Biochemical characterization of Aprataxin, the protein deficient in Ataxia with Oculomotor Apraxia type 1

Neurodegenerative disorders are heterogenous in nature and include a range of ataxias with oculomotor apraxia, which are characterised by a wide variety of neurological and ophthalmological features. This family includes recessive and dominant disorders. A subfamily of autosomal recessive cerebellar ataxias are characterised by defects in the cellular response to DNA damage. These include the well characterised disorders Ataxia-Telangiectasia (A-T) and Ataxia-Telangiectasia Like Disorder (A-TLD) as well as the recently identified diseases Spinocerebellar ataxia with axonal neuropathy Type 1 (SCAN1), Ataxia with Oculomotor Apraxia Type 2 (AOA2), as well as the subject of this thesis, Ataxia with Oculomotor Apraxia Type 1 (AOA1). AOA1 is caused by mutations in the APTX gene, which is located at chromosomal locus 9p13. This gene codes for the 342 amino acid protein Aprataxin. Mutations in APTX cause destabilization of Aprataxin, thus AOA1 is a result of Aprataxin deficiency. Aprataxin has three functional domains, an N-terminal Forkhead Associated (FHA) phosphoprotein interaction domain, a central Histidine Triad (HIT) nucleotide hydrolase domain and a C-terminal C2H2 zinc finger. Aprataxins FHA domain has homology to FHA domain of the DNA repair protein 5’ polynucleotide kinase 3’ phosphatase (PNKP). PNKP interacts with a range of DNA repair proteins via its FHA domain and plays a critical role in processing damaged DNA termini. The presence of this domain with a nucleotide hydrolase domain and a DNA binding motif implicated that Aprataxin may be involved in DNA repair and that AOA1 may be caused by a DNA repair deficit. This was substantiated by the interaction of Aprataxin with proteins involved in the repair of both single and double strand DNA breaks (XRay Cross-Complementing 1, XRCC4 and Poly-ADP Ribose Polymerase-1) and the hypersensitivity of AOA1 patient cell lines to single and double strand break inducing agents. At the commencement of this study little was known about the in vitro and in vivo properties of Aprataxin. Initially this study focused on generation of recombinant Aprataxin proteins to facilitate examination of the in vitro properties of Aprataxin. Using recombinant Aprataxin proteins I found that Aprataxin binds to double stranded DNA. Consistent with a role for Aprataxin as a DNA repair enzyme, this binding is not sequence specific. I also report that the HIT domain of Aprataxin hydrolyses adenosine derivatives and interestingly found that this activity is competitively inhibited by DNA. This provided initial evidence that DNA binds to the HIT domain of Aprataxin. The interaction of DNA with the nucleotide hydrolase domain of Aprataxin provided initial evidence that Aprataxin may be a DNA-processing factor. Following these studies, Aprataxin was found to hydrolyse 5’adenylated DNA, which can be generated by unscheduled ligation at DNA breaks with non-standard termini. I found that cell extracts from AOA1 patients do not have DNA-adenylate hydrolase activity indicating that Aprataxin is the only DNA-adenylate hydrolase in mammalian cells. I further characterised this activity by examining the contribution of the zinc finger and FHA domains to DNA-adenylate hydrolysis by the HIT domain. I found that deletion of the zinc finger ablated the activity of the HIT domain against adenylated DNA, indicating that the zinc finger may be required for the formation of a stable enzyme-substrate complex. Deletion of the FHA domain stimulated DNA-adenylate hydrolysis, which indicated that the activity of the HIT domain may be regulated by the FHA domain. Given that the FHA domain is involved in protein-protein interactions I propose that the activity of Aprataxins HIT domain may be regulated by proteins which interact with its FHA domain. We examined this possibility by measuring the DNA-adenylate hydrolase activity of extracts from cells deficient for the Aprataxin-interacting DNA repair proteins XRCC1 and PARP-1. XRCC1 deficiency did not affect Aprataxin activity but I found that Aprataxin is destabilized in the absence of PARP-1, resulting in a deficiency of DNA-adenylate hydrolase activity in PARP-1 knockout cells. This implies a critical role for PARP-1 in the stabilization of Aprataxin. Conversely I found that PARP-1 is destabilized in the absence of Aprataxin. PARP-1 is a central player in a number of DNA repair mechanisms and this implies that not only do AOA1 cells lack Aprataxin, they may also have defects in PARP-1 dependant cellular functions. Based on this I identified a defect in a PARP-1 dependant DNA repair mechanism in AOA1 cells. Additionally, I identified elevated levels of oxidized DNA in AOA1 cells, which is indicative of a defect in Base Excision Repair (BER). I attribute this to the reduced level of the BER protein Apurinic Endonuclease 1 (APE1) I identified in Aprataxin deficient cells. This study has identified and characterised multiple DNA repair defects in AOA1 cells, indicating that Aprataxin deficiency has far-reaching cellular consequences. Consistent with the literature, I show that Aprataxin is a nuclear protein with nucleoplasmic and nucleolar distribution. Previous studies have shown that Aprataxin interacts with the nucleolar rRNA processing factor nucleolin and that AOA1 cells appear to have a mild defect in rRNA synthesis. Given the nucleolar localization of Aprataxin I examined the protein-protein interactions of Aprataxin and found that Aprataxin interacts with a number of rRNA transcription and processing factors. Based on this and the nucleolar localization of Aprataxin I proposed that Aprataxin may have an alternative role in the nucleolus. I therefore examined the transcriptional activity of Aprataxin deficient cells using nucleotide analogue incorporation. I found that AOA1 cells do not display a defect in basal levels of RNA synthesis, however they display defective transcriptional responses to DNA damage. In summary, this thesis demonstrates that Aprataxin is a DNA repair enzyme responsible for the repair of adenylated DNA termini and that it is required for stabilization of at least two other DNA repair proteins. Thus not only do AOA1 cells have no Aprataxin protein or activity, they have additional deficiencies in PolyADP Ribose Polymerase-1 and Apurinic Endonuclease 1 dependant DNA repair mechanisms. I additionally demonstrate DNA-damage inducible transcriptional defects in AOA1 cells, indicating that Aprataxin deficiency confers a broad range of cellular defects and highlighting the complexity of the cellular response to DNA damage and the multiple defects which result from Aprataxin deficiency. My detailed characterization of the cellular consequences of Aprataxin deficiency provides an important contribution to our understanding of interlinking DNA repair processes.

