Binding mechanism of affinity ligands for purification of plasmid DNA

Plasmid DNA for therapeutic and vaccination purposes must be highly purified. The high selectivity of affinity chromatography makes it ideal for the isolation of pDNA from complex biological feed stocks. Affinity chromatography makes use of the biological function and/or individual chemical structure of the interacting molecules. However, the success of any affinity purification protocol is dependent on the availability of suitable ligands. In this study, surface plasmon resonance (SPR) based Biacore system has been employed for the detection and quantification of the binding between lac operon (lacO) sequence contained in a pDNA and synthetic peptides based on the DNA-binding domain of the lac repressor protein, lad. The equilibrium dissociation constant (K D) and association and dissociation rate constants (ka, kd) for the interaction between plasmid DNA and designed peptides were determined.

EPC: a provably secure permutation based compression function

The security of permutation-based hash functions in the ideal permutation model has been studied when the input-length of compression function is larger than the input-length of the permutation function. In this paper, we consider permutation based compression functions that have input lengths shorter than that of the permutation. Under this assumption, we propose a permutation based compression function and prove its security with respect to collision and (second) preimage attacks in the ideal permutation model. The proposed compression function can be seen as a generalization of the compression function of MD6 hash function.

On the Collision and Preimage Resistance of Certain Two-Call Hash Functions

In this paper we present concrete collision and preimage attacks on a large class of compression function constructions making two calls to the underlying ideal primitives. The complexity of the collision attack is above the theoretical lower bound for constructions of this type, but below the birthday complexity; the complexity of the preimage attack, however, is equal to the theoretical lower bound. We also present undesirable properties of some of Stam’s compression functions proposed at CRYPTO ’08. We show that when one of the n-bit to n-bit components of the proposed 2n-bit to n-bit compression function is replaced by a fixed-key cipher in the Davies-Meyer mode, the complexity of finding a preimage would be 2 n/3. We also show that the complexity of finding a collision in a variant of the 3n-bits to 2n-bits scheme with its output truncated to 3n/2 bits is 2 n/2. The complexity of our preimage attack on this hash function is about 2 n . Finally, we present a collision attack on a variant of the proposed m + s-bit to s-bit scheme, truncated to s − 1 bits, with a complexity of O(1). However, none of our results compromise Stam’s security claims.

Grøstl – a SHA-3 candidate

Grøstl is a SHA-3 candidate proposal. Grøstl is an iterated hash function with a compression function built from two fixed, large, distinct permutations. The design of Grøstl is transparent and based on principles very different from those used in the SHA-family. The two permutations are constructed using the wide trail design strategy, which makes it possible to give strong statements about the resistance of Grøstl against large classes of cryptanalytic attacks. Moreover, if these permutations are assumed to be ideal, there is a proof for the security of the hash function. Grøstl is a byte-oriented SP-network which borrows components from the AES. The S-box used is identical to the one used in the block cipher AES and the diffusion layers are constructed in a similar manner to those of the AES. As a consequence there is a very strong confusion and diffusion in Grøstl. Grøstl is a so-called wide-pipe construction where the size of the internal state is significantly larger than the size of the output. This has the effect that all known, generic attacks on the hash function are made much more difficult. Grøstl has good performance on a wide range of platforms and counter-measures against side-channel attacks are well-understood from similar work on the AES.

Grøstl - a SHA-3 candidate

Grøstl is a SHA-3 candidate proposal. Grøstl is an iterated hash function with a compression function built from two �fixed, large, distinct permutations. The design of Grøstl is transparent and based on principles very different from those used in the SHA-family. The two permutations are constructed using the wide trail design strategy, which makes it possible to give strong statements about the resistance of Grøstl against large classes of cryptanalytic attacks. Moreover, if these permutations are assumed to be ideal, there is a proof for the security of the hash function. Grøstl is a byte-oriented SP-network which borrows components from the AES. The S-box used is identical to the one used in the block cipher AES and the diffusion layers are constructed in a similar manner to those of the AES. As a consequence there is a very strong confusion and diffusion in Grøstl

Stability analysis and implementation of Power-Hardware-in-the-Loop for power system testing

This project develops the required guidelines to assure stable and accurate operation of Power-Hardware-in-the-Loop implementations. The proposals of this research have been theoretically analyzed and practically examined using a Real-Time Digital Simulator. In this research, the interaction between software simulated power network and the physical power system has been studied. The conditions for different operating regimes have been derived and the corresponding analyses have been presented.

Modelling busway operation with mixed stopping and non-stopping buses

This thesis investigated the complexity of busway operation with stopping and non-stopping buses using field data and microscopic simulation modelling. The proposed approach made significant recommendations to transit authorities to achieve the most practicable system capacity for existing and new busways. The empirical equations developed in this research and newly introduced analysis methods will be ideal tools for transit planners to achieve optimal reliability of busways.

