Re-visioning a "novel concept" : beyond vision and revision to advanced editing strategies

This thesis is a work of creative practice-led research comprising two components. The first component is a speculative thriller novel, entitled Diamond Eyes. (Contracted for publication in 2009 by Harper Collins: Voyager as the first in a trilogy, under the name AA Bell.) The second component is an exegesis exploring the notion of re-visioning a novel. Re-visioning, not to be confused with revision, refers to advance editing strategies required when the original vision of a novel changes during development.

The development of a serological-based diagnostic test for Dasheen mosaic potyvirus (DsMV)

Dasheen mosaic potyvirus (DsMV) is an important virus affecting taro. The virus has been found wherever taro is grown and infects both the edible and ornamental aroids, causing yield losses of up to 60%. The presence of DsMV, and other viruses,prevents the international movement of taro germplasm between countries. This has a significant negative impact on taro production in many countries due to the inability to access improved taro lines produced in breeding programs. To overcome this problem, sensitive and reliable virus diagnostic tests need to be developed to enable the indexing of taro germplasm. The aim of this study was to generate an antiserum against a recombinant DsMV coat protein (CP) and to develop a serological-based diagnostic test that would detect Pacific Island isolates of the virus. The CP-coding region of 16 DsMV isolates from Papua New Guinea, Samoa, Solomon Islands, French Polynesia, New Caledonia and Vietnam were amplified,cloned and sequenced. The size of the CP-coding region ranged from 939 to 1038 nucleotides and encoded putative proteins ranged from 313 to 346 amino acids, with the molecular mass ranging from 34 to 38 kDa. Analysis ofthe amino acid sequences revealed the presence of several amino acid motifs typically found in potyviruses,including DAG, WCIE/DN, RQ and AFDF. When the amino acid sequences were compared with each other and the DsMV sequences on the database, the maximum variability was21.9%. When the core region ofthe CP was analysed, the maximum variability dropped to 6% indicating most variability was present in the N terminus. Within seven PNG isolates ofDsMV, the maximum variability was 16.9% and 3.9% over the entire CP-coding region and core region, respectively. The sequence ofPNG isolate P1 was most similar to all other sequences. Phylogenetic analysis indicated that almost all isolates grouped according to their provenance. Further, the seven PNG isolates were grouped according to the region within PNG from which they were obtained. Due to the extensive variability over the entire CP-coding region, the core region ofthe CP ofPNG isolate Pl was cloned into a protein expression vector and expressed as a recombinant protein. The protein was purified by chromatography and SDS-PAGE and used as an antigen to generate antiserum in a rabbit. In western blots, the antiserum reacted with bands of approximately 45-47 kDa in extracts from purified DsMV and from known DsMV -infected plants from PNG; no bands were observed using healthy plant extracts. The antiserum was subsequently incorporated into an indirect ELISA. This procedure was found to be very sensitive and detected DsMV in sap diluted at least 1:1,000. Using both western blot and ELISA formats,the antiserum was able to detect a wide range ofDsMV isolates including those from Australia, New Zealand, Fiji, French Polynesia, New Caledonia, Papua New Guinea, Samoa, Solomon Islands and Vanuatu. These plants were verified to be infected with DsMV by RT-PCR. In specificity tests, the antiserum was also found to react with sap from plants infected with SCMV, PRSV-P, PRSV-W, but not with PVY or CMV -infected plants.

Receptor-DNA interactions: EMSA and footprinting

Defining the precise promoter DNA sequence motifs where nuclear receptors and other transcription factors bind is an essential prerequisite for understanding how these proteins modulate the expression of their specific target genes. The purpose of this chapter is to provide the reader with a detailed guide with respect to the materials and the key methods required to perform this type of DNA-binding analysis. Irrespective of whether starting with purified DNA-binding proteins or somewhat crude cellular extracts, the tried-and-true procedures described here will enable one to accurately access the capacity of specific proteins to bind to DNA as well as to determine the exact sequences and DNA contact nucleotides involved. For illustrative purposes, we primarily have used the interaction of the androgen receptor with the rat probasin proximal promoter as our model system.

Bioengineered 3D platform to explore cell-ECM interactions and drug resistance of epithelial ovarian cancer cells