Should mental health issues be addressed in primary care, and can it be done? Views of rural general practitioners in Queensland

Objective: The aim of this paper was to examine self-efficacy and perceived appropriateness among rural general practitioners (GPs) in regards to screening and intervention for physical, lifestyle and mental health issues. ----- Method: Fifty GPs from 25 practices in eight rural Queensland towns completed a written survey designed for the study. ----- Results: General practitioners rated opportunistic screening or assessment for smoking and for detection of relapse of mental disorders as the most appropriate, with even cardiovascular and diabetes risk falling behind these. Self-efficacy was highest for medical disorders for smoking assessment. It was significantly lower for alcohol, mental health issues, and addressing risks of physical disorder in people with mental disorders. ----- Conclusions: High appropriateness ratings suggest that current strategies to boost self-efficacy of GPs in addressing mental health issues are timely.

Hard Lessons : Reflections on Governance and Crime Control in Late Modernity

The essays in this book catalogue a wide and varied range of instances where 'things go wrong' in the practice of criminal justice. The contributions document instances where laws, policies and practices have produced unintended consequences of the most deleterious kind, drawing attention to 'boot camps', detention centres and specific penal policies such as 'short, sharp shock' and 'three strikes and you're out'. Also examined are policing practices such as 'zero tolerance', 'saturation policing' and punitive laws in the area of drug use, sex offences, and prostitution. It will be demonstrated that in each of these cases, the objectives of government resulted in the creation of new and unforeseen problems requiring further reform to the justice system.

