a basis for the development of a system evolving architectural envelopes in a generic and abstract manner. Recent research by the authors has focused on the implementation of a virtual environment for the automatic generation and exploration of complex forms and architectural envelopes based on solid modelling techniques and the integration of evolutionary algorithms, enhanced computational and mathematical models. Abstract data types are introduced for genotypes in a genetic algorithm order to develop complex models using generative and evolutionary computing techniques. Multi-objective optimisation techniques are employed for defining the fitness function in the evaluation process.

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.

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.

Sustainable Australia : containing travel in master planned estates

Low density suburban development and excessive use of automobiles are associated with serious urban and environmental problems. These problems include traffic congestion, longer commuting times, high automobile dependency, air and water pollution, and increased depletion of natural resources. Master planned development suggests itself as a possible palliative for the ills of low density and high travel. The following study examines the patterns and dynamics of movement in a selection of master planned estates in Australia. The study develops new approaches for assessing the containment of travel within planned development. Its key aim is to clarify and map the relationships between trip generation and urban form and structure. The initial conceptual framework of the paper is developed in a review of literature related to urban form and travel behaviour. These concepts are tested empirically in a pilot study of suburban travel activity in master planned estates. A geographical information systems methodology is used to determine regional journey-to-work patterns and travel containment rates. Factors that influence selfcontainment patterns are estimated with a regression model. This research is a useful preliminary examination of travel self-containment in Australian master planned estates.

Research Monograph: Building Online Participatory Systems: Towards the Community Based Interactive Environmental Decision Support Systems

The importance of broadening community participation in environmental decision-making is widely recognized and lack of participation in this process appears to be a perennial problem. In this context, there have been calls from some academics for the more extensive use of geographic information systems (GIS) and distance learning technologies, accessible via the Internet, as a possible means to inform and empower communities. However, a number of problems exist. For instance, at present the scope for online interaction between policy-makers and citizens is currently limited. Contemporary web-based environmental information systems suffer from this lack of interactivity on the one hand and on the other hand from the apparent complexity for the lay user. This paper explores the issue of online community participation at the local level and attempts to construct a framework for a new (and potentially more effective) model of online participatory decision-making. The key components, system architecture and stages of such a model are introduced. This model, referred to as a ‘Community Based Interactive Environmental Decision Support System’, incorporates advanced information technologies, distance learning and community involvement tools which will be applied and evaluated in the field through a pilot project in Tokyo in the summer of 2002.

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.

Implication of 3D culture system for study of prostate cancer (CaP) mediated bone metastasis

Introduction : For the past decade, three dimensional (3D) culture has served as a foundation for regenerative medicine study. With an increasing awareness of the importance of cell-cell and cell-extracellular matrix interactions which are lacking in 2D culture system, 3D culture system has been employed for many other applications namely cancer research. Through development of various biomaterials and utilization of tissue engineering technology, many in vivo physiological responses are now better understood. The cellular and molecular communication of cancer cells and their microenvironment, for instance can be studied in vitro in 3D culture system without relying on animal models alone. Predilection of prostate cancer (CaP) to bone remains obscure due to the complexity of the mechanisms and lack of proper model for the studies. In this study, we aim to investigate the interaction between CaP cells and osteoblasts simulating the natural bone metastasis. We also further investigate the invasiveness of CaP cells and response of androgen sensitve CaP cells, LNCaP to synthetic androgen.----- Method : Human osteoblast (hOB) scaffolds were prepared by seeding hOB on medical grade polycaprolactone-tricalcium phosphate (mPLC-TCP) scaffolds and induced to produce bone matrix. CaP cell lines namely wild type PC3 (PC3-N), overexpressed prostate specific antigen PC3 (PC3k3s5) and LNCaP were seeded on hOB scaffolds as co-cultures. Morphology of cells was examined by Phalloidin-DAPI and SEM imaging. Gelatin zymography was performed on the 48 hours conditioned media (CM) from co-cultures to determine matrix metalloproteinase (MMP) activity. Gene expression of hOB/LNCaP co-cultures which were treated for 48 hours with 1nM synthetic androgen R1881 were analysed by quantitative real time PCR (qRT-PCR).----- Results : Co-culture of PCC/hOB revealed that the morphology of PCCs on the tissue engineered bone matrix varied from homogenous to heterogenous clusters. Enzymatically inactive pro-MMP2 was detected in CM from hOBs and PCCs cultured on scaffolds. Elevation in MMP9 activity was found only in hOB/PC3N co-culture. hOB/LNCaP co-culture showed increase in expression of key enzymes associated with steroid production which also corresponded to an increase in prostate specific antigen (PSA) and MMP9.----- Conclusions : Upregulation of MMP9 indicates involvement of ECM degradation during cancer invasion and bone metastases. Expression of enzymes involved in CaP progression, PSA, which is not expressed in osteoblasts, demonstrates that crosstalk between PCCs and osteoblasts may play a part in the aggressiveness of CaP. The presence of steroidogenic enzymes, particularly, RDH5, in osteoblasts and stimulated expression in co-culture, may indicate osteoblast production of potent androgens, fuelling cancer cell proliferation. Based on these results, this practical 3D culture system may provide greater understanding into CaP mediated bone metastasis. This allows the role of the CaP/hOB interaction with regards to invasive property and steroidogenesis to be further explored.

Fear, trust and Aborigines : The historical experience of state institutions and current encounters in the health system

Troubled dynamics between residents of an Aboriginal town in Queensland and the local health system were established during colonisation and consolidated during those periods of Australian history where the policies of 'protection' (segregation), integration and then assimilation held sway. The status of Aboriginal health is, in part, related to interactions between the residents' current and historical experiences of the health and criminal justice systems as together these agencies used medical and moral policing to legitimate dispossession, marginalisation, institutionalisation and control of the residents. The punitive regulations and ethnocentric strategies used by these institutions are within the living memory of many of the residents or in the published accounts of preceding generations. This paper explores current residents' memories and experiences.