Bayesian methodology for genetics of complex diseases

Genetic research of complex diseases is a challenging, but exciting, area of research. The early development of the research was limited, however, until the completion of the Human Genome and HapMap projects, along with the reduction in the cost of genotyping, which paves the way for understanding the genetic composition of complex diseases. In this thesis, we focus on the statistical methods for two aspects of genetic research: phenotype definition for diseases with complex etiology and methods for identifying potentially associated Single Nucleotide Polymorphisms (SNPs) and SNP-SNP interactions. With regard to phenotype definition for diseases with complex etiology, we firstly investigated the effects of different statistical phenotyping approaches on the subsequent analysis. In light of the findings, and the difficulties in validating the estimated phenotype, we proposed two different methods for reconciling phenotypes of different models using Bayesian model averaging as a coherent mechanism for accounting for model uncertainty. In the second part of the thesis, the focus is turned to the methods for identifying associated SNPs and SNP interactions. We review the use of Bayesian logistic regression with variable selection for SNP identification and extended the model for detecting the interaction effects for population based case-control studies. In this part of study, we also develop a machine learning algorithm to cope with the large scale data analysis, namely modified Logic Regression with Genetic Program (MLR-GEP), which is then compared with the Bayesian model, Random Forests and other variants of logic regression.

Occurrence of iron and associated bacterial populations in soils of a forested subtropical coastal catchment

Iron (Fe) biogeochemistry is potentially of environmental significance in plantation-forested, subtropical coastal ecosystems where soil disturbance and seasonal water logging may lead to elevation of Fe mobilization and associated water quality deterioration. Using wet-chemical extraction and laboratory cultivation, we examined the occurrence of Fe forms and associated bacterial populations in diverse soils of a representative subtropical