Designing for engagement : building IT systems

Context The School of Information Technology at QUT has recently undertaken a major restructuring of their Bachelor of Information Technology (BIT) course. Some of the aims of this restructuring include a reduction in first year attrition and to provide an attractive degree course that meets both student and industry expectations. Emphasis has been placed on the first semester in the context of retaining students by introducing a set of four units that complement one another and provide introductory material on technology, programming and related skills, and generic skills that will aid the students throughout their undergraduate course and in their careers. This discussion relates to one of these four fist semester units, namely Building IT Systems. The aim of this unit is to create small Information Technology (IT) systems that use programming or scripting, databases as either standalone applications or web applications. In the prior history of teaching introductory computer programming at QUT, programming has been taught as a stand alone subject and integration of computer applications with other systems such as databases and networks was not undertaken until students had been given a thorough grounding in those topics as well. Feedback has indicated that students do not believe that working with a database requires programming skills. In fact, the teaching of the building blocks of computer applications have been compartmentalized and taught in isolation from each other. The teaching of introductory computer programming has been an industry requirement of IT degree courses as many jobs require at least some knowledge of the topic. Yet, computer programming is not a skill that all students have equal capabilities of learning (Bruce et al., 2004) and this is clearly shown by the volume of publications dedicated to this topic in the literature over a broad period of time (Eckerdal & Berglund, 2005; Mayer, 1981; Winslow, 1996). The teaching of this introductory material has been done pretty much the same way over the past thirty years. During this period of time that introductory computer programming courses have been taught at QUT, a number of different programming languages and programming paradigms have been used and different approaches to teaching and learning have been attempted in an effort to find the golden thread that would allow students to learn this complex topic. Unfortunately, computer programming is not a skill that can be learnt in one semester. Some basics can be learnt but it can take many years to master (Norvig, 2001). Faculty data typically has shown a bimodal distribution of results for students undertaking introductory programming courses with a high proportion of students receiving a high mark and a high proportion of students receiving a low or failing mark. This indicates that there are students who understand and excel with the introductory material while there is another group who struggle to understand the concepts and practices required to be able to translate a specification or problem statement into a computer program that achieves what is being requested. The consequence of a large group of students failing the introductory programming course has been a high level of attrition amongst first year students. This attrition level does not provide good continuity in student numbers in later years of the degree program and the current approach is not seen as sustainable.

The ADHD debate and the philosophy of truth

There is ongoing and wide-ranging dispute over the proliferation of childhood behaviour disorders. In particular, the veracity of the category Attention Deficit Hyperactivity Disorder (ADHD), has been the subject of considerable scepticism. With no end to the debate in sight, it will be argued here that the problem might effectively be approached, not by addressing the specific features of ADHD itself, but rather by a philosophical analysis of one of the terms around which this entire problem revolves: that is, the notion of truth. If we state: “It is true that ADHD is a real disorder”, what exactly do we mean? Do we mean that it is an objective fact of nature? Do we mean that it fits seamlessly with other sets of ideas and explanations? Or do we simply mean that it works as an idea in a practical sense? This paper will examine the relationship between some of the dominant models of truth, and the assertions made by those in the field of ADHD. Specifically, the paper will contrast the claim that ADHD is a real disorder, with the claim that ADHD is a product of social governance. The intention is, first, to place some significant qualifications upon the validity of the truth-claims made by ADHD advocates, and second, to re-emphasise the potential and promise of philosophical investigation in providing productive new ways of thinking about some obstinate and seemingly intractable educational problems.

Waterfront Development for Residential Property in Malaysia

Rivers and water are valuable natural resources for human life, environment and national development. Recognition of water resources as national heritage will contribute towards more long term sustainable property development. Waterfront development is already a well-established phenomenon internationally. In Malaysia, as the economy began to change in 1980s, so did the land uses along many of the river and waterfront locations. The pressures of new technology coupled with an urban population growth and urbanization began to force a transition from water dependent industry to a variety of non-water dependent developments such as apartments, offices, and retail shopping areas. Residential waterfront development has taken advantage of available land and water amenities and incorporated as a feature or “selling point” of the development. It has been found that wide views of water add an average of 59% to the value of waterfront property, as well as providing attractive landscaping and better property neighborhoods respectively. Development of waterfront lands in Malaysia occurred with limited federal, state, or municipal planning guidance; resulting in cost aspects like flooding and pollution. Although some waterfront development projects continue to remain profitable with a maintained successful public access component, many have not. This paper provides a brief introduction to the research project to address this issue, which is currently on-going.