The behaviour of cells cultured within three-dimensional (3D) structures rather than onto two-dimensional (2D) culture plastic more closely reflects their in vivo responses. Consequently, 3D culture systems are becoming crucial scientific tools in cancer cell research. We used a novel 3D culture concept to assess cell-matrix interactions implicated in carcinogenesis: a synthetic hydrogel matrix equipped with key biomimetic features, namely incorporated cell integrin-binding motifs (e.g. RGD peptides) and the ability of being degraded by cell-secreted proteases (e.g. matrix metalloproteases). As a cell model, we chose epithelial ovarian cancer, an aggressive disease typically diagnosed at an advanced stage when chemoresistance occurs. Both cell lines used (OV-MZ-6, SKOV-3) proliferated similarly in 2D, but not in 3D. Spheroid formation was observed exclusively in 3D when cells were embedded within hydrogels. By exploiting the design flexibility of the hydrogel characteristics, we showed that proliferation in 3D was dependent on cell-integrin engagement and the ability of cells to proteolytically remodel their extracellular microenvironment. Higher survival rates after exposure to the anti-cancer drug paclitaxel were observed in cell spheroids grown in hydrogels (40-60%) compared to cell monolayers in 2D (20%). Thus, 2D evaluation of chemosensitivity may not reflect pathophysiological events seen in patients. Because of the design flexibility of their characteristics and their stability in long-term cultures (28 days), these biomimetic hydrogels represent alternative culture systems for the increasing demand in cancer research for more versatile, physiologically relevant and reproducible 3D matrices.

Transitions

Transitions represents a selection of works presented by 3rd year QUT design students undertaken as part of their coursework entitled "Environments in Transitions". The work focuses upon the migration of ideas and aesthetics from East to West, with particular consideration for the influence of Japanese woodblock prints, Wabi-Sabi themes and decorative motifs upon European design during the turn of the 19th century. The works exhibited included design artifacts of various themes, and associated print work which informed the design process. A small exhibition publication accompanied the exhibition and talk.

Three-dimensional hydrogen-bonded structures in the guanidinium salts of the monocyclic dicarboxylic acids rac-trans-cyclohexane-1,2-dicarboxylic acid (2:1, anhydrous), isophthalic acid (1:1, monohydrate) and terephthalic acid (2:1, trihydrate).

The structures of bis(guanidinium)rac-trans-cyclohexane-1,2-dicarboxylate, 2(CH6N3+) C8H10O4- (I), guanidinium 3-carboxybenzoate monohydrate CH6N3+ C8H5O4- . H2O (II) and bis(guanidinium) benzene-1,4-dicarboxylate trihydrate, 2(CH6N3+) C8H4O4^2- . 3H2O (III) have been determined and the hydrogen bonding in each examined. All three compounds form three-dimensional hydrogen-bonded framework structures. In anhydrous (I), both guanidinium cations give classic cyclic R2/2(8) N--H...O,O'(carboxyl) and asymmetric cyclic R1/2(6) hydrogen-bonding interactions while one cation gives an unusual enlarged cyclic interaction with O acceptors of separate ortho-related carboxyl groups [graph set R2/2(11)]. Cations and anions also associate across inversion centres giving cyclic R2/4(8) motifs. In the 1:1 guanidinium salt (II), the cation gives two separate cyclic R1/2(6) interactions, one with a carboxyl O-acceptor, the other with the water molecule of solvation. The structure is unusual in that both carboxyl groups give short inter-anion O...H...O contacts, one across a crystallographic inversion centre [2.483(2)\%A], the other about a two-fold axis of rotation [2.462(2)\%A] with a half-occupancy hydrogen delocalized on the symmetry element in each. The water molecule links the cation--anion ribbon structures into a three-dimensional framework. In (III), the repeating molecular unit comprises a benzene-1,4-dicarboxylate dianion which lies across a crystallographic inversion centre, two guanidinium cations and two water molecules of solvation (each set related by two-fold rotational symmetry), and a single water molecule which lies on a two-fold axis. Each guanidinium cation gives three types of cyclic interactions with the dianions: one R^1^~2~(6), the others R2/3(8) and R3/3(10) (both of these involving the water molecules), giving a three-dimensional structure through bridges down the b cell direction. The water molecule at the general site also forms an unusual cyclic R2/2(4) homodimeric association across an inversion centre [O--H...O, 2.875(2)\%A]. The work described here provides further examples of the common cyclic guanidinium cation...carboxylate anion hydrogen-bonding associations as well as featuring other less common cyclic motifs.

4-Carbamoylpiperidinium phenylacetate hemihydrate

In the structure of the title compound, C6H13N2O+ C8H7O2- . 0.5H2O, the asymmetric unit comprises two isonipecotamide cations, two phenylacetate anions and a water molecule of solvation. The hydrogen-bonding environments for both sets of ion pairs are essentially identical with the piperidinium and amide 'ends' of each cation involved in lateral heteromolecular hydrogen-bonded cyclic N---H...O associations [graph set R2/2(11)] which incorporate a single carboxyl O-atom acceptor. These cyclic motifs enclose larger R5/5(21) cyclic systems forming sheet substructures which lie parallel to (101) and are linked across b by the single water molecule via water O---H...O(carboxyl) associations to give a two-dimensional duplex-sheet structure

Optimization problems for controlled mechanical systems : bridging the gap between theory and application

