UQ Theses Collection (RHD) - UQ staff and students only - UQ eSpace

Behold the man : the life, times and circle of Daniel Isaac Eaton, 1753-1814

Michael T. Davis — 2012-07-04T00:00:00Z

Bellum piraticum: pompey, piracy, and the lex gabinia of 67 BC

Press, Daniel Patrick — 2012-09-12T00:00:00Z

Belonging in the mining museum: an examination of Chinese Australian identity and belonging in discourses of the Gold Rush

Han, Alan — 2013-03-09T03:02:15Z

Benthic foraminifera as Holocene to Recent indicators in marginal marine environments: modern distribution and the palaeoecological response to environmental changes in Moreton Bay, southeastern Queensland, Australia

Yogeeta Roshni Narayan — 2011-09-17T00:00:00Z

Estuarine embayments and coastal areas occurring adjacent to large, populated river catchments are presently threatened by multiple anthropogenic and natural environmental stressors, including: intense human activities, overharvesting, coastal land modification, sediment/nutrient and pollutant input, storms, flooding and freshwater plumes. This is further exacerbated by predicted relative sea level rise and global climatic changes. Effective marine resource management of environmental threats requires an understanding of the: (i) present conditions and the ecological response by organisms (ii) future forecasted scenarios; and (iii) long-term historical range in natural variability (HRNV), which conveys the magnitude of modern environmental degradation. To carry this out, a useful ecological indicator(s) is needed. Here, I focus on the (palaeo)ecology of benthic foraminiferal assemblages (Protista) to understand modern, decadal and millennial-scale changes, specifically the: (1) modern relationship between ecology and environment; (2) decadal changes in community structure over the last ~40 years in the lower river estuary and reef environment; and (3) response by benthic foraminifers to long-term, historical (millennial) changes in the subtropical, marginal reef environments of Moreton Bay, southeast Queensland, Australia. From the analysis of 47 surface sediment samples taken from habitats across the Bay, I identified 69 species, three distinct foraminiferal assemblages and six sub-assemblages. I found a positive relationship between foraminiferal assemblages and substrate conditions that resulted in a geographic gradient from: an urban-impacted assemblage in the westernmost part of the Bay, to a hyposaline, estuarine-influenced assemblage in the western Bay to a nearly normal marine to hypersaline assemblage in the eastern Bay. The Foraminifera in Reef Assessment and Monitoring (FORAM) Index of Hallock et al. (2003), which provides a quantitative measurement of reef “health”, was applied and demonstrated marginal conditions. The western Bay foraminiferal assemblages from the estuarine and marginal reef flats reflect high turbidity and variable nutrient conditions, whereas the assemblages from the eastern Bay, near-oceanic, tidal (seagrass-dominated) flats, reflect optimal conditions for zooxanthellate organisms (i.e. corals and large symbiont-bearing foraminifera). Currently, the Brisbane River catchment is experiencing rapid population growth, urbanisation, industrialisation and climate-induced impacts such as the recent major flooding events (i.e. 1974 and 2011). The availability of existing foraminifera samples collected during the 1970s by the Geological Survey of Queensland provide an excellent and rare opportunity to carry out quantitative comparisons between new (2007-08) and existing (1972) data, to assess changes between today and ~40 years ago. I compared community structure between the two time periods and across two different environments: the lower Brisbane River estuary and the adjacent lagoonal-reef flats of Waterloo Bay, in western Moreton Bay. Species diversity and bio-environmental indicators reflect a predominantly human-dominated influence in the lower Brisbane River estuary and reef environments. However, in comparison to the 1970s, recent temporal trends in the foraminiferal assemblages reveal incipient recovery, suggesting potential for remediation of an environment that has previously been influenced by severe anthropogenic modification. This study demonstrates the potential of benthic communities to at least partially recover from severe degradation in nearshore ecosystems. I also examined the spatial and temporal distribution patterns of foraminifera from Holocene sediment cores from three extant Moreton Bay marginal reef sites: Wellington Point, southwest Peel Island and Myora Reef. The foraminiferal assemblages from the three reefs are significantly different from one another, reflecting a W to E spatial gradation (improving eastwards) and a younger to older temporal gradation in water quality and palaeo-water depths. The approximate timing of assemblage shifts with decreasing palaeo-depths over time, generally corresponds with the timing of known faunal and sedimentary patterns associated with the following: regional sea level highstand and progradation of subtidal reefal facies; sea level fall and progradation of shallow-reefal facies; and lastly episodic reefal “turn-off” and progradation of land-derived facies. However, we find that the magnitude of sea level change exceeds known relative sea level change in the region (by a factor of ~1.5-2). The physiographic nature of Moreton Bay, which tends to amplify ecological changes, would have contributed to the higher magnitude of change seen in reefs, throughout the Holocene. Holocene studies also highlight the historical importance of larger benthic symbiont-bearing foraminiferal assemblages (Peneroplis spp. and Alveolinella quoyi/Heterostegina depressa spp.) as indicators of environmental change in Moreton Bay’s reefs. They can be used as a measure of improvement in water quality or as a signal for recovery of environments, particularly in the western Bay reefs. Lastly, this study demonstrates a clear response by benthic foraminiferal assemblages to changes in sea level throughout the Holocene. It suggests that Moreton Bay’s reefs have endured natural instability and gradual, progressive change over a time frame of ~7000 years. In contrast, more recent anthropogenically-driven changes affecting water quality, have resulted in dramatic shifts in the benthic ecological assemblages of Moreton Bay in a shorter time-frame of ~200 years.

Beta-Arrestin Expression and Function in Macrophages

Jane Lattin — 2009-04-06T00:00:00Z

Monocytes and macrophages are critical cellular mediators of inflammation. However, aberrant activation of these cells contributes to the pathology of acute (for example septic shock) and chronic (for example rheumatoid arthritis) inflammatory diseases. These cell types express an extensive repertoire of G-Protein Coupled Receptors (GPCRs), which are widely targeted in drug discovery. Novel macrophage-expressed GPCRs are likely to impact on inflammatory and immune responses and hence represent targets for development of novel therapeutics. This thesis focused on identifying GPCRs and GPCR signalling molecules expressed by macrophages and investigating their function in this lineage. In Chapter 3 of this thesis, a systematic micro-array analysis of primary mouse macrophages compared to other cell populations was performed to identify GPCRs that are enriched in macrophages. The P2Y family of GPCRs were identified as being highly expressed and/or regulated in macrophages, and the regulated expression of two P2Y family members (P2RY5 and P2RY6) was further investigated in this chapter. Expression profiling was also used to identify macrophageexpressed GPCR signalling molecules, and Chapter 4 focused on the expression and function of one of these, beta-arrestin (ARRB) 2. The macrophage-enriched expression of ARRB2 was confirmed at the mRNA and protein level, and its regulation by inflammatory stimuli in macrophages was also investigated. Given that ARRB2 is a key regulator of GPCR signalling and has also recently emerged as regulator of Toll-like Receptor (TLR) signalling, further research focused on this signalling molecule in an attempt to identify novel functions in macrophages. By expression profiling of ARRB2 deficient BMM, and through the use of a novel cell permeable peptide antagonist of ARRB2, this signalling molecule was identified as a critical regulator of basal and LPS-inducible complement C1q expression. Furthermore, ARRB2 limited factor-independent survival and regulated activation of ERK-1/2 and JNK MAPK in macrophages. Chapter 5 documented a defect in LPS-inducible expression of the histone deacetylase, Hdac1 in ARRB2-/- macrophages, and explored the consequences of this on macrophage inflammatory pathways. Thus Chapters 4 and 5 identified novel pathways by which ARRB2 positively regulates LPS-inducible gene expression in macrophages. Given that loss of C1q expression is associated with systemic lupus erythematosus (SLE) and that HDAC1 is a feedback regulator of macrophage activation, understanding the mechanisms by which ARRB2 regulates the expression of these genes will provide further insight into inflammatory disease processes.

Beta-cell development and maintenance : disruption of the normal processes in the disease state, hyperinsulinism of infancy

Jack, Michelle Marion. — 2011-06-29T00:00:00Z

Betaine as a Dietary Additive for Heat Exposed Beef Cattle

Stephen Bonner — 2011-10-02T00:00:00Z

The heat stress response in cattle functions to minimise accumulation of excessive body heat, and to facilitate its removal. Prolonged and continuous exposure to high heat load can cause physiological imbalances. Nutritional strategies may be used to ameliorate the disturbance of homeostasis resulting from heat stress. The research presented in this thesis was designed to assess the potential of betaine as a dietary additive to ameliorate the negative aspects of the heat stress response in beef cattle. This was accomplished by; i) testing the effects of betaine on the heat stress response of steers exposed to hot conditions, ii) evaluating the influence of betaine within the rumen, iii) assessing betaine effects on rumen bacterial species, iv) the effect of betaine on the physiology and blood parameters of steers under hot conditions, and v) assessing the response of steers to dietary betaine on blood parameters over 120 days in a feedlot. A 5 day heating protocol was imposed on steers under controlled climatic conditions within 2 studies (Chapters 3 and 6). Steers were fed a grain ration containing 20 g of betaine (BET) or no betaine (CON) in Chapter 3. Three dietary treatments were used in Chapter 6; identical to Chapter 3, plus betaine (20 g) with buffer (BET+). DMI fell for all steers during the 5 day hot phases. The change in DMI (relative to DMI pre-heat) was larger (P<0.001, P<0.001) for betaine treatments in both studies. The rate of increase of rectal temperature (RT_slope) and respiration rate (RR_slope) for CON steers was greatest on day 3 of heat, in contrast to peaks for RT_slope and RR_slope occurring for BET steers on day 4 of heat. This may indicate that the response of CON steers to heat was more acute, particularly in day 3. During the hot days (Chapter 6), CON steers had the smallest (P<0.05) change in rectal temperature (ΔRT) compared with BET and BET+, and yet had the highest (P<0.05) increase in respiration rate (ΔRR). Conversely, both BET and BET+ steers had the highest core temperature throughout 5 hot days, while simultaneously having lower ΔRR compared with CON. Serum urea was higher (P<0.01) for BET and BET+, however, this may be influenced by dietary protein. Across all treatments, serum creatinine appeared sensitive to elevated temperatures. Creatinine was higher for hot days compared with thermoneutral days, and increased as ambient temperatures became more severe. This may indicate that creatinine expression is sensitive to hot conditions, and therefore having potential as a marker of heat stress in beef cattle. An in vivo study was conducted using sheep to evaluate the effect of betaine within the rumen. Two treatments were fed the same diet, while betaine was added directly to the rumen of the betaine treatment. Similar to other studies (Mitchell et al. 1979), betaine clearance from the rumen was rapid. The half-life of betaine within the rumen was within 0.9 - 2.1 h. Rumen ammonia concentration was lower (P<0.05) for betaine treatment at 6, 7 and 9 hours following betaine addition to the rumen. Betaine did not affect rumen VFA concentration, digestibility or protozoal counts. To evaluate betaine upon rumen bacterial species, an in vitro rumen culturing experiment was conducted using rumen fluid from sheep fed the same concentrate diet with and without betaine. All in vitro cultures contained betaine, while 2 rumen fluid inocula were taken from sheep previously receiving betaine (B), and 2 without betaine (C). Profiling rumen bacterial populations with DGGE demonstrated changes at 24 and 48 h. In particular, the intensity of band D increased at 24 and 48 h for C treatment, but was present for B treatment. This band was identified to the family level as Streptococcacae. Ammonia accumulation was lower (P<0.05) for C treatment in the 0 - 24 h culture. These data indicate that initial exposure of rumen bacteria to betaine in the in vitro cultures may increase the relative proportion of certain bacterial species. As a component of a larger study, steers fed for 120 days over summer in a sub-tropical environment and fed 0, 10, 20 or 40 g of betaine, or glycerol, with a shaded and unshaded treatment for all diets. Blood samples were collected on days 0, 30, 60, 90 and 110. Production data from this study is published elsewhere (Gaughan et al. 2010). Correlations between blood parameters and physiological measures (body temperature, panting score, DMI and liveweight) were observed for sodium, urea, glucose, haematocrit and red blood cells. These studies have highlighted the complexity of the heat stress response in cattle, and the indirect nature of employing nutritional strategies to attend to resulting imbalances. Successful nutritional strategies for heat stress may not always result in direct production benefits. These studies emphasise the impact of dietary nitrogen on the heat stress response and a likely interaction with betaine supplementation.