Biotechnology education : topics of interest to students and teachers

This paper presents the findings of a survey that investigates the biotechnology topics of interest according to students and teachers for inclusion in biology lessons and reports on the similarities and differences in teachers’ and students’ biotechnology topics of interest. The study is of significance as biotechnology has been identified as a key area of technological and economic importance worldwide yet there is scant literature relating to teachers’ and students’ interests concerning biotechnology education topics. 500 students and their 15 teachers completed the survey. Interviews were conducted with 3 teachers and 60 students. Responses indicate there is a mismatch in the interests of students and teachers, and what they perceive as being possible topics for inclusion in biology and biotechnology lessons. Where teachers are provided with the freedom to design and assess their own units of work, this mismatch of interests causes problems. The study found students withdrawing from biology courses in post compulsory settings due to lack of interest, and perceived lack of relevance of the course. It is possible that this lack of agreement on topics of interest is a factor in the world wide decline of enrolments in the sciences.

Identity, relationships and culture

The purpose of this paper is to consider contemporary developments in the knowledge area dealing with culture, relationships and individual identity. It has three main objectives: the first is to examme the ways in which knowledge is currently produced within the discipline; the second is to look at an alternative approach to the issues, an approach which stresses more piecemeal and contingent ways of understanding; finally, this paper looks at how this new theoretical knowledge is being applied, or can be applied, to areas which impact directly upon educational practices.

Mainstreaming sustainability into pre-service teacher edcuation in Australia

There is a growing interest in and support for education for sustainability in Australian schools. Australian Government schemes such as the Australian Sustainable Schools Initiative (AuSSI), along with strategies such as Educating for a Sustainable Future: A National Environmental Education Statement for Australian Schools(NEES(Australian Government and Curriculum Corporation (2005) and Living Sustainably: The Australian Government’s National Action Plan for Education for Sustainability (Australian Government 2009), recognise the need and offer support for education for sustainability in Australian schools. The number of schools that have engaged with AuSSI indicates that this interest also exists within Australian schools. Despite this, recent research indicates that pre-service teacher education institutions and programs are not doing all they can to prepare teachers for teaching education for sustainability or for working within sustainable schools. The education of school teachers plays a vital role in achieving changes in teaching and learning in schools. Indeed, the professional development of teachers in education for sustainability has been identified as ‘the priority of priorities’. Much has been written about the need to ‘reorient teacher education towards sustainability’. Teacher education is seen as a key strategy that is yet to be effectively utilised to embed education for sustainability in schools. Mainstreaming sustainability in Australian schools will not be achieved without the preparation of teachers for this task. The Mainstreaming Sustainability model piloted in this study seeks to engage a range of stakeholder organisations and key agents of change within a system to all work simultaneously to bring about a change, such as the mainstreaming of sustainability. The model is premised on the understanding that sustainability will be mainstreamed within teacher education if there is engagement with key agents of change across the wider teacher education system and if the key agents of change are ‘deeply’ involved in making the change. The model thus seeks to marry broad engagement across a system with the active participation of stakeholders within that system. Such a systemic approach is a way of bringing together diverse viewpoints to make sense of an issue and harness that shared interpretation to define boundaries, roles and relationships leading to a better defined problem that can be acted upon more effectively. Like action research, the systemic approach is also concerned with modelling change and seeking plausible solutions through collaboration between stakeholders. This is important in ensuring that outcomes are useful to the researchers/stakeholders and the system being researched as it creates partnerships and commitments to the outcomes by stakeholder participants. The study reported on here examines whether the ‘Mainstreaming Sustainability’ model might be effective as a means to mainstream sustainability in pre-service teacher education. This model, developed in an earlier study, was piloted in the Queensland teacher education system in order to examine its effectiveness in creating organisational and systemic change. The pilot project in Queensland achieved a number of outcomes. The project: • provided useful insights into the effectiveness of the Mainstreaming Sustainability model in bringing about change while also building research capacity within the system • developed capacities within the teacher education community: o developing competencies in education for sustainability o establishing more effective interactions between decision-makers and other stakeholders o establishing a community of inquiry • changed teaching and learning approaches used in participating teacher education institutions through: o curriculum and resource development o the adoption of education for sustainability teaching and learning processes o the development of institutional policies • improved networks within the teacher education system through: o identifying key agents of change within the system o developing new, and building on existing, partnerships between schools, teacher education institutions and government agencies • engaged relevant stakeholders such as government agencies and non-government organisations to understand and support the change Our findings indicate that the Mainstreaming Sustainability model is able to facilitate organisational and systemic change – over time – if: • the individuals involved have the conceptual and personal capacities needed to facilitate change, that is, to be a key agent of change • stakeholders are engaged as participants in the process of change, not simply as ‘interested parties’ • there is a good understanding of systemic change and the opportunities for leveraging change within systems. In particular, in seeking to mainstream sustainability in pre-service teacher education in Queensland it has become clear that one needs to build capacity for change within participants such as knowledge of education for sustainability, conceptual skills in systemic thinking, action research and organisational change, and leadership skills. It is also of vital importance that key agents of change – those individuals who are ‘hubs’ within a system and can leverage for change across a wide range of the system – are identified and engaged with as early as possible. Key agents of change can only be correctly identified, however, if the project leaders and known participants have clearly identified the boundary to their system as this enables the system, sub-system and environment of the system to be understood. Through mapping the system a range of key organisations and stakeholders will be identified, including government and nongovernment organisations, teacher education students, teacher education academics, and so on. On this basis, key agents of change within the system and sub-system can be identified and invited to assist in working for change. A final insight is that it is important to have time – and if necessary the funding to ‘buy time’ – in seeking to bring about system-wide change. Seeking to bring about system-wide change is an ambitious project, one that requires a great deal of effort and time. These insights provide some considerations for those seeking to utilise the Mainstreaming Sustainability model to bring about change within and across a pre-service teacher education system.