Injecting Creative Commons Licensing into university policy and publishing

Australian universities are publishing previously unpublished works such as theses in institutional repositories or by publishing scholarly journals on their own presses. This re-invented role of publisher is due in part, to the availability of digital age technologies which scaffold the publishing process and facilitate inexpensive production of digital-only journals. The global push for Open Access to the outputs of publicly-funded research has also been a major driver. Research funder mandates and institutional Open Access policies apply only to publications for which the authors have no expectation of commercial gain. In all cases the primary motivation is to disseminate widely for maximum uptake with attribution to the author thereby increasing impact. This makes works published in institutional repositories and on university presses ideal candidates for Creative Commons licences.

High-throughput bone and cartilage micropellet manufacture, followed by assembly of micropellets into biphasic osteochondral tissue

Engineered biphasic osteochondral tissues may have utility in cartilage defect repair. As bone-marrow-derived mesenchymal stem/stromal cells (MSC) have the capacity to make both bone-like and cartilage-like tissues, they are an ideal cell population for use in the manufacture of osteochondral tissues. Effective differentiation of MSC to bone-like and cartilage-like tissues requires two unique medium formulations and this presents a challenge both in achieving initial MSC differentiation and in maintaining tissue stability when the unified osteochondral tissue is subsequently cultured in a single medium formulation. In this proof-of-principle study, we used an in-house fabricated microwell platform to manufacture thousands of micropellets formed from 166 MSC each. We then characterized the development of bone-like and cartilage-like tissue formation in the micropellets maintained for 8–14 days in sequential combinations of osteogenic or chondrogenic induction medium. When bone-like or cartilage-like micropellets were induced for only 8 days, they displayed significant phenotypic changes when the osteogenic or chondrogenic induction medium, respectively, was swapped. Based on these data, we developed an extended 14-day protocol for the pre-culture of bone-like and cartilage-like micropellets in their respective induction medium. Unified osteochondral tissues were formed by layering 12,000 osteogenic micropellets and 12,000 chondrogenic micropellets into a biphasic structure and then further culture in chondrogenic induction medium. The assembled tissue was cultured for a further 8 days and characterized via histology. The micropellets had amalgamated into a continuous structure with distinctive bone-like and cartilage-like regions. This proof-of-concept study demonstrates the feasibility of micropellet assembly for the formation of osteochondral-like tissues for possible use in osteochondral defect repair.

Applications of real-time machine vision to the control of mining equipment

The mining industry presents us with a number of ideal applications for sensor based machine control because of the unstructured environment that exists within each mine. The aim of the research presented here is to increase the productivity of existing large compliant mining machines by retrofitting with enhanced sensing and control technology. The current research focusses on the automatic control of the swing motion cycle of a dragline and an automated roof bolting system. We have achieved: * closed-loop swing control of an one-tenth scale model dragline; * single degree of freedom closed-loop visual control of an electro-hydraulic manipulator in the lab developed from standard components.

Positioning as a source of competitive advantage: Benchmarking Rotorua’s position as a domestic short break holiday destination

Travellers are spoilt by holiday choice, and yet will usually only seriously consider a few destinations during the decision process. With thousands of destination marketing organisations (DMOs) competing for attention, places are becoming increasingly substitutable. The study of destination competitiveness is an emerging field, and thesis contributes to an enhanced understanding by addressing three topics that have received relatively little attention in the tourism literature: destination positioning, the context of short break holidays, and domestic travel in New Zealand. A descriptive model of positioning as a source of competitive advantage is developed, and tested through 12 propositions. The destination of interest is Rotorua, which was arguably New Zealand’s first tourist destination. The market of interest is Auckland, which is Rotorua’s largest visitor market. Rotorua’s history is explored to identify factors that may have contributed to the destination’s current image in the Auckland market. A mix of qualitative and quantitative procedures is then utilised to determine Rotorua’s position, relative to a competing set of destinations. Based on an applied research problem, the thesis attempts to bridge the gap between academia and industry by providing useable results and benchmarks for five regional tourism organisations (RTOs). It is proposed that, in New Zealand, the domestic short break market represents a valuable opportunity not explicitly targeted by the competitive set of destinations. Conceptually, the thesis demonstrates the importance of analysing a destination’s competitive position, from the demand perspective, in a travel context; and then the value of comparing this ‘ideal’ position with that projected by the RTO. The thesis concludes Rotorua’s market position in the Auckland short break segment represents a source of comparative advantage, but is not congruent with the current promotional theme, which is being used in all markets. The findings also have implications for destinations beyond the context of the thesis. In particular, a new definition for ‘destination attractiveness’ is proposed, which warrants consideration in the design of future destination positioning analyses.