Beta-lactam antibiotic dosing in critical care units: bolus vs continuous dosing

Jason Roberts — 2009-04-07T00:00:00Z

In critically ill patients, the pathophysiology of sepsis can affect the interactions between the antibiotic, the bacteria and the patient, leading to potential therapeutic failure and the development of antibiotic resistance. It is well acknowledged that research that optimises antibiotic exposure will assist improvement of outcomes in this patient group. Although beta-lactam antibiotics, such as piperacillin and meropenem, are commonly selected for empiric therapy of sepsis, dosing is unlikely to be optimal. In patients without renal dysfunction, data suggests that disease-induced alterations to pharmacokinetic parameters result in low trough concentrations for significant periods within a dosing interval. Administration of these time-dependent antibiotics by continuous infusion has been suggested to improve the pharmacokinetic-pharmacodynamic profile. Knowledge of concentrations in the extracellular fluid of human tissue, which is the target site of most pathogens, is particularly instructive. Extracellular fluid concentrations can be determined using techniques such as microdialysis. Therefore, the principal aims of this Thesis were to determine the plasma and subcutaneous tissue pharmacokinetics of piperacillin and meropenem administered by bolus dosing and continuous infusion in critically ill patients with sepsis; and to use Monte Carlo simulations to compare the ability of different dosing strategies to achieve pharmacodynamic endpoints. This Thesis also sought to compare the clinical outcomes of bolus dosing and continuous infusion of a beta-lactam antibiotic, ceftriaxone, in a prospective randomised controlled trial and to perform a meta-analysis on clinical outcomes from other similar published studies. Finally, this Thesis aimed to systematically review the published literature to determine any correlation between antibiotic dosing and the development of antibiotic resistance. The results of the pharmacokinetic studies, using piperacillin and meropenem, indicate that beta-lactam distribution into subcutaneous tissue, in critically ill patients with sepsis, is less than that observed in previous studies in healthy volunteers yet superior to studies in patients with septic shock. This supports the notion that the peripheral concentration of drugs may be inversely related to the level of sickness severity. Administration by continuous infusion was found to maintain statistically significantly higher trough beta-lactam concentrations in both plasma and subcutaneous tissue. Further analysis of the plasma data using population pharmacokinetic modeling and Monte Carlo simulations described significant pharmacodynamic advantages for administering meropenem or piperacillin by continuous infusion to organisms with high minimum inhibitory concentrations. Given the documented pharmacodynamic advantages for administering beta-lactams by continuous infusion, a prospective randomized controlled clinical trial was conducted using the beta-lactam antibiotic ceftriaxone. In 57 critically ill patients, we found equivalence between continuous infusion and bolus dosing in the intention-to-treat analysis. However, our a priori analysis criteria, requiring patients receive at least 4-days antibiotic treatment, found significant clinical and bacteriological advantages for administration by continuous infusion. To further investigate any clinical differences between bolus dosing and continuous infusion of beta-lactam antibiotics, we performed a meta-analysis of all published studies. Our analysis of the 13 published prospective randomized controlled trials (846 hospitalised patients) showed equivalence of continuous infusion and bolus dosing. Possible confounders observed within, and between the studies, make interpretation of these results challenging. However, two large retrospective cohorts not included in the meta-analysis, found definitive clinical and bacteriological advantages suggesting further research may be appropriate. The possible relationship between antibiotic dosing, or exposures, on the development of resistance was investigated using a structured review of the published literature. Our analysis of relevant papers found a wealth of data describing increasing levels of resistance with sub-optimal antibiotic dosing, particularly for fluoroquinolone antibiotics, but also for other classes including beta-lactams. These results demonstrate the importance of optimizing antibiotic dosing to decrease the development of antibiotic susceptibility from sub-optimal dosing, particularly for critically ill patients who are likely to have low drug concentrations. The results of this Thesis, suggest that a large, prospective, multi-centre randomised controlled trial in critically ill patients with sepsis, is required to definitively determine the clinical utility of administration of beta-lactam antibiotics by continuous infusion.

Between movements of crisis and movements of affluence : an analysis of the campaign against the Jabiluka uranium mine, 1997-2000

Paasonen, Karl-Erik — 2008-11-21T00:00:00Z

Between Scylla and Charybdis: Navigating Amendment Law in the Australian Patent System

McBratney, Amanda Jane — 2008-11-21T00:00:00Z

This thesis examines the historical development and current state of amendment law in the Australian patent system. Initial research on modern amendment cases immediately showed that the confused, inconsistent and complex state of the law is a significant problem. There is a plethora of different analytical tools and legal tests being applied to assess an amendment, yet they were developed in a different area of patent law, that of fair basing. Such tools and tests are ill equipped to provide any real assistance to decision-makers faced with assessing an amendment. In fact, they seem to lead decision-makers away from applying the correct investigation as set out in the amendment provisions of the legislation. The thesis examines the history of amendment law so as to place its discussion of the current problems in context and provide a better understanding of why the problems arose. Four major events are discussed in the thesis. Together, these events have shaped Australian amendment law over the past century: (i) the development and introduction of the substantially larger than or substantially different from test into the British and Australian statutory amendment provisions; (ii) the development and introduction of the concept of fair basing into British and Australian patent law; (iii) the development and introduction of the modern British and Australian statutory test for amendments and the tiered amendment scheme; and (iv) the analogies drawn in modern British and Australian cases between fair basing and amendment that ultimately led to fair basing tests being cross-applied in Australia to assess the allowability of amendments. The thesis shows how the very harsh early British treatment of requests for amendment ultimately led to statutory change. It also locates, for the first time, the common law origins of the notion of fair basing. The 1949 British legislation implemented a new and different statutory test that was intended to liberalise the whole area of amendment law. It also added the requirement of fair basing into the legislation. However, the thesis shows that this last development occurred via well-intentioned legislators with a significant misunderstanding of patent law. The notion of fair basing injected a great deal of uncertainty into an area of law that was previously settled. Theoretically, and in practical application, it caused problems. Then, when decision-makers sought guidance on the new amendment provision, they applied the tests developed in fair basing cases to assess amendments, with the consequent deleterious effects. The Australian experience largely mirrored the British experience until 1977 when the British Act changed. The significance of the thesis is that it clearly demonstrates that the currently accepted dogma that fair basing is equivalent to the in substance disclosure statutory test for amendments, so fair basing tests can be used to assess amendment is unsound. The thesis isolates the problems inherent in the dogma and the examination of relevant case law confirms the main hypothesis that the current approach should be rejected. It simply operates to the prejudice of inventors, their competitors, the public and the patent system itself. Most importantly, the thesis shows that reform is urgently needed. Some possibilities for reform are suggested.

BETWEEN TWO WORLDS: CLAUDIO POMPILI, ITALIAN-AUSTRALIAN COMPOSER

Claudio Pompili — 2009-04-08T00:00:00Z

Between Two Worlds, with its implied dualities, alludes both to my Italian and Australian backgrounds and to my popular and art music experiences. The dissertation comprises of analyses of and critical commentary on a selection of compositions from instrumental through electroacoustic to musico-dramatic works. Further, Part I presents a précis of relevant background in order to locate the compositions within both Australian contemporary classical music and international settings, and Part I includes sections on analytical methodology and compositional technique. Compositions examined in Part II illustrate the salient features of compositional technique, specific influences and aesthetic concerns. Both instrumental works, Fra l’urlo e il tacere and Ridendo vado sul fiume, were written during the earlier period of the doctoral candidature. The discussion presents not only the seminal influences including the use of interval-class (ic) construction and music technologies but is also intended to guide the reader from solo and chamber instrumental writing through sound design and electronic soundscape composition towards the larger-scale, musico-dramatic works. Part III discusses the major contribution. It is concerned with three mixed-media musictheatre compositions that were created in the period 2000–08 and which explore crossdisciplinary relationships. Whilst maintaining a continuous development of style, the works are on a larger scale in all respects: involve national (The Last Child and Touch Wood) and international (Lontano Blu) production teams and a greater number of performers; are interdisciplinary, conceptually more complex and multilayered, and longer in duration; include extensive use of music technologies, multimedia and multichannel surround sound in performance; and use graphic/text/prose scores. By their very nature, these compositions involved significant collaborative endeavour not only with the key members of the creative teams, such as artistic directors, writers and set designers, but also the performers in general and musicians in particular. The collaborations included development of the conceptual structures of the works with the creative teams and ‘hands on’ interaction with the musicians in shaping the sound in real time through group-devised processes where appropriate.

Beyond Alethia: A Critique of Heideggerian Einaiology

Colledge, Richard John David — 2008-11-21T00:00:00Z

The work of Martin Heidegger holds a pre-eminent place in contemporary ontological metaphysics, and this, it is argued, is a deeply two-edged sword. Proceeding on the basis of the unity of Heideggers life-long project, the thesis critically evaluates Heideggerian thought, with a particular emphasis on its early formative texts (1923-35), highlighting what are seen as both its radical insights and its important shortcomings. The essay essentially follows Heideggers own philosophical practice in two senses. First, it takes a strongly historical approach both to the etymology and semantics of the language of ontology, as well as to the context of Heideggerian thought in the tradition of western metaphysics. Second, beyond the method of immanent critique alone, it adopts a version of Heideggers own methodology of retrieval (Wiederholung) in its confrontation with his thought: on one hand affirming the radically insightful nature of key elements of his work, while on the other hand looking to bring out of Heideggers (and his precursors) own texts something of their drawing back from the deepest latent implications of his (and their) own insights. The essay begins with a historico-linguistic survey of the language of western ontology, from its origins in ancient Greek and Hellenistic metaphysics, through to its reception into medieval Latin, and onto its deployment in contemporary German and English, in this way establishing a key aspect of the pre-history of the ontological difference in terms of infinitival-participial renderings of the question. The interpretation offered here is then contrasted with key elements of Heideggers own reading of the ancient origins of the tradition, and thus the first major strand of the essays critique of Heideggerian thought is established along both linguistic and conceptual lines: i.e., that is amounts to an einaiolisation of the broad question of ontology. On the basis on this critique, the essay then sets out the understanding of be ειναι, esse, Sein) to be defended in what follows, a reading that situates itself between the Heideggerian and Thomistic positions, affirming and opposing key elements of each. On one hand, the vast wealth of Heideggers alethiological phenomenology of world is affirmed as a radical advance on traditional static notions of essence, while on the other hand the collapse of any genuine understanding of the depth dimension of to exist (υπαρχειν, ex(s)istere) is identified as a major point of contention with Heideggers einaiology. In this way, the second major strand of the essays critique of Heideggerian thought is established: i.e., that it amounts to a partialising alethiolisation of ontology. Within the context provided by the essay to this point, a more explicit retrieval of Heideggerian thought is then enacted first of all by situating his thought within the broad transcendental-phenomenological tradition in which it is so deeply embedded. In particular, this entails close readings of the methodological exclusion (εποχη) of exist(ence) seen in texts by Kant and Husserl, a strategy that in both cases is inadequately ameliorated by allusions to that which is surplus (Überschuß) to predication, meaning, sense, essence. Within the rich context provided by this analysis, the nature of Heideggers innovation within, and yet deep adherence to, the transcendental-phenomenological tradition is sketched. The essays fourth and final chapter involves a detailed confrontation with Heideggers delimitation of the Seinsfrage to alethiological and einaiological concerns alone. This involves a close reading of some major early texts on the question of the independent integrity of beings from world(ing) and thus the meaning of Heideggers category of Vorhandenheit, noting some substantial ambiguities on this question. It also involves a more systematic assessment of the consequential deep inner-contradictions of Heideggers project as a whole, including some reflections on strands of early Heideggerian thought that appear to be attempts to address these deeply embedded tensions and problems. The essays conclusion very briefly links the enacted critique of Heideggerian ontology to the broader question of the understanding of contingency in contemporary continental philosophy, thereby indicating something of the place of these reflections within a larger project of thought concerning philosophy as a hermeneutics of awe for which it serves as an essential prolegomena.

Beyond gentrification : a new phase of inner city resettlement?

Shaw, Kirstyn E. L — 2013-01-10T09:12:56Z

Beyond revascularisation and recovery of regional ventricular function: Implications of myocardial viability for medical treatment and remodelling.