Applying Stafford and Warr’s Reconceptualization of Deterrence Theory to drug driving : can it predict those likely to offend?

In December 2007, random roadside drug testing commenced in Queensland, Australia. Subsequently, the aim of this study was to explore the preliminary impact of Queensland’s drug driving legislation and enforcement techniques by applying Stafford and Warr’s [Stafford, M. C., & Warr, M. (1993). A reconceptualization of general and specific deterrence. Journal of Research in Crime and Delinquency, 30, 123-135] reconceptualization of deterrence theory. Completing a comprehensive drug driving questionnaire were 899 members of the public, university students, and individuals referred to a drug diversion program. Of note was that approximately a fifth of participants reported drug driving in the past six months. Additionally, the analysis indicated that punishment avoidance and vicarious punishment avoidance were predictors of the propensity to drug drive in the future. In contrast, there were indications that knowing of others apprehended for drug driving was not a sufficient deterrent. Sustained testing and publicity of the legislation and countermeasure appears needed to increase the deterrent impact for drug driving.

Internal audit quality, audit committee independence, growth opportunities and firm performance

This study explores whether the relation between internal audit quality and firm performance is associated with firm characteristics of information asymmetry and uncertainty (growth opportunities) and certain governance controls (audit committee effectiveness). The results from this preliminary study of 60 Malaysian companies show that the association between internal audit quality and firm performance is stronger for firms with high growth opportunities and that this positive association is weakened by increasing audit committee independence. These findings demonstrate the internal auditors conflicting roles and question the governance recommendations that require all members of the audit committee to be non-executive directors.

Members abroad - Australia - Brisbane and the Gold Coast

Brisbane's sub-tropical climate, vegetation and urban history as a British settlement, endow the region with many characteristics that are familiar in KwaZulu-Natal. Brisbane settlement, firstly as a penal conlony to accommodate the hardiest criminals dispatched from Sydney, was established in 1825 on a wide river, several kilometers upstream from Moreton Bay with the Pacific Ocean beyond. The penal colony was short lived and was soon opened up to free settlement in 1842. The growth of the fledgling town was characterized by brick warehouse and service buildings to the port that was established on its riverbanks, resembling those of the old Point Road area in Durban. Government and administration buildings heralded Brisbane as the captial city of the State of Queensland, annexed from New South Wales in 1859. Morphological studies reveal that Brisbane had reached its first zenith around 1930 as a commerical city of four and five storey buildings. The urban form remained stagnant until the post-1960's building boom and the developments from this period on, consolidated land amalgamations largely ignoring the urban characteristics of the established city. Public space was poorly observed, resulting in a city that had turned its back on the river. It is only in recent times that the currency of good urban design, under the custodial direction of the City Council, has fostered a re-engagemed urban realm that, enabled by the recent building boom, has delivered high quality urban environments