Improving fluid registration through white matter segmentation in a twin study design

Robust and automatic non-rigid registration depends on many parameters that have not yet been systematically explored. Here we determined how tissue classification influences non-linear fluid registration of brain MRI. Twin data is ideal for studying this question, as volumetric correlations between corresponding brain regions that are under genetic control should be higher in monozygotic twins (MZ) who share 100% of their genes when compared to dizygotic twins (DZ) who share half their genes on average. When these substructure volumes are quantified using tensor-based morphometry, improved registration can be defined based on which method gives higher MZ twin correlations when compared to DZs, as registration errors tend to deplete these correlations. In a study of 92 subjects, higher effect sizes were found in cumulative distribution functions derived from statistical maps when performing tissue classification before fluid registration, versus fluidly registering the raw images. This gives empirical evidence in favor of pre-segmenting images for tensor-based morphometry.

The rapid manufacture of uniform composite multicellular-biomaterial micropellets, their assembly into macroscopic organized tissues, and potential applications in cartilage tissue engineering

We and others have published on the rapid manufacture of micropellet tissues, typically formed from 100-500 cells each. The micropellet geometry enhances cellular biological properties, and in many cases the micropellets can subsequently be utilized as building blocks to assemble complex macrotissues. Generally, micropellets are formed from cells alone, however when replicating matrix-rich tissues such as cartilage it would be ideal if matrix or biomaterials supplements could be incorporated directly into the micropellet during the manufacturing process. Herein we describe a method to efficiently incorporate donor cartilage matrix into tissue engineered cartilage micropellets. We lyophilized bovine cartilage matrix, and then shattered it into microscopic pieces having average dimensions < 10 μm diameter; we termed this microscopic donor matrix "cartilage dust (CD)". Using a microwell platform, we show that ~0.83 μg CD can be rapidly and efficiently incorporated into single multicellular aggregates formed from 180 bone marrow mesenchymal stem/stromal cells (MSC) each. The microwell platform enabled the rapid manufacture of thousands of replica composite micropellets, with each micropellet having a material/CD core and a cellular surface. This micropellet organization enabled the rapid bulking up of the micropellet core matrix content, and left an adhesive cellular outer surface. This morphological organization enabled the ready assembly of the composite micropellets into macroscopic tissues. Generically, this is a versatile method that enables the rapid and uniform integration of biomaterials into multicellular micropellets that can then be used as tissue building blocks. In this study, the addition of CD resulted in an approximate 8-fold volume increase in the micropellets, with the donor matrix functioning to contribute to an increase in total cartilage matrix content. Composite micropellets were readily assembled into macroscopic cartilage tissues; the incorporation of CD enhanced tissue size and matrix content, but did not enhance chondrogenic gene expression.

Creative adaptations: Integrating Feldenkrais principles in contemporary dance technique to facilitate the transition into tertiary dance education

As conservatoire-style dance teaching has traditionally utilised a hierarchical approach through which the student must conform to the ideal requirements of the conventional technique, current discourse is beginning to question how dance training can develop technical acuity without stifling students' ability to engage creatively. In recent years, there has been growing interest in the field of somatics and its relationship to tertiary dance training due to the understanding that this approach supports creative autonomy by radically repositioning the student's relationship to embodied learning, skill acquisition, enquiry and performance. This research addresses an observable disjuncture between the skills of dancers graduating from tertiary training and Australian dance industry needs, which increasingly demand the co-creative input of the dancer in choreographic practice. Drawing from Action Research, this paper will discuss a project which introduces somatic learning approaches, primarily from Feldenkrais Method and Hanna Somatics, to first-year dance students in their transition into tertiary education. This paper acknowledges previous research undertaken, most specifically the Somdance Manual by the University of Western Sydney, while directing focus to the first-year student transition from private dance studio training into the pre-professional arena.

Expression and characterization of digestive enzyme genes from hepatopancreatic transcripts from redclaw crayfish (Cherax quadricarinatus)

Redclaw crayfish, Cherax quadricarinatus, possess a number of biological and commercial attributes that make them ideal for commercial aquaculture. While some studies have investigated digestive enzyme activity and nutritional requirements of this species, little information exists about the expression of digestive enzyme genes and their role in regulating digestive capacity. The current study therefore sequenced and annotated a RNASeq library constructed from a redclaw hepatopancreas to identify genes involved in digestive enzyme production. We observed that most of the transcripts that were annotated as digestive enzyme genes are associated with carbohydrate metabolism, thus confirming that redclaw have an innate capacity to digest a range of carbohydrate substrates. While endoglucanases were the most abundant group of digestive enzymes found, a number of novel transcripts were also detected. Here, we provide the first report for the presence and expression of endo-b-mannanase in freshwater crayfish. This novel gene showed significant alignment with a GH5 family protein from marine Limnoriids, wood borers that do not possess symbiotic microbes in their gut system. Overall, the data generated here provide an important resource to better understand the suite of digestive enzymes in redclaw that are very useful to fully utilize the species’ digestive capacity and will assist development of specific artificial feeds.