Khoury, Vincent K. — 2007-08-24T00:00:00Z

Beyond root causes: understanding risk and resilience in the prevention of mass atrocities

McLoughlin, Stephen — 2012-08-10T00:00:00Z

Beyond the Cootharaba Mill: An archaeology of social interaction, practice and community in colonial Australia

Karen Murphy — 2011-04-20T00:00:00Z

This thesis explores a new approach for understanding communities in the historical past. It examines community as a fluid entity, constructed through the social interactions and practices of its members. This approach is used to investigate the community associated with the operation of the Cootharaba sawmill, in late 19th century southeast Queensland. Previous approaches to understanding community in the archaeological discipline have been founded on the paradigm of a ‘natural’ community; a naturally-occurring, spatially-bounded, static entity. More recent approaches have considered the issue by viewing the community as ‘imagined’; a unit with ties to external entities and comprising active internal agents. My research adopts the latter approach using concepts of agency and practice as a foundation to a model which aims to understand the community as both a physical and a mental phenomenon. This practice-oriented approach recognises that the community is a social institution that structures and is structured by internal agents and external forces. As Canuto (2002) proposes, a community can be seen as comprising four elements — locale, habitus, agency and pacing — which enables spatial, ideational, interactive and temporal interpretations to be made about a community. A study of a community must consider the multiple scales of interaction and the broader external contexts in which the community operates. My research provides a methodological contribution to studying historical period communities by providing a framework of indicators to address the physical nature of the archaeological remains of a community’s actions and practices in order to examine the mental and social aspects of the community. Archaeological data for this study were generated from extensive survey and excavation of the residential area of the site of the Cootharaba sawmill settlement. Historical research included the investigation of a range of primary documents and secondary sources concerning the lives and characters of the Cootharaba story. The archaeological and documentary evidence enabled each of the indicators to be examined in order to identify the actions and practices of the community at the domestic, local and regional scales, as follows: • The organisation of individual residences within the residential area of the mill settlement reflecting the daily, residential, doxic practice in the domestic locale. • The organisation of the mill settlement and associated operations resulting from periodic, discursive group action in the local locale. • The nature of the regions surrounding the mill settlement as evidence of irregular, external, orthodox practice in the regional locale. The social group of the community of Cootharaba was a complex, interacting social institution that operated in different ways at different scales. The company operating the sawmill, McGhie, Luya and Co., was the key to the establishment and ongoing existence of this community and as such the company and the organisation of its operations was the overarching structuring factor of the community. Examining the community solely through this lens, however, provides a biased view and marginalises the majority of the population — the women and the children. Using three scales of practice to examine the interaction and social constitution of the community of Cootharaba provides for the elucidation of the complexities and variances both between and within groups in the community. This research demonstrates that communities are not simply equable to a spatially bounded location; the relationship between community and locality is not necessarily a one-to-one relationship. For the Cootharaba community there were relationships between people in different localities but who still belonged to the same community group. The linkages and inter-relationships between the people of the Cootharaba community, the localities where they lived and interacted and the material culture they created and used all occurred within a broader social and historical context. This research examines the relationship between the people, localities, and material culture of the Cootharaba community within its context of 19th century Queensland. The community development, maintenance and dissolution was reliant on natural resources and their extraction and was tied to the economic highs and lows of the Queensland colony. The actions and practices of the community members were also tied into the social expectations and requirements of the society of 19th century Queensland and their mainly British and Irish cultural backgrounds. The study of the Cootharaba community demonstrates the importance of social interaction and individual practices in the formation of social groups, and in the maintenance of community at different scales and across different localities. The community was not just made up of the group of people living at the physical settlement at Cootharaba. The Cootharaba community was an active, interacting social institution that was structuring and being structured by the internal actions and practices of its members at the domestic, local and regional scales, as well as by external forces well beyond the mill.

Beyond the Visible: Disability and Performing Bodies

McHenry, Lalita — 2008-11-21T00:00:00Z

This thesis emerges from my work in the disability field and engagement in disability arts. After attending the first High Beam Festival in Adelaide in 1998, I became interested in the ways that disabled bodies were reclaiming identity and performing issues about disability as a challenge to those offered through dominant cultural representations. Work in the disability field over the past 50 years that has been dominated by medical and social frameworks, but disability studies and creative works by people with disabilities are shifting the focus and insisting on the centrality, rather than marginality, of the disabled bodyarguing for a new cultural space. These cultural practices are witness to the reconstruction, transformation and subversion of the discourses that historically circumscribe disability. Common to much disability arts practice is a desire to make visible a repressed and othered body, rewrite the scripts of disability by drawing on the real experience of people with disabilities and, perhaps most importantly, to provoke a rethinking of disability (primarily in the able-bodied majority) by reversing the gaze. Despite these efforts, disability continues to exist in an untenable binary with the able-bodied. In addition, questions of subjectivity and embodiment beyond the purview of physical and visible disability remain under-explored. This has led to a broader interest in a politics of the image and an analysis of the normative gaze, issues this thesis places under considerable scrutiny. As the title of this thesis indicates, I ask questions that go beyond the visible by exploring disability and performing bodies. At the forefront of this enquiry is a concern with the relations of looking, the nature of Otherness and questions of the gaze. The research is conducted through observation of live performance, in-depth interviews with disabled performers, theatre producers and artists, and a detailed analysis of the processes involved. Questions of the body are at the heart of numerous disciplines including feminism, disability studies, cultural studies, postcolonial and performance studies. The body can be said to be under a radical deconstructive agenda. The thought that theatre reflects an unproblematic reality no longer holds true because the performers self is not just a question of assuming a character or playing a role. What then of work that relies on these tropes as important markers of cultural resistance? I introduce the important developments in the field of disability and performance and address a series of research questions: In what ways can the cultural sphere of the arts work as a site of intervention able to respond to the problems of extant constructions of disability? How might disability be performed in ways that address issues of exclusion and abjection and at the same time avoid perpetuating the very oppressive spaces that are under challenge? What are the limitations of a pure visibility politics? What are the ideological interpellations and emotional and political effects of performing in a disability arts context? What might be gained from problematising the disabled body itself? In this thesis, I bring together a number of divergent cultural sites through which to challenge the concept of disability and the performing disabled body. These cultural sites include disability arts theory and practice, live performance, contemporary freak shows and the practices of self-demand amputation and extreme body modification. These sites provoke an examination of subjectivity and a rethinking of how disability and the disabled subject are presently understood. It is necessary to deconstruct the disabled subject and rethink notions of the Other in order to provoke any real challenge to the discourses of perfection and wholeness that dominate the cultural imaginary. The term Other is generally used in disability theory in ways that inevitably resort to a binary relationship and a problematic understanding of the operations of the gaze. In the work of both Emmanuel Levinas and Jacques Lacan, the term Other dramatically shifts in meaning and offers a profound rethinking of the premises of much disability theory and arts practice. Levinass work offers the possibility for an alternative ethics of performance for an audience and a different way of thinking about the relations between self and other and disability. Lacans work on the Other and the gaze assists in unpacking the binary distinctions often constructed in the visual field between notions of the normal observer and the disabled subject. I endeavour to move beyond visibility, to highlight the limitations of a politics steeped in mobilising a disabled subject and identity without eclipsing the significance of the visual in the formation of subjectivity. By engaging with a few select performances and other cultural projects not currently read through the lens of disability, yet corporeally linked to questions about body image, the Other and desire my hope is that a more critical perspective on the concept of disability can be adopted. This provides the conditions to further the development of a critical disability studies.

Bifurcations, Phase Transitions and Teleportation in Entangled Quantum Systems

John Paul Barjaktarevic — 2008-12-04T00:00:00Z

Bilingual Child-rearing in Linguistic Intermarriage: Negotiating Language, Power, and Identities between English-Speaking Fathers and Japanese-Speaking Mothers in Japan

Lachlan Jackson — 2010-03-15T00:00:00Z

This is a qualitative sociolinguistic study that investigates the parental experiences of bilingual child-rearing for linguistically intermarried couples in Japan. In particular, it focuses on the role of native English-speaking fathers. Through the incorporation of questionnaire, logbook, and in-depth interview data, the study presents eight unique and richly-nuanced cases of language contact in the family domain. The thesis builds on influential works that have both questioned the ease with which children acquire two languages (Yamamoto, 2001b) and highlighted bilingual child-rearing as an emotionally draining and labour-intensive pursuit (Okita, 2002). In accordance with recent suggestions to more readily acknowledge the socio-political dimensions of bilingualism (e.g. Heller, 2007, p. 1; Myers-Scotton, 2006; Li Wei, 2008, p. 17), this study shows bilingual child-rearing to be an innately political phenomenon. The study supports the supposition that the individual circumstances of linguistically intermarried couples rarely align neatly with the prescriptive advice found in much of the popular literature on how to raise children in two (or more) languages (Piller, 2001b). In particular, abstractions of power and discursively constructed identities are shown to structure both the specific language choices and the broader parental practices of the couples in this study. For linguistically intermarried couples, bilingual child-rearing is shown to be a fluid process of negotiation, whereby language choices and decisions about transmission strategies are tied to social positioning of both self and other. Drawing from a broader literature pertaining to the social psychology of parenting, this thesis also proposes a model to analyse the ecological context of bilingual child-rearing. The linguistic behaviours of the parents, as well as their decisions concerning family language planning are shown to emerge from each family’s unique and fluctuating set of social circumstances. These include, but are not limited to, the quality of the spousal relationship, the family’s economic resources, (shifting) cultural affiliations of all family members, future plans, minority language contact opportunities, the medium of instruction at the child’s school, the needs and wishes of extended family members, as well as the agency of the child.

Bilirubin metabolism during arsenic toxicity of the liver: involvement of murine cytochrome P450 2a5 and its human orthologue CYP2A6

Dionne Arthur — 2011-03-01T00:00:00Z

Arsenic exposure causes chronic disease and cancer in various organs in humans. The liver is a target organ for arsenic toxicity. The most accepted mechanism of arsenic toxicity involves oxidative stress. The initial response to oxidative stress is defensive, and involves numerous antioxidant defence systems. Two enzyme systems that have been reported to play an important role in cellular defence during metal-induced oxidative stress include haem oxygenase-1 (HO-1) and cytochrome P450 2a5 (Cyp2a5). It was found that both enzymes are involved in bilirubin (BR) homeostasis, where Cyp2a5-dependant BR oxidation is elevated when BR levels increase due to HO-1 induction. The oxidative metabolism of BR is an important pathway of detoxification in addition to glucuronidation however the oxidative products were not identified. In this thesis various bilirubin oxidative metabolites (BOMs) formed as a result of BR oxidation by cytochrome P450 are reported. Bilirubin was incubated with yeast microsomal fractions (wild type, recombinant yeast expressing the murine Cyp2a5 or its human orthologue, CYP2A6). The origin of the products from BR was confirmed by comparing oxidation products of mesobilirubin, an analogue of BR. The products of enzymic incubation were also compared to those of the chemical oxidation of BR. The major products found in both enzymic and chemical oxidation system were identical and were as followed: ion A m/z 301; ion B m/z 333; ion D m/z 315 and ion biliverdin m/z 583. Additionally, in a study using recombinant yeast expressing CYP2A6, BR inhibited coumarin 7-hydroxylation (a CYP2A6 catalysed reaction) in a concentration dependent manner with an IC50 of 4.98 μM BR. The inhibitory effects of BR on the rate of coumarin 7-hydroxylation is that of competitive inhibition as BR increased the Km but not the Vmax for CYP2A6-dependent coumarin 7-hydroxylation. The Ki value of BR was found to be 2.82 μM, which is in the same range as the Km for coumarin 7-hydroxylation (2.44 μM). Furthermore, a monoclonal antibody for Cyp2a5 (which cross-reacts with CYP2A6), caused a dose-dependent inhibition of BR degradation activity by about 70 %. These observations suggest the affinity of BR to CYP2A6 is similar to that of coumarin. In a study using DBA/2J mice, a strain with high Cyp2a5 basal activity, evidence was found that shows the induction of HO-1 and Cyp2a5 is an adaptive response to viii arsenite-mediated oxidative stress to protect the liver against lipid peroxidation. Mice treated with a subacute dose of arsenite showed an induction of HO-1 and Cyp2a5 at both mRNA and protein levels in the liver, which was associated with oxidative stress. This response correlated with a decline in total cytochrome P450; a modest elevation in total bilirubin followed by a decrease in lipid peroxidation; and an increase in microsomal BR degradation rate followed by an increase in urinary elimination of BOMs identified in the enzymic incubations with BR. Furthermore, exposure of human liver cells (HepG2) to arsenic resulted in a time dependant induction of CYP2A6 protein and activity levels. This implies a similar adaptive response towards arsenic may also occur in human liver cells. In sum, these observations suggest that (i) both murine Cyp2a5 and human CYP2A6 enzymes oxidise BR to form BOMs; (ii) concurrent induction of HO-1 and Cyp2a5 during arsenic-mediated oxidative stress may protect the liver against lipid peroxidation; and (iii) production of BOMs may be mediated by Cyp2a5 BR oxidation and subsequently eliminated in the urine.