Mechanical control systems have become a part of our everyday life. Systems such as automobiles, robot manipulators, mobile robots, satellites, buildings with active vibration controllers and air conditioning systems, make life easier and safer, as well as help us explore the world we live in and exploit it’s available resources. In this chapter, we examine a specific example of a mechanical control system; the Autonomous Underwater Vehicle (AUV). Our contribution to the advancement of AUV research is in the area of guidance and control. We present innovative techniques to design and implement control strategies that consider the optimization of time and/or energy consumption. Recent advances in robotics, control theory, portable energy sources and automation increase our ability to create more intelligent robots, and allows us to conduct more explorations by use of autonomous vehicles. This facilitates access to higher risk areas, longer time underwater, and more efficient exploration as compared to human occupied vehicles. The use of underwater vehicles is expanding in every area of ocean science. Such vehicles are used by oceanographers, archaeologists, geologists, ocean engineers, and many others. These vehicles are designed to be agile, versatile and robust, and thus, their usage has gone from novelty to necessity for any ocean expedition.

A geometric approach to trajectory design for an autonomous underwater vehicle : surveying the bulbous bow of a ship

In this paper, we present a control strategy design technique for an autonomous underwater vehicle based on solutions to the motion planning problem derived from differential geometric methods. The motion planning problem is motivated by the practical application of surveying the hull of a ship for implications of harbor and port security. In recent years, engineers and researchers have been collaborating on automating ship hull inspections by employing autonomous vehicles. Despite the progresses made, human intervention is still necessary at this stage. To increase the functionality of these autonomous systems, we focus on developing model-based control strategies for the survey missions around challenging regions, such as the bulbous bow region of a ship. Recent advances in differential geometry have given rise to the field of geometric control theory. This has proven to be an effective framework for control strategy design for mechanical systems, and has recently been extended to applications for underwater vehicles. Advantages of geometric control theory include the exploitation of symmetries and nonlinearities inherent to the system. Here, we examine the posed inspection problem from a path planning viewpoint, applying recently developed techniques from the field of differential geometric control theory to design the control strategies that steer the vehicle along the prescribed path. Three potential scenarios for surveying a ship?s bulbous bow region are motivated for path planning applications. For each scenario, we compute the control strategy and implement it onto a test-bed vehicle. Experimental results are analyzed and compared with theoretical predictions.

A geometrical analysis of trajectory design for underwater vehicles

Designing trajectories for a submerged rigid body motivates this paper. Two approaches are addressed: the time optimal approach and the motion planning ap- proach using concatenation of kinematic motions. We focus on the structure of singular extremals and their relation to the existence of rank-one kinematic reduc- tions; thereby linking the optimization problem to the inherent geometric frame- work. Using these kinematic reductions, we provide a solution to the motion plan- ning problem in the under-actuated scenario, or equivalently, in the case of actuator failures. We finish the paper comparing a time optimal trajectory to one formed by concatenation of pure motions.

Robust tracking control of autonomous underwater vehicles in the presence of disturbance inputs

An autonomous underwater vehicle (AUV) is expected to operate in an ocean in the presence of poorly known disturbance forces and moments. The uncertainties of the environment makes it difficult to apply open-loop control scheme for the motion planning of the vehicle. The objective of this paper is to develop a robust feedback trajectory tracking control scheme for an AUV that can track a prescribed trajectory amidst such disturbances. We solve a general problem of feedback trajectory tracking of an AUV in SE(3). The feedback control scheme is derived using Lyapunov-type analysis. The results obtained from numerical simulations confirm the asymptotic tracking properties of the feedback control law. We apply the feedback control scheme to different mission scenarios, with the disturbances being initial errors in the state of the AUV.

A geometrical approach to the motion planning problem for a submerged rigid body

The main focus of this paper is the motion planning problem for a deeply submerged rigid body. The equations of motion are formulated and presented by use of the framework of differential geometry and these equations incorporate external dissipative and restoring forces. We consider a kinematic reduction of the affine connection control system for the rigid body submerged in an ideal fluid, and present an extension of this reduction to the forced affine connection control system for the rigid body submerged in a viscous fluid. The motion planning strategy is based on kinematic motions; the integral curves of rank one kinematic reductions. This method is of particular interest to autonomous underwater vehicles which can not directly control all six degrees of freedom (such as torpedo shaped AUVs) or in case of actuator failure (i.e., under-actuated scenario). A practical example is included to illustrate our technique.

Guidance and control for underactuated autonomous underwater vehicles

The main focus of this paper is on the motion planning problem for an under-actuated, submerged, Omni-directional autonomous vehicle. Underactuation is extremely important to consider in ocean research and exploration. Battery failure, actuator malfunction and electronic shorts are a few reasons that may cause the vehicle to lose direct control of one or more degrees-of-freedom. Underactuation is also critical to understand when designing vehicles for specific tasks, such as torpedo-shaped vehicles. An under-actuated vehicle is less controllable, and hence, the motion planning problem is more difficult. Here, we present techniques based on geometric control to provide solutions to the under-actuated motion planning problem for a submerged underwater vehicle. Our results are validated with experiments.