Information enrichment for quality recommender systems

The explosive growth of the World-Wide-Web and the emergence of ecommerce are the major two factors that have led to the development of recommender systems (Resnick and Varian, 1997). The main task of recommender systems is to learn from users and recommend items (e.g. information, products or books) that match the users’ personal preferences. Recommender systems have been an active research area for more than a decade. Many different techniques and systems with distinct strengths have been developed to generate better quality recommendations. One of the main factors that affect recommenders’ recommendation quality is the amount of information resources that are available to the recommenders. The main feature of the recommender systems is their ability to make personalised recommendations for different individuals. However, for many ecommerce sites, it is difficult for them to obtain sufficient knowledge about their users. Hence, the recommendations they provided to their users are often poor and not personalised. This information insufficiency problem is commonly referred to as the cold-start problem. Most existing research on recommender systems focus on developing techniques to better utilise the available information resources to achieve better recommendation quality. However, while the amount of available data and information remains insufficient, these techniques can only provide limited improvements to the overall recommendation quality. In this thesis, a novel and intuitive approach towards improving recommendation quality and alleviating the cold-start problem is attempted. This approach is enriching the information resources. It can be easily observed that when there is sufficient information and knowledge base to support recommendation making, even the simplest recommender systems can outperform the sophisticated ones with limited information resources. Two possible strategies are suggested in this thesis to achieve the proposed information enrichment for recommenders: • The first strategy suggests that information resources can be enriched by considering other information or data facets. Specifically, a taxonomy-based recommender, Hybrid Taxonomy Recommender (HTR), is presented in this thesis. HTR exploits the relationship between users’ taxonomic preferences and item preferences from the combination of the widely available product taxonomic information and the existing user rating data, and it then utilises this taxonomic preference to item preference relation to generate high quality recommendations. • The second strategy suggests that information resources can be enriched simply by obtaining information resources from other parties. In this thesis, a distributed recommender framework, Ecommerce-oriented Distributed Recommender System (EDRS), is proposed. The proposed EDRS allows multiple recommenders from different parties (i.e. organisations or ecommerce sites) to share recommendations and information resources with each other in order to improve their recommendation quality. Based on the results obtained from the experiments conducted in this thesis, the proposed systems and techniques have achieved great improvement in both making quality recommendations and alleviating the cold-start problem.

Exercise and lymphoedema : Is it good or bad?

Being physically active during and following treatment for breast cancer has been associated with a range of benefits including improved fitness and function, body composition and immune function and reductions in stress, depression and anxiety, as well as the number and severity of treatment-related side-effects such as nausea, fatigue and pain, all of which contribute to improvements in quality of life. There is also emerging evidence linking active lifestyles with improved survival. Therefore, there is little doubt that participating in regular exercise following breast cancer is ‘good’. Unfortunately, research investigating the role of exercise for women considered at high-risk of lymphoedema or who have developed lymphedema following breast cancer is lacking. For fear of initiating or exacerbating lymphoedema, these women have traditionally been cautioned rather than encouraged to be regularly active. However, recent preliminary findings suggest that being inactive may increase risk of developing lymphedema, and that for those with lymphoedema, participation in an exercise program does not exacerbate the condition. This presentation will address what we know about the role of exercise following a breast cancer diagnosis and will provide some practical recommendations about becoming and staying regularly active following breast cancer, for those with and without lymphoedema.

Exercise and activity – how it helps lymphoedema?

Research investigating the role of exercise in the prevention and/or management of lymphoedema is lacking. For fear of initiating or exacerbating lymphoedema, and its associated symptoms, those with lymphoedema have traditionally been cautioned against engaging in physical activity rather than encouraged to be regularly active. However, recent preliminary findings suggest that being inactive may increase risk of developing lymphedema, and that for those with lymphoedema, participation in an exercise program does not exacerbate the condition. This presentation will address why engaging in regular physical activity is important, what we know about the role of exercise with respect to lymphoedema prevention and management, and will provide some practical recommendations about becoming and staying regularly active for those with lymphoedema.