Bioactive secondary metabolites from Australian invertebrates, Indonesian marine sponges, and an Indonesian terrestrial plant

Swasono, Respati Tri. — 2012-09-11T00:00:00Z

Bioactivity Grafting of Cyclic Peptides: Structure Activity Studies of Grafted Cyclotides and SFTI-1

Sunithi Gunasekera — 2009-02-28T00:00:00Z

Peptides are considered as drugs of the future because of their advantageous features of high specificity and low toxicity. However, the complete therapeutic potential of peptides has not yet been realized because of the in vivo instability displayed by most potential peptides. In this thesis, two naturally derived cyclic peptides, cyclotides and sunflower trypsin inhibitor 1 (SFTI-1), were utilized to impart stability to linear bioactive epitopes and enhance their therapeutic potential in a biological environment. Cyclotides are plant derived mini-proteins with compact folded structures and exceptional stability. Their stability derives from a head-to-tail cyclised backbone coupled with a cystine knot arrangement of three-conserved disulfide bonds. Sunflower typsin inhibitor 1 (SFTI-1) is a stable cyclic peptide containing a single disulfide bond. Taking advantage of these stable cyclic peptide frameworks, novel drug leads to inhibit/stimulate angiogenesis were developed by using the approach of ‘epitope grafting’ in which linear epitopes were grafted onto the cyclic peptide frameworks. Angiogenesis is a physiological condition that is unregulated in the progression of many diseases, including cancers and cardiovascular diseases. Thus the drug leads designed in the current project have potential therapeutic applications to combat cancers and cardiovascular diseases. To fully exploit cyclotides as drug scaffolds, it is imperative to understand their folding. Two main subfamilies, referred to as the Möbius and bracelet cyclotides have been identified and interestingly, they require dramatically different in vitro folding conditions to achieve formation of the conserved cyclic cystine knot motif. To determine the underlying structural elements that influence cyclotide folding, the in vitro folding of a suite of hybrid cyclotides based on combination of the Möbius cyclotide kalata B1 and the bracelet cyclotide cycloviolacin O1 was examined in this thesis. The pathways of folding of the two cyclotide subfamilies were found to be different and primarily dictated by specific residues harboured within inter-cysteine loops 2 and 6. Two changes in these loops, an amino acid substitution in loop 2 and an amino acid addition in loop 6 enabled the folding of cycloviolacin O1 under conditions where folding does not occur in vitro for the native peptide. Thus, the study identified key residues that are not in close proximity in the primary sequence or three-dimensional structure which assist folding in cyclotides. A key intermediate species in the folding pathway was isolated and characterised, and found to contain a native-like hairpin structure that appears to be a nucleation locus early in the folding process. The intermediate does not have native disulfide connectivities, but disulfide shuffling processes ultimately lead to a rearrangement to the native form. Overall these mechanistic findings on the folding of cyclotides are potentially valuable for protein engineering applications that utilize cystine-rich peptides as scaffolds in the design of new drug leads. The current study has also enabled the extention of the grafting studies to the bracelet cyclotide subfamily, which was intractable to grafting prior to this work. Cyclotides are gene encoded macrocyclic proteins and another way to exploit their potential as drug scaffolds, would be to develop combinatorial cyclotide libraries. The most efficient way to generate engineered cyclotides would be via recombinant expression, which currently remains unsuccessful, partly due to lack of understanding of the mechanism of cyclotide backbone cyclization. Understanding how the cyclotide precursor folds may provide clues to how cyliclization occurs. A conserved region known as the N-terminal repeat (NTR) region in the cyclotide precursor has been speculated to play an important role in precursor folding. In this thesis, the function of the NTR in the folding of the cyclotide precursor in vitro was examined via the design of a series of constructs for the precursor protein for the prototypic kalata B1 cyclotide, with incremental additions of the NTR region. Analysis of the constructs by NMR spectroscopy for evidence of secondary structure revealed that the NTR does not assist folding of the cyclotide precursor in vitro. Using diffusion NMR, the unstructured nature of the constructs was localized to the NTR region. In a complementary study, structural analysis of the full length cyclotide precursor was carried out by expressing the precursor gene for kalata B1 in a bacterial expression system. The full-length precursor was found to be unstructured in solution despite approximately half of the precursor comprising the mature domain and NTR, both of which are structured in isolation. The unstructured nature of the cyclotide precursor suggested that a different environment, or indeed interaction of the NTR with a particular enzyme involved in processing, is necessary for it to adopt a well-defined conformation and allow processing to produce the mature circular protein. The information that NTR alone may not assist folding of the cyclotide precursors has provided new impetus to examine the role of other potential folding auxiliaries such as protein disulfide isomerase in cyclotide folding and has indirectly advanced the production of cyclotides via transgenic means. In summary, this thesis has provided a fundamental insight into the folding of cyclotides, both when expressed as part of a precursor protein and in isolation via solid phase chemical synthesis, and has exploited the potential of cyclic peptide scaffolds in drug design applications.

Bioassay-guided and computer-aided investigation of marine-derived kinase inhibitors: applications to control neurodegenerative disorders

Plisson, Fabien Gerard Christian — 2012-09-26T00:00:00Z

Bioavailability of carbon in microaggregates formed from clay minerals and metal oxyhydroxides

Jessie Horton — 2012-04-16T00:00:00Z

The sequestration of organic matter (OM) in soil is an important issue in relation to soil health and productivity and the cycling of carbon on a global scale. Commonly up to 80% of OM in soil is associated within the microstructure, defined here as the microaggregates within the soil fraction <100 ìm. Research of this fraction within a soil sample has generally focussed on the extraction of the OM under varying conditions and the nature of the fractions using microscopy. However, little is known about the soil processes that cause the OM to become sequestered in this fraction. A fundamental approach has been used in this research to study the factors that affect the processes of aggregation and the subsequent carbon sequestration in the microstructure of soils, by creating soil microaggregates under controlled laboratory conditions using well characterised minerals. The components used in the preparation of microaggregates included various types of OM (extracted from soil and leaf litter and commercial organic compounds), cations (iron, aluminium and calcium) and soil mineral particles (bentonite and kaolinite) under a range of conditions. A review of the literature suggests that the factors that affect the aggregation processes in these microaggregates might include typical soil conditions (wetting and drying cycles, salts, pH, temperature and time), nature of the soil components, and the sequence of interactions between these components. The impact of these factors on the extent of aggregation and the stability of the aggregates were determined by particle size analysis and sonication respectively. Microaggregates formed from kaolinite were not able to withstand more than one wetting and drying cycle before being dispersed. OM type, sequence of addition, pH, cation type and concentration had minimal impact on microaggregate size, but this may be mostly due to the unstable nature of the aggregates formed from kaolinite. Microaggregates formed from bentonite increased in size and in stability with an increase in the ratio of cation to clay and cation to organic matter. The solution pH did not impact on the size of the aggregates after sonication. Aluminium produced larger aggregates than iron, and iron produced larger aggregates than calcium. Whereas wetting and drying cycle had an impact on aggregate size, OM type did not. The second stage of this research was to quantify the bioavailability of the OM associated within these microaggregates, and hence the quantity of sequestered carbon. This involved the inoculation of the microaggregates with bacteria isolated from natural soil, and monitoring their subsequent respiration using gas chromatography. Carbon sequestration is the removal and long-term storage of carbon dioxide from the atmosphere. Carbon that is sequestered in soil is not bioavailable and hence bioavailability was chosen here as an indirect measure of sequestration. It is also known that the majority of carbon lost from the natural soil environment is due to microbial action. The bentonite aggregates were used in the bioavailability studies because they were larger and more stable than the kaolinite aggregates. Increasing size and stability was assumed to be associated with decreasing bioavailability of the incorporated carbon. Lysine was chosen as the organic substrate because it had a low molecular weight and was readily degradable by soil bacteria. The rate and amount of lysine bioavailable to the bacteria was dependent on the ‘factors’ used to form the bentonite aggregates. For example, microaggregates formed in solution from iron oxyhydroxides (in the absence of bentonite) resulted in the least amount of bioavailable carbon. Microaggregates formed in solution from bentonite, and bentonite/aluminium, and bentonite/iron mixtures, were also found to have significantly less bioavailable carbon than the control. Microaggregates formed in solution from aluminium oxyhydroxides alone did not impact on the amount of bioavailable carbon within the aggregates. This research has improved our understanding of the interaction between clay minerals, metal oxyhydroxides, and organic matter in soil, and how this interaction influences aggregation and carbon sequestration in soil. The knowledge gained and the new methods developed in this research can be further developed and used to improve our fundamental knowledge aggregation and carbon sequestration in soil.

BIOBANKS: PROFESSIONAL, DONOR & PUBLIC PERCEPTIONS OF TISSUE BANKS &THE ETHICAL & LEGAL CHALLENGES OF CONSENT, LINKAGE &THE DISCLOSURE OF RESEARCH RESULTS.

Fleming, Jennifer M. — 2008-07-21T00:00:00Z

Biodegradation of the cyanotoxin cylindrospermopsin

Maree J. Smith — 2007-08-24T00:00:00Z

Biodiversity Conservation and Poverty Alleviation: Factors Influencing their Integration in Cambodia

Kara Scally-irvine — 2011-06-02T00:00:00Z

Aligning conservation objectives with those of poverty alleviation in developing countries has been an elusive goal for the last two – three decades. An approach known as Integrated Conservation and Development Projects (ICDPs) became an extremely popular means to achieve this. Unfortunately, despite considerable enthusiasm, widespread implementation, and financial support the performance of these has been underwhelming. The laudable aspiration of achieving conservation and development together has been questioned. Reviews of ICDPs have identified flaws in previous applications of the concept. General advice on how practical elements of future ICDPs might be modified has been proffered, however there is an absence of substantive suggestions about how the approach should be modified to address the problems it has suffered from. An interdisciplinary divide between conservation and related disciplines also hinders the cross-fertilisation of ideas and insights. Using Cambodia as a case study, the conundrum of integrating conservation and development was re-examined using a research approach addressing deficiencies identified in the literature. A holistic perspective using a mixture of methods to maximise opportunities for new insights was adopted. The objective was to identify factors that influence conservation and development and their integration in Cambodia, to compare these with factors already identified in the literature, and draw conclusions that can be applied to integrated conservation and development (ICD) in general. A systems view, which acknowledges that real world problems are non-linear and complex, was adopted. Soft Systems Methodology (SSM) was used to structure the research, which followed two streams of inquiry. The first ‘cultural’ stream used grounded theory: a qualitative approach that identifies core issues via an emergent analytical process that avoids preconception and forcing of data. The second ‘logic’ stream used Bayesian Belief Networks (BBN) to quantitatively model the situation in Cambodia to explore its dynamics and reveal leverage points where positive changes could be made. A pluralist paradigm permitted this combination of quantitative and qualitative methods. The grounded theory analysis revealed a triad of central concepts; Engagement, Power and Control, with Engagement the most important. Engagement comprised four sub-categories; Capacity, Benefits, Time and Conceptual Buy-In, with Conceptual Buy-In emerging as the richest. The analysis confirmed many concepts such as building capacity and benefits that are typically discussed in relation to ICD. However a number of other critical issues, which receive much less attention, emerged during analysis, suggesting there are gaps in knowledge of ways to improve ICD. These primarily related to social and political processes (social capital), and highlighted the role trust and power dynamics play. Linkages were made to ‘resilience’ theory to suggest ways the socio-ecological systems that dictate ICD may be optimised to improve outcomes. BBN modelling suggested that in Cambodia, biodiversity conservation and poverty alleviation are complementary and compatible goals. This contrasts more pessimistic conclusions sometimes found in the conservation literature. The presence or absence of non-governmental organisations was found to be an extremely influential factor determining the success of conservation and poverty alleviation initiatives, which has a number of practical implications. The model also suggested reducing dependence on natural resources by introducing medium and high value alternatives was one way in which conservation and development goals can be achieved simultaneously, as was reducing natural resource damage by minimising areas under concession. Building capacity, offering appropriate benefits and continuing to build awareness were reinforced as valuable objectives. Although the BBN model provided an adequate representation of the situation in Cambodia, the role political forces play and the social forces identified as critically important in the grounded theory analysis were conspicuously absent. Overall, BBNs are well suited to examining concrete and quantifiable factors but failed to capture other more abstract concepts that are not easily translated into quantifiable measures. This highlights the value of adopting a broad multimethodological approach in progressing ICD theory and practice. This research makes contributions to improving the integration of conservation and development in several ways. First, adopting a multimethodological approach in general, and including qualitative analysis in particular, to identify issues that influence the success of ICD is valuable. Second, the fundamental role social and political processes play were highlighted. If ICDPs are aware of, address, and support the effective functioning of these in their activities projects and programmes, sustainable and robust interventions are more likely. Third, practical recommendations can be derived from the analytical products of this work. This research suggests there is hope for achieving integrated conservation and development, but changes in perspective and approach are necessary. The disciplinary divide must be crossed if conservation is to effectively tackle the social and political forces that dictate the context in which it operates, and which play a central role in determining its success. Failure to do so will mean the conservation community may miss what is in front of them, due to artefacts of quantitative approaches that dominate its science-based tool box.

BIOELECTRICAL IMPEDANCE ANALYSIS OF MUSCLE FUNCTION AND ACTIVITY: (BIODYNAMIC ANALYSIS)

William Mccullagh — 2009-10-23T00:00:00Z

Abstract There is a need in medicine and research for noninvasive, painless, safe and simple bed-side techniques to measure physiological processes associated with muscle function and activity. Bioelectrical Impedance Analysis (BIA) is a widely used, noninvasive, painless, safe and simple procedure for the measurement of body composition. However, although capable of producing accurate and reproducible data, it is known to be prone to movement artifacts. This poses the interesting question “Could impedance changes be used to monitor movement and, consequently, be related to muscle function or activity?” This project investigated the utility of impedance change as a monitoring technique for physiological processes that involve movement such as muscular contraction, the calf muscle pump, and swallowing. The impedance of leg muscle segments during locomotion, whilst riding a stationary exercise cycle, was measured at discrete frequencies and by bioimpedance spectroscopy to monitor muscle function or activity. Impedance traces were compared to information obtained by electromyography (EMG). Impedance, at a discrete frequency, was able to measure the cadence of cycling and its magnitude was related to the position of the pedal during the pedal cycle. When the cycling action was measured by bioimpedance spectroscopy, R0 and Zc showed a statistically significant difference, (p<0.05), between all angles of the pedal crank cycle while R∞ showed a statistically significant difference between angles in the lower hemisphere of the pedal crank cycle. The cyclical changes in impedance during cycling may be attributed to changes in shape and volume of the muscle during contraction as well as a volume change due to blood and lymph being pumped from the limb by the action of the calf muscle pump. Based on procedures used in the cycling studies, an impedance-based method for the measurement of calf muscle pump function during an exercise protocol, originally designed for use with air plethysmography, was developed. It was shown that impedance measured at 5 kHz provides a simple, non-invasive method for the measurement of the ejection fraction and ejection volume of the calf muscle pump as well as other haemodynamic variables. The impedance-based method was less technically challenging than accepted volumetric methods, such as air plethysmography and strain gauge plethysmography, and non-invasive c.f. ambulatory venous pressure, enabling it to be used repeatedly. Muscle function and activity is not confined to the legs so impedance changes in the arm and forearm during exercise were measured. Impedance measurements, at discrete frequencies and using bioimpedance spectroscopy, of the forearm during contractions of the hand were able to distinguish the difference between a ramp and a pulse contraction. When the impedance of the arm and forearm were plotted against the angle of the forearm to the horizontal during a bicep curl, there was an hysteresis effect. Impedance traces of a bicep curl were compared to an EMG trace of the same action. The larynx is a hollow muscular organ situated in the front of the neck above the trachea consisting of a framework of cartilages bound together by muscles and ligaments. The two major functions of the larynx are deglutition and phonation. Dysphagia, which is becoming more prevalent as the population ages, is defined as difficulty in swallowing thin liquids such as water or juices which splash into the trachea because the patient is unable to control the thin liquid bolus. Aspiration pneumonia and dehydration can be prevented by using thickened liquids which allow patients to achieve a safer swallowing response, but it is difficult to assess this response without interfering with the swallowing process. Impedance pharynography (IPG) is a technique using BIA to monitor an impedance waveform of the swallowing process that presents no radiation hazard to the patient, is non-invasive and does not require specialist trained personnel to operate it. Resistance changes across the neck were measured while subjects swallowed solutions of different viscosities. The resistance changes were distinctive and reproducible for each of the solutions of different viscosities which were swallowed. Measuring the function of the larynx by this method could be useful in the diagnosis and treatment of dysphagia. In conclusion, the studies described in this thesis demonstrate the potential usefulness of the measurement of change in impedance as a measure of muscle activity. Impedance-based methods can measure volume changes associated with changes in cross-sectional area of the muscles involved in contraction as well as compartmental fluid changes caused by the force of the contraction on the surrounding tissues including the vasculature. In particular, measuring the ejection fraction and other haemodynamic variables of the calf muscle pump by impedance has the potential to become the method of choice in the future because it is easy to use, inexpensive, non-invasive, safe, and hygenic. Measuring resistance changes across the neck during swallowing yields distinctive waveforms with features corresponding to the physiological phases of the swallowing process as well as identifying distinctive swallowing patterns associated with the different viscosities of liquids swallowed. Function of the larynx and the associated diseases of the larynx will potentially be easier to diagnose and treat with a safe, non-invasive, inexpensive, portable bed-side method of assessment such as BIA.

Biogeography and variation of Cynopterus brachyotis in Southeast Asia

Abdullah, Mohd Tajuddin — 2007-08-24T00:00:00Z

Biogeography of avifauna and patterns of variation in the little spiderhunter (Arachnothera longirostra) in Southeast Asia

Mustafa Abdul Rahman — 2007-08-24T17:47:33Z

Bioinformatic identification of functional noncoding elements and expressed noncoding RNAs

Chol Hee Jung — 2010-09-22T00:00:00Z

The majority of the genome in multicellular organisms is composed of non-protein-coding (noncoding) sequences, the amount of which increases with developmental complexity. This observation and other evidence support the contention that these noncoding regions house numerous functional sequence elements including cis-acting protein-binding sites and regulatory noncoding RNAs (ncRNAs), many of which are conserved. Over recent years, the number of identified ncRNA genes has increased. Indeed, it is likely that higher eukaryotes produce a comparable if not greater number of ncRNAs than protein-coding mRNAs. All annotated conserved regions of the genome are associated with functional elements and transcripts, but most are unannotated, suggesting that many more of these elements remain to be identified. On this basis, I analyzed both conserved noncoding regions and sequenced fragments of expressed ncRNAs of the genomically and transcriptomically well-characterized model organism Drosophila melanogaster to identify potentially functional sequence elements and ncRNAs. The first approach was based upon a search for over-represented sequence motifs, on the hypothesis that different classes of regulatory RNAs or cis-acting regulatory sequences might possess core sequence motifs, such as those found in small nucleolar RNAs (snoRNAs), which may be used to parse these sequences and identify new subclasses. The conserved noncoding regions of D. melanogaster were searched for over-represented tetranucleotide pairs (which best covers the possibilities while being computationally tractable) separated by certain distances up to 100 bp apart (termed 'pattern-cores'). Among over 17,000 over-represented pattern-cores, 473 showed the highest information content in their surrounding sequences and were extended using the program MEME into longer motifs defined by position-specific scoring matrices (PSSMs). These motifs were then classified into 23 groups based on their similarity. The whole genome was scanned for genomic sites of the motifs with certain threshold values that effectively separated true from false positives. The results identified five groups of known functional elements: a subset of tRNAs, motifs immediately downstream of Histone genes, and three types of protein-binding sites, including one recognized by the chromatin insulator protein Su(Hw). Two novel groups with large numbers of instances, DLM3 and DLM4, were investigated in more detail and showed strong evidence for functional potential including their abundance in the genome, conservation across other (and only within) Drosophilae, location in specific genomic regions (DLM3), strong predicted RNA folding energy (DLM4) and positive signals in Northern hybridization analysis (DLM4). Motifs in some other groups also showed functional potential such as enrichment in promoter regions of genes with specific categories of biological processes or genomic loci covered by short RNA sequence data. These findings suggest that there may be many more such motifs, especially lineage-specific motifs, to be discovered in other genomes by these strategies. The second approach employed an empirical analysis of short-read high density RNA sequencing data. Published datasets of short RNA sequences from D. melanogaster were combined and used to assemble tag-contigs. Tag-contigs identified most known small ncRNAs (such as tRNAs, snRNAs and snoRNAs), and showed distinctive characteristics associated with different classes of small ncRNAs. By using these characteristics in conjunction with the typical sequence motifs of snoRNAs, 7 novel box H/ACA and 26 box C/D snoRNAs were identified. In addition, one novel snRNA and hundreds of putative ncRNAs candidates of uncharacterized classes were predicted, 15 out of 21 of which showed corresponding signals in subsequent Northern hybridization analysis. The combined use of small RNA sequence data from various tissues also successfully inferred the expression profiles of the putative ncRNA candidates. This approach was then extended to the nematode Caenorhabditis elegans to identify hundreds of putative ncRNAs with specific expression profiles. The pattern-core approach accurately identified over-represented sequence motifs and can be modified to accommodate different gap-sizes between two tetranucleotides or to alter the size of co-dependent two short sequence elements. The tag-contig approach is a simple yet effective way to gather preliminary candidates of novel noncoding RNAs, but it (as yet) only skims the surface of the great complexity of small RNA species. Moreover, excessive accumulation of sequence data can cause ambiguity in 5' / 3' cleavage sites of the candidates. Thus, additional computational and data-driven analyses need to be developed for better prediction, identification and understanding of ncRNAs. Additionally, since some species of small noncoding RNAs can be defined by distinctive sequence features within them, applying the pattern-core approach to the tag-contig data would be one way to better classify putative noncoding RNAs.

Biological Activities of Plant Extracts and Essential Oils against Helicoverpa armigera

Hidayat, Yusup — 2008-11-21T00:00:00Z

Hexane, benzene, chloroform and methanol extracts of Ajuga australis, Lantana camara and Tithonia diversifolia, and the essential oils of Backhousia citriodora, Melaleuca alternifolia and Melaleuca quinquenervia were investigated for their biological activities against the cotton bollworm, Helicoverpa armigera Hubner. Most noticeable was the antifeedant effect of most of the plant extracts tested on H armigera. Based on the results of the choice feeding assays, the most effective extracts of each plant were hexane for A. australis (AIso=13.5 ~g/cm2), benzene for T diversifolia (AIso=43.5 ~g/cm2) and benzene for L. camara (AIso=99.7 ~g/cm2). For the three essential oils tested, only the essential oil of B. citriodora showed an antifeedant effect (Also choice test = 282.4 ~g/cm2). Among all plant extracts and essential oils investigated in this study, the hexane extract ofA. australis was the most potent antifeedant. None of the plant extracts tested significantly affected the survival of H armigera in either feeding or contact assays. Generally, ingesting plant extracts for 12-15 hours in a no-choice feeding assay had no significant effects on the growth and development of H armigera. Exceptions were the hexane and chloroform extracts of A. australis and the chloroform extract of L. camara, which slightly lengthened the larval development time, and the hexane extract ofL. camara which slightly reduced the pupal weight. Unlike the plant extracts, or the essential oils of M alternifolia and M. quinquenervia, the essential oil of B. citriodora had an effect on the survival ofH armigera. In a contact assay at the highest dose (200 ~g/larvae), this essential oil killed 33.3 % of the larvae tested after 48 hours. In a no-choice feeding assay, also at the highest dose (500 ~g/cm2), the essential oil of B. citriodora had no significant effect on larval survival, but heavily influenced the later development stages of the insect where more abnormal pupae were formed, and not a single adult emerged. Although it is without toxic effect, the Australian native plant, A. australis is considered to have the most potential for insect control. Its strong antifeedant effect at a low dose on H armigera may have a significant potential role in the implementation of an Integrated Pest Management (IPM) program for this insect.

Biological and physicochemical properties of tobacco streak virus

Sdoodee, Ratana. — 2012-05-15T00:00:00Z

Biological effects of backyard feeding the Australian magpie (Gymnorhina tibicen) in south-east Queensland

Ishigame, Go. — 2012-02-13T00:00:00Z

Biological filtration processes for the removal of the cyanobacterial toxin, cylindrospermopsin

Wijesundara, Shiromani Wasantha Kumari — 2008-07-10T00:00:00Z

Biologically-based insecticides for mosquito control and environmental conservation in south-east Queensland

Russell, Tanya Louise — 2008-11-21T00:00:00Z

Mosquitoes transmit a range of pathogens, such as malaria protozoans, dengue, Ross River and Barmah Forest viruses. Human infection with any of these pathogens may lead to the onset of debilitating disease, and due to limited vaccine availability, mosquito control is essential to interrupt the transmission of disease. During control operations, the larvae are targeted and there are two classes of biologically-based insecticides available: microbials (Bacillus thuringiensis var. israelensis de Barjac [Bti] and Bacillus sphaericus Neide [Bs]) and insect growth regulators (s-methoprene and pyriproxyfen). The aims of this thesis were to: 1) undertake specific research to enhance mosquito control operations; and 2) evaluate the ecological impacts of insecticide use in saltmarsh habitats. Initially, the efficacy of new formulations of biologically-based insecticides were investigated in the laboratory. Bioassays were conducted using third-instars of six common Australian mosquito species, Aedes aegypti (Linnaeus), Aedes vigilax (Skuse), Aedes notoscriptus (Skuse), Culex sitiens Wiedemann, Culex annulirostris Skuse and Culex quinquefasciatus Say. The normal model for log-linear mortality was used to determine LC50 and LC95 values. The newly developed VectoBac WG (3,000 Bti International Toxic Units [ITU]/mg) was highly effective against the range of larvae, contrasting with the unregistered insect growth regulator, pyriproxyfen, which was not effective against some species. Sequentially, the efficacy of Bti formulations was assessed in the field. Larvae were exposed to Bti as free-swimming larvae and in mesh cages, and mortality was calculated after 48 h to examine appropriate sampling techniques. The accuracy of sampling free-swimming larvae with 250-ml ‘dips’ was highly variable, where monitoring mortality of caged larvae was highly accurate; this information was used to design the sequential field trials. In freshwater pools, replicated cohorts of caged Cx. annulirostris were exposed to the water dispersible (VectoBac WG) and liquid (VectoBac 12AS: 1,200 Bti ITU/mg) formulations. Treatment concentrations of 0.008 ppm VectoBac WG and 0.04 ppm VectoBac 12AS and above produced significant larval control (>96% mortality) at 48 h, with no residual control after 1 week. In saltmarsh pools, cohorts of caged Ae. vigilax were exposed to the granular (VectoBac G: 200 Bti ITU/mg) formulation; which was effective (>99% mortality) at application rates of 4 kg/ha and above at 48 h. Next, the distribution of the granular (VectoBac G) formulation was assessed after an aerial treatment using catch-trays. The accuracy of the catch-trays was defined using mathematical models. Specifically, the analysis revealed that the size of catch-trays can affect the interpretation of results, especially if smaller than 2 m². The mass of product captured in 1 m² catch-trays, due to random sampling processes alone, would be expected to range between the equivalent of 2.9 to 7.8 kg/ha for 95% of replicates when targeting 5 kg/ha. During the field trial, 1 m² catch-trays were used, this catch-tray size was selected as it was the nominated size used by contractors for quality assurance of aerial granular applications. The average flight lane separation of the rotary-wing aircraft was 14.70 m (SD: ± 4.52 m) and the average treatment rate was 5.76 kg/ha (SD: ± 3.46 kg/ha; CV = 60%). This was close to the targeted lane separation of 14 m and treatment rate of 5 kg/ha. However, the product was not distributed evenly. Nonetheless, there was 100% mortality of third-instar Ae. vigilax that were exposed to the treatment in mesh cages. The most important factors that affected the observed spatial distribution of product were the uneven flight path of the helicopter and the low sensitivity of the small catch-trays. Despite the fact that Bti and s-methoprene are considered to be among the most target specific of insecticides, there are indications that non-target organisms may be impacted in different ecosystems. In response, changes in the density and diversity of non-target communities, after application of either Bti or s-methoprene, were examined. The main taxa collected from ephemeral pools were Copepoda; and from terrestrial plots were Collembola, Coleoptera, Heteroptera, Hymenoptera and Diptera. Applications of both products altered the community composition; however, differences were not consistent over the two localities. After applications of Bti to ephemeral pools, lower numbers of Copepoda were recorded at only one location. No differences were recorded after treatments of s-methoprene to ephemeral pools. After applications of s-methoprene to terrestrial plots, higher numbers of Acariformes were recorded at both localities, and this was also recorded after application of Bti to one of the locations. However, these differences were not spatially and temporally consistent or in agreement with predictions. The results of these trials suggest that applications of Bti and smethoprene will not impact on the long-term structure and composition of arthropod assemblages in saltmarshes. Authors of previous studies from the northern hemisphere had indicated that s-methoprene was more broadly toxic to non-target organisms than Bti; however, this is not true in Australia. The results of this thesis found that Bti can be used to effectively control mosquito immatures under different field conditions. Applications of Bti and s-methoprene did not decrease the diversity or abundance of non-target arthropods in south-east Queensland. As such, future applications of Bti and s-methoprene are supported in preference to organophosphate alternatives; this is based on a comparison with previously published literature that has demonstrated organophosphate insecticides to be directly toxic to non-target arthropods. Considering that the appropriate use of Bti and s-methoprene can reduce the incidence of arbovirus transmission among the local human population, the future application of these products is supported. The use of insecticides should be integrated with public education, biological control, physical habitat modification and early detection systems.

Biologically inspired vision for autonomous vehicle guidance

Fernandes, Joshua Leslie Noel — 2012-09-11T00:00:00Z

Biological markers of renal transplant rejection in humans

Armitage, Michael Shane. — 2011-05-18T00:00:00Z

Biological Nutrient Removal for High Strength Wastewater Using Combined Anaerobic Ponds and Sequencing Batch Reactor: Feasibility Study

Mr Kanthavanam Subramaniam — 2008-10-10T00:00:00Z

Biological Processes for Dissolved Organic Carbon Removal

Christopher Pipe-martin — 2011-11-04T00:00:00Z

Biological water treatment has the potential to be a readily available, robust, effective and low energy intensity treatment technology. This report investigates the application of biological treatment processes for the removal of remaining organic compounds from a domestic wastewater treatment plant effluent. Biologically activated carbon (BAC) was found to be the preferred media for biological filtration, with removal of dissolved organic compounds by activated carbon being more than three times higher than in comparable sand filters. A two-stage sand-BAC filter was effective in achieving high DOC removal and had advantages during filter cleaning, as well as being compatible with the preferred configuration of the large slow rate filters required for high DOC removal. Methods for enhancing the filtration process were investigated. Pretreatment with alum coagulation and Dissolved Air Flotation/Filtration removed up to 40% of DOC and achieved excellent solids removal, leading to stable biological activity in BAC filters over long periods with surface skimming as the only maintenance and without the need for backwashing . Ozonation increased the DOC removal by BAC filtration. The DOC removal by BAC at low flow rates without ozonation exceeded that for ozone/BAC treatment at typical (higher) flow rates, meaning that the use of ozone may not be necessary to significantly reduce DOC in all cases. In the absence of ozonation, aeration was essential to achieve high DOC removal as the oxygen consumption in the filters was very high. It was found that longer contact times than are typically used for BAC filtration are required for high DOC removal, although the contact time is dependent on the level of pretreatment. Longer treatment time implies larger filter sizes, and a bigger footprint for the treatment plant. This increase in size and cost can be offset by the fact that equipment for ozone treatment may not be required. Coagulation/filtration removed 40% of DOC from secondary treated effluent, BAC filtration removed a further 22% with an EBCT of 140±30 minutes to give a total DOC reduction of 62%. Ozone/BAC treatment was able to achieve a 30% reduction (relative to influent) of the DOC remaining after coagulation/ filtration at an EBCT of 140±30 minutes to give a total DOC reduction of 70%. The effectiveness of biological treatment on the different components of the DOC was also explored. Very hydrophobic and slightly hydrophobic acids combined made up about 80% of the identified DOC fractions in the feed water, and also after alum pretreatment. BAC filters were able to remove 40% of this fraction, while ozone/BAC treatment removed over 50%. There was some variability in the effectiveness of BAC (with or without ozone) for removing hydrophilic compounds. It was also found that BAC, with or without ozone, was able to remove a wide range of pharmaceutical compounds and other micropollutants to below detection limits, with the two exceptions of caffeine and the pharmaceutical gabapentin, which were more than 90% removed in both treatment trains. The toxicity of the BAC treated water (again with or without ozone pretreatment) was significantly lower than that of the feedstock, and was comparable with that of pure water used as blank control. As measured by IC50, the toxicity was reduced to approximately 30% of that of the feed water. The estrogenic effect after treatment, with or without ozone, was below the detection limit. Slow flow BAC treatment appears to be an extremely effective means of removing micropollutants from water, even without the ozone pretreatment. The use of the UV Excitation Emission Matrix (EEM) technique as a rapid method for evaluating DOC removal was explored. It proved to be a useful analytical tool, able to distinguish the proportion of the different fractions such as neutral hydrophilic compounds, charged hydrophilic compounds and hydrophobic compounds (in combination with resin treatments) as well as the total residual DOC after treatment.

Biology and bionomics of the biting midge Culicoides subimmaculatus Lee and Reye (Diptera: Ceratopogonidae) and other coastal Culicoides in Southeast Queensland

Edwards, Penelope Bronwyn — 2012-04-30T00:00:00Z

BIOLOGY AND CONTROL OF VERRALLINA FUNEREA (DIPTERA: CULICIDAE)

Jeffery, Jason Andrew Loh — 2008-11-21T00:00:00Z

Verrallina funerea (Theobald) is a brackish water mosquito species common in the north eastern coastal regions of Australia. It is a recognised pest species and has been implicated in the transmission cycles of Australias two most common arboviruses, Ross River virus (RRV) and Barmah Forest virus (BFV). The aims of this study were to investigate aspects of the biology and ecology of Ve. funerea as a prerequisite to designing more appropriate control strategies against this species. To prioritise the control of Ve. funerea, the vector competence of this species for BFV and RRV was investigated. Experiments were performed on laboratory-reared Ve. funerea to evaluate the susceptibility of this species to the BF1611 strain of BFV. Verrallina funerea were found to be moderately susceptible to infection, with an ID50 of 103.6 CCID50 (Vero) per mosquito. Virus was detected in 5% of salivary glands only 2 days (d) after infection: however, maximum salivary gland infection (65%) was not observed until 8 d after infection. Transmission to mice was demonstrated, with 52% of mosquitoes transmitting 9􀀐12 d after infection. Vector competence experiments were also carried out with laboratory-reared Ve. funerea and the B94/20 strain of RRV. Virus was detected in 10% of salivary glands only 2 d after infection: maximum salivary gland infection (50%) was not observed until 10 d after infection. To determine whether the susceptibility of Ve. funerea to BFV and RRV was consistent between populations of this species across southeast Queensland (Qld) and northern New South Wales, adult mosquitoes were trapped from across that region on the same night and fed the same blood/virus (either BFV or RRV) mixture. No statistically significant variations in whole body, disseminated and salivary gland infection rates were detected for either virus. Using wing length as an indicator of adult body size, there was no apparent association between smaller mosquitoes and their ability to become infected. To assess whether the results of experiments using Ve. funerea from southeast Qld would be applicable to other populations of Ve. funerea throughout Australia, the genetic population structure of this species was investigated. Sequence analyses were performed on sections of the cytochrome oxidase I (COI) and internal transcribed spacer 2 (ITS2) genes from individuals collected from localities representative of the distribution of Ve. funerea in Australia. Verrallina funerea populations were relatively genetically consistent. No ITS2 variation was found. For COI, only 12 haplotypes were identified from 94 individuals. Haplotype 1 was found at all locations, and represented the most common haplotype, being present in more than 73% of individuals at all localities. There was some indication of isolation by distance based on significant Fst values and Mantel regressions. These significant values were between the Darwin/Cairns and the Ballina/Russell Island groups of populations, which represent the extremes of the distribution of Ve. funerea in Australia. Therefore, although Ve. funerea has a relatively genetically consistent population structure in Australia, there is some evidence of the beginnings of a cline in variation between populations at the extremes of its distribution. Since insecticides need to be applied when mosquito immatures are at their most susceptible stage, immature development time and survival of Ve. funerea was defined in the laboratory. This was done in response to a range of temperatures (17􀀐34oC) and salinities (0􀀐35 parts per thousand [ppt]). The expression of autogeny in this species was also assessed. Salinity only had a slight effect on mean development time from hatching to adult emergence (7.0􀀐7.4 d at salinities of 0, 17.5 and 31.5 ppt) and survival was uniformly high (97.5􀀐99.0%). Mean development times were shorter at 26, 29, and 32oC (7.0, 6.8, and 6.8 d, respectively) and longest at 17oC (12.2 d). The threshold temperature (t) was 5.8oC and the thermal constant (K) was 142.9 degree-days above t. Survival to adulthood decreased from greater than 95% (at 17􀀐29oC) to 78% (at 32oC) and 0% (at 34oC). No expression of autogeny was observed. Immature development times of Ve. funerea, Aedes vigilax (Skuse) and Aedes procax (Skuse) were then determined under field conditions at Maroochy Shire. Following tidal and rain inundation, cohorts of newly hatched larvae were monitored daily by dipping, and time until pupation was noted. Tidal inundation triggered hatching of Ve. funerea and Ae. vigilax larvae whereas Ae. procax larvae were found only after rain inundation. Estimates of Ve. funerea and Ae. vigilax field development times were similar (8􀀐9 d) while Ae. procax development time was slightly longer (9􀀐10 d). Mean salinities of pools containing Ve. funerea and Ae. vigilax ranged from 17 to 28 ppt and 10 to 28 ppt, respectively. Mean salinities for Ae. procax positive pools ranged from 9 to 21 ppt. The efficacy of various registered and novel insecticides against Ve. funerea was then assessed using laboratory dose-response assays. Verrallina funerea was highly susceptible to Abate 100E (temephos), VectoBac 12AS (Bacillus thuringiensis var. israelensis), Altosid Liquid Larvicide (s-methoprene) and technical grade pyriproxyfen, but was highly refractory to VectoLex WG (Bacillus sphaericus). The survival of adults exposed as larvae to sub-lethal doses of ALL was reduced for those doses greater than the EI50, although sex ratios were unaffected. The efficacy of VectoBac 12AS was observed to increase in higher salinities whereas the efficacy of ALL decreased. Following these laboratory assays, small-plot field trials using caged larvae in saline water pools demonstrated that Ve. funerea was susceptible to VectoBac G at 7 kg/ha and Altosand at 4 kg/ha, with these products giving greater than 99 and 98% control, respectively. A significant increase in immature mortality in Altosand treated pools was observed, suggesting that s-methoprene field trials based solely on emergence inhibition of pupae may underestimate the efficacy of this insecticide. The results presented in this thesis provide evidence that Ve. funerea is a vector of BFV, and confirms and further elucidates its role as a vector of RRV. Based on moderate susceptibility to experimental infection with these viruses, this species is likely to be an amplification vector of both viruses during epidemics. Because of its genetic structure, this is most likely applicable to all populations of Ve. funerea throughout Australia. This study provides justification for prioritising the control of Ve. funerea in areas where it is abundant. Although Altosand and VectoBac G were shown to be effective in small-plot field trials, the potential effectiveness of sustained-release formulations and the ability of these products to penetrate the Casuarina canopy that covers Ve. funerea habitats should be evaluated.

Biology and Population Ecology of Manta Birostris in Southern Mozambique

Andrea Denise Marshall — 2009-01-16T00:00:00Z

Despite being the world’s largest batoid fish, manta rays have been the focus of very little research in the last century. Almost nothing is currently known about their ecology or distribution throughout the world’s oceans. Manta rays are considered to be near-threatened to vulnerable by the World Conservation Union’s Redlist of endangered species, yet many populations still face threats from target fishing for their fin cartilage, branchial filaments and meat. The taxonomic history of the genus Manta has been questionable and convoluted,with Manta having one of the most extensive generic and species synonymies of any living genus of cartilaginous fish. Currently this genus is considered to be monotypicwith a single recognized species, Manta birostris. Behavioural and morphological data collected during this study showed that there are two distinct, sympatric species of manta ray in Mozambique. This discovery has led to an examination of manta ray distribution worldwide, with the two species hypothesis receiving further support from study sites in the Indian and Pacific Oceans. This thesis examined large populations of both putative species in Mozambique. Development and application of a photographic-identification methodology allowed identification of individuals based on their unique ventral surface markings (spots). The ability to recognise individuals enabled many aspects of both populations to be examined. A total of 449 individual rays were identified of Manta birostris variant A and 101 individual rays were identified of Manta birostris variant B. Both populations exhibited a highly significant female bias in observed sex ratios of 1:3.5 and 1:7.4 respectively. The photographic identification approach was used in studies of population size and structure and to examine the reproductive ecology of these two distinct populations. Population estimates incorporating four years of re-sighting data on Manta birostris variant A and five years of data on Manta birostris variant B were conducted using the program MARK resulting in super population estimates of 890 and 600 individuals respectively. The region encompassing the study site was identified as a mating ground for Manta birostris variant A based on observations of mating events and fresh pectoral fin tip scars on female rays produced when the male rays bite onto the fins during copulation. The distribution of scars was highly biased, with 99% on the left pectoral fin, indicative of a strong lateralised behavioural trait in this species. No other elasmobranch has been reported to display behavioural lateralisation. The study region also acts as a birthing ground, with individuals giving birth in the summer after a gestation period of approximately one year. Reproductive periodicity in M. birostris variant A was most commonly biennial, but a few individuals were seen to be pregnant in consecutive years, confirming an annual ovulatory cycle. The production of a single pup appears to be the normal situation, although observations in the wild as well as during opportunistic dissections of individuals killed in fisheries revealed that two pups are conceived on occasion. Morphometric analysis of late-term foetus (M. birostris variant A) was contrasted with measurements taken from adult rays. These are the only detailed measurements on M. birostris variant A from the western Indian Ocean. Predatory scarring and bite injuries on individuals of both variant A and B were consistent with attacks from sharks of various sizes. The frequency and effect of these predatory injuries on the two populations were examined over a three-year period. Acoustic tags were attached to fourteen rays and their presence/absence at sites around the major inshore reefs was explored to evaluate how the rays utilised their environment on a temporal scale. Cleaning activity of both putative species of manta rays by small fishes occurred on these reefs and was considered to be the main reason why the rays were present at these sites. Parasite removal and wound healing were implicated as the benefits received. Host cleaner fish species partition the manta ray body to avoid interspecific competition while the two putative species appear to partition cleaning habitats, with very little overlap apparent. This research on manta rays is the first of its kind in African waters. Many aspects of the study have contributed to the limited baseline data currently available for this genus. The study additionally provided sufficient empirical evidence to warrant the separation of these two putative species of Manta and a full revision of the genus with the systematic examination of specimens throughout Manta’s range. The results of this study may be useful in this endeavour as diagnostic characteristics have been isolated that may help to differentiate members of this genus. The results of this research study are directly applicable to management strategies for both putative species of manta rays off the East Coast of Africa as well as populations worldwide and have highlighted the potential need for different conservation strategies

Biology, demography and conservation of rays in Moreton Bay, Queensland, Australia.

Simon Pierce — 2009-05-12T00:00:00Z

Thirteen elasmobranch species were collected during a four year seine-net survey of the intertidal margins of Moreton Bay, a large subtropical embayment in southeast Queensland, Australia. The inshore elasmobranch fauna of Moreton Bay is relatively species rich in comparison to sites elsewhere in Australia, emphasising the regional importance of this ecosystem. Stingrays were the most common large predators in the intertidal, with overall catches dominated numerically by the blue-spotted maskray Neotrygon kuhlii (53.8%) and the estuary stingray Dasyatis fluviorum (22.2%). The biological and demographic characteristics of these two species were examined in detail. Neotrygon kuhlii ranged in size from 11.5 – 46.5 cm disc width (WD), with 50% maturity in females at 31.4 cm WD and 6.32 years old and at 29.4 cm WD and 3.95 years in males. Neotrygon kuhlii has a synchronous annual reproductive cycle, producing one litter of 1 – 3 pups (mean of 1.67 ± 0.71 S.D.) in the late Austral summer after a four month gestation. Maximum age estimates of 13 and 10 years were obtained from females and male N. kuhlii, respectively. Annual band pair deposition was confirmed through the recapture of four wild calcein-injected individuals from 22.7 to 30.2 cm WD. A three parameter power function provided the best statistical fit to age-at-size data for both sexes, providing parameter estimates of y0 = 163.13, a = 58.52 and b = 0.58 for females and y0 = 165.13, a = 59.02 and b = 0.54 in males. Individual growth rates obtained from tagged specimens were not qualitatively different to modelled growth predictions. Tagging studies produced a total recapture rate of 16.1%, with individual rays at liberty for up to 1081 days. Direct estimates of instantaneous mortality for N. kuhlii were derived by creating catch curves for both sexes from age-frequency keys. Mortality was estimated at 0.171 ± 0.024.yr-1 S.E. in females, corresponding with a population growth rate of 1.00.yr-1 based on deterministic matrix demographic model predictions, and 0.345 ± 0.022.yr-1 S.E. in males. Seven age-independent and two age-dependent indirect mortality estimates produced negative population growth rates of 0.84 to 0.98.yr-1. Elasticity results were relatively robust to mortality estimates, with juvenile survivorship contributing 74-75% of total elasticity under all scenarios. Dasyatis fluviorum is endemic to near-shore, estuarine and riverine habitats along the eastern coast of Australia. Previous records of the species from northern Australia and New Guinea appear to be misidentifications of other, similar species. Dasyatis fluviorum was caught at 15.5 cm to 76.2 cm WD in Moreton Bay, with 50% maturity occurring at 63 cm WD (13.40 years) in females and 41.2 cm WD (6.97 years) in males. Maximum age estimates of 21 and 16 years were obtained from females and males, respectively. The Gompertz growth function provided the best fit to estimated age data in female D. fluviorum, providing parameter estimates of WD∞ = 100.3 cm, k = 0.09.yr-1 and t0 = 5.66. The modified two-parameter von Bertalanffy growth function provided the best fit to male size-at-age data, providing parameter estimates of WD∞ = 73.4 cm, k = 0.10.yr-1 and b = 0.86. An annual reproductive cycle in female D. fluviorum was hypothesised based on preliminary reproductive data. Fecundity estimates were derived from the related D. americana for input into deterministic and stochastic demographic models. Six out of nine indirect mortality estimates produced positive population growth in deterministic models, with a probabilistic estimate of 1.02.yr-1. Elasticity results were robust to model structure, mortality and fecundity estimates, with juvenile survivorship comprising 74-78% of total elasticity under all scenarios. Both N. kuhlii and D. fluviorum provide interesting case studies in elasmobranch conservation. Neotrygon kuhlii is a common bycatch of demersal prawn-trawl fisheries in Australia. Although mandatory turtle exclusion devices (TEDs) exclude most large vertebrates from trawl catches in Australian waters, their benefits in the reduction of smaller elasmobranch bycatch has not been empirically tested. The results of deterministic demographic models show that TEDs can, in principle, mitigate the impacts of trawl fisheries by partially excluding highly-elastic large juvenile age-classes. However, N. kuhlii is the largest of the four Neotrygon species found in Australian waters and bycatch of the three smaller species may be less reduced by current bycatch reduction technologies. Dasyatis fluviorum is affected by a suite of anthropogenic threats in its near-shore and estuarine habitats including commercial and recreational fisheries, habitat modification and pollution. Within Moreton Bay, 10.8% of the surveyed population bore evidence of past interactions with fisheries as evidenced by retained hooks or mutilated tails. Deep-hooking resulted in significant pathological effects including fibrocollagenous scar tissue masses, peritonitis and hepatitis. Stochastic demographic scenarios were created to model the potential effects of low (0.02 yr-1), medium (0.05 yr-1) and high (0.10 yr-1) rates of additive anthropogenic mortality to simulate stage-specific conservation interventions on D. fluviorum. Removing anthropogenic mortality on juvenile age-classes provided the largest benefits in terms of reducing population decline. The probability of the species’ conservation status declining further to Endangered, based on IUCN criteria, ranged from 39% to 100% under these mortality scenarios if no conservation measures were applied.

Biology of Botrytis cinerea infecting waxflower (Chamelaucium) flowers and potential elicitation of host defence in this pathosystem

Son-Quang Dinh — 2009-07-08T00:00:00Z

Waxflower (Chamelaucium spp. and hybrids) is the singlemost important Australian export cut-flower. The major problem in waxflower trading is flower abscission after harvest. While several factors are involved, ethylene production resulting from preharvest infection with the fungus Botrytis cinerea is the most important cause. The general objectives of this study were to investigate the biology of Botrytis infecting waxflower flowers and potential elicitation of host defence against this pathogen. Effects of anti-ethylene and S-carvone treatments on Botrytis-induced flower abscission were also evaluated. Infection of flowers by Botrytis was studied on two waxflower cvs. Mullering Brook and My Sweet Sixteen using light and electron microscopy. Conidial germination and protoappressorial formation occurred within 8 h post-inoculation (hpi). Infection of most floral organs, including petals, anthers and filaments, stigma, and hypanthium, was within 24 hpi. Infection cushions on stamen bases were formed at 36 hpi by saprophytic hyphae that originated from anthers. This infection route probably gives rise to the typical tan-coloured Botrytis symptoms that appear to radiate from this part of the flower. Subcuticular hyphae were present at very high density near stamen bases. They evidently resulted at multiple penetrations from single infection cushions. Flower abscission occurred at 72 hpi. At this time, floral tube tissues remained uninfected. This temporal pattern infers the possible transmission of a signal (e.g. ethylene) upon Botrytis infection (6–36 hpi) that intiates a defence response of shedding infected flowers (72 hpi). Susceptibility of waxflower before and after harvest to B. cinerea under various environmental conditions (laboratory, greenhouse, and field) was investigated. Flowers, either on plants or on cut stems showed similar susceptibility to B. cinerea and abscised under cool temperatures (~20 ºC) and high humidity (>95% RH) conditions following infection. Compared to cv. Mullering Brook, cv. My Sweet Sixteen was somewhat more resistant to B. cinerea infection under field conditions. Constitutive and inducible antifungal compounds in waxflower flower tissues were screened in cvs. CWA Pink, Stephan’s Delight, Mullering Brook and My Sweet Sixteen using thin layer chromatography bioassays with isolates of B. cinerea and Alternaria alternata (pathogenic) and Cladosporium cladosporioides (non-pathogenic). Common inhibition zone observed at Rf 0.28–0.38, 0.46–0.56 and 0.67–0.76 contained phenolic compounds. There were at least five (cv. Mullering Brook) and one (cv. My Sweet Sixteen) inducible antifungal phenolic compounds as judged by increases in inhibition area as a result of B. cinerea infection and methyl jasmonate treatment. The total areas of B. cinerea- and MeJA-induced inhibition zones were approximately 2.0- and 2.5-folds greater, respectively, than zones from control flowers. Preharvest sprays of three different known host plant defence elicitors, methyl jasmonate (MeJA), benzothiadiazole (BTH), and silicon (Si), were applied to waxflower cvs. Mullering Brook and My Sweet Sixteen plants. BTH or Si sprays generally had no significant effect on postharvest Botrytis severity on either cultivar. MeJA sprays did not reduce B. cinerea on cv. Mullering Brook. MeJA slightly suppressed B. cinerea on cv. My Sweet Sixteen at 500 and 750 µM. Overall, field applications of these host plant defence elicitor chemicals as spray treatments had little effect on vase life, water uptake and relative fresh weight of the cut sprigs. Moreover, they did not appreciably suppress B. cinerea or associated postharvest floral abscission. The efficacy of combined elicitor treatments and combined pre- and postharvest MeJA treatments were assessed. Preharvest foliar applications of MeJA (1000 µM; 2 or 4 times), MeJA (1000 µM) combined with BTH (150 mg/L), and MeJA combined with Si (1500 mg SiO2/L) generally did not suppress postharvest B. cinerea development and flower abscission from harvested sprigs. A pre- plus post-harvest 1000 µM MeJA spray treatment consistently but only slightly suppressed B. cinerea infection on flowers from both pot- and field-grown plants. Pre- and post-harvest MeJA treatments reduced B. cinerea development, but increased flower abscission. Combined MeJA and anti-ethylene treatments were then screened for potential to suppress B. cinerea while preventing flower abscission. However, the combined MeJA and 1-MCP treatment reduced neither Botrytis disease nor flower abscission on sprigs from pot- and field-grown plants. The combined MeJA and STS treatment reduced disease severity for up to 6 days on sprigs harvested from pot-grown plants but tended to increase Botrytis severity on sprigs from field-grown plants 6 days after inoculation. Antifungal effects of the essential oil S-carvone against B. cinerea germination and mycelial growth were demonstrated in vitro. Inhibition increased with increasing S-carvone concentrations from 0.64 mM to 5.08 mM. However, in planta, S-carvone concentrations in this range did not affect either Botrytis disease levels or flower abscission on cut waxflower flowers.

Biology of Five Benthic Elasmobranch Species from Northern and North-eastern Australia, Including a Taxonomic Review of Indo-West Pacific Gymnuridae.

Ian Jacobsen — 2008-06-12T00:00:00Z

Biology of Sex Determination and Sexual Development in the Cane Toad (Bufo marinus)

Oganes Abramyan — 2010-08-18T00:00:00Z

To date, the majority of studies into sex determination and sexual development have focused on the mammalian system due to the mouse model being an excellent tool for developmental biology as well as obvious implications to human health and development. However, the focus on the mammalian system has caused a large fraction of other vertebrate groups to be overlooked. The last decade has seen an array of studies into various non-mammalian organisms like fishes, birds, reptiles, and amphibians. These studies have unveiled a remarkably conserved molecular background utilized for sexual differentiation amongst all vertebrates, ranging from the alligator which employs temperature dependent sex determination to the mouse, which employs genotypic sex determination In this project, I implemented molecular methods traditionally used to study model organisms, to investigate an amphibian species, the cane toad (Bufo marinus). The cane toad was chosen due to its invasive status in Australia, as well as being a representative of one of the most successful and specious families of vertebrates, Bufonidae. Since, its introduction, this species has rapidly spread across the continent, adversely effecting native species throughout its introduced range. Recent studies have identified the disruption of the sex-determination pathway as a realistic goal in an otherwise, seemingly futile, effort to curtail their expansion. We decided to approach the study of cane toad sex determination and development on three levels, in order to have a broader understanding of the similarities between toads and other groups, and additionally, to better assess the feasibility of utilizing molecular means to control cane toads in non-native habitats. Firstly, I used a candidate gene approach to clone and characterize five genes which were previously known to be involved in both mammalian as well as amphibian sex determination: Sox9, Dmrt1, p450arom, Sf1, and Dax1. I chose Sox9 and Dmrt1 due to their known involvement in the male-specific pathway of mammals. Dmrt1 was also known to be male specific in other groups, including amphibians. Conversely, I also decided to investigate p450arom and Dax1, due to their affiliation with the female pathway, while Sf1 has a role in both sexes. All of these genes were expressed in the gonads of both sexes of cane toads. However, Sox9 exhibited strong transcriptional up-regulation in testes at the time of sexual differentiation, similar to mammals. Thus, using the candidate gene approach, I was successful in identifying a sex-specific marker which could be utilized in the manipulation of the sex determination pathway (e.g. female to male sex reversal). VIIThe second approach involved the study of sex determination on a cytogenetic level. Traditionally, Bufonids have been assumed to utilize a ZZ/ZW (male homogametic/female heterogametic) sex chromosome system, yet only one recent study has been successful in the identification of sex chromosomes in a toad species. Moreover, the authors identified the sex chromosomes in only one population (of 18 studied), highlighting the scarcity of discernible sex chromosomes in toads. When we began to investigate the karyotype of cane toads, we were able to identify a female-specific length polymorphism in the nucleolus organizer region (NOR) of chromosome 7, making this chromosome pair a strong candidates for the Z and W sex chromosomes. In order to verify our hypothesis, we also performed chromomycin A3 staining to reveal a differential signal between the chromosome pair, indicative of heterochromatin accumulation on the brighter NOR. This study lent strong support to the observed difference between the chromosomes, yet we required further investigation in order to identify the W and the Z chromosomes, specifically. By utilizing comparative genomic hybridization (CGH), I was able to identify a female specific region on the chromosome with the larger NOR, identifying it as the W chromosome. This study was successful in identifying the sex chromosomes in the cane toad. Moreover, it allows us to make a more accurate prediction of the possible sex determination method utilized: either a dosage dependent male determination system, or a female-specific gene in a female determination system. The third approach focused on the Bidder’s organ and its role in sexual development of cane toads. The Bidder’s organ is a gonadal structure comprised of ovary-like tissue, found in both males and females, with no known function. Since our study was focused on female to male sex-reversal of cane toads, we decided to investigate the potential of the Bidder’s organ to interrupt this process. By utilizing the candidate genes, which I had previously cloned, I was able to identify the Bidder’s organ as having an entirely distinct transcriptional pattern in comparison to the gonads of either sex. Additionally, the Bidder’s organ showed significantly higher levels of p450arom expression than the gonads, identifying it as a possible key player in the production of aromatase enzyme for oestrogen production. Moreover, gene expression patterns in the Bidder’s organ strongly correlated with the significant developmental time points in the sexual development of the toads, implying a possible function in the development process of toads. In conclusion, I have performed the first study of the molecular, cytogenetic and anatomical aspects of sexual development in a toad. I was able to verify that cane toads utilize a ZZ/ZW chromosome system and furthermore, likely utilize the mammalian male-linked gene, Sox9, in male development. I was also able to show that the Bidder’s organ is transcriptionally active at key time points, likely indicative of a functional role during development.

Biomarkers for chronic arsenic poisoning

Faye Fang Liu — 2007-08-24T00:00:00Z

Biomarkers of Motor Neurone Disease: Neurophysiological studies of lower motor neuron degeneration

Fusun Baumann — 2012-05-24T00:00:00Z

Motor neurone disease (MND) is a fatal disease characterized by relentless degeneration of both upper motor neurones (UMN) and lower motor neurones (LMN) leading to progressive muscular paralysis, with death usually occurring 1 to 5 years after the onset. Despite the recent advances in research, the cause of motor neuron death and the pathological determinants of disease progression in MND still remain poorly understood. There is no efficient treatment of the disease and further clinical trials are required to test potential therapies. Clinical heterogeneity is a recognized feature of MND and is reflected in differences in survival time and rate of progression. From a pathophysiological point of view, this raises the question of whether MND is a single disease entity or a syndrome of different clinical entities arising from distinct biologic mechanisms. Clinical assessment by way of the traditional clinical examination remains the best way to assess neurodegeneration and to follow the process in real time but is not able to detect subclinical UMN or LMN involvement. Therefore, objective biomarkers of UMN and LMN dysfunction are useful not only as endpoint measures sensitive to early therapeutic effects but have the potential to shed light on the disease pathogenesis in MND and might also resolve complexities of clinical heterogeneity in clinical trials. We hypothesized that Bayesian motor unit number estimation (MUNE) is a sensitive biomarker of lower motor neuron degeneration in MND. We performed serial studies in a large cohort of MND patients to evaluate motor unit (MU) loss in different regions of the spinal cord and among clinical subtypes of MND The half life of MUs determined by serial Bayesian MUNE was able to demonstrate selective vulnerability of different motor neuron pools during the disease process and the spread of disease from the site of onset. It also distinguished the clinical subtypes with different survival time. Our findings were supported by previous reports using clinical and neuropathological methods in human subjects and animal models of MND. Therefore Bayesian MUNE has the potential to be a sensitive biomarker of disease process in MND subjects. Furthermore, since both the MU number and size have not been considered in previous MUNE methods, Bayesian MUNE provides useful information about MU sprouting in MND. Our results of serial studies of Bayesian MUNE have confirmed its potential as a biomarker of disease progression and as a reliable, reproducible, practical and tolerable method.

Biomimetic Orientated Total Synthesis of Neovibsane Natural Products and Comparison of Synthetic Neovibsanes on Neurite Outgrowth Promotion in PC12 Cells

Annette Chen — 2010-06-09T00:00:00Z

Neovibsanin A and B are natural products which induced neurite outgrowth in PC12 cells. They belong in the neovibsane class under the rare vibsane natural product family, whose structures are characterized by polycyclic, polyoxygenated cores. Based on a proposed biosynthesis, the synthetic strategy towards neovibsanin A and B involved synthesizing a key enone intermediate. Initial investigation using this intermediate lead to the total synthesis of 2-O-methylneovibsanin H. Crucial to this concise synthesis was an acid-catalyzed, one-pot, four-step cascade reaction. Modifying the reaction condition leads to a different five-step cascade pathway, resulting in the total synthesis of 4,5-bis-epi-neovibsanin A and B. The synthetic trials and tribulations encountered on the road to these final compounds are explored. It is envisaged that other related neovibsane natural products may arise based on this synthetic sequence. 4,5-Bis-epi-neovibsanin A and B, as well as several other structural analogues collected during the synthesis, were biologically assayed using NGF-stimulated PC12 cells. All compounds induced a significant proportion of neurons to extend neurite processes compared to control cultures. The structure-activity relationship studies indicated that the tricyclic core, as well as the 3,3-dimethylacroyl enol ester side chain, may be responsible for promoting a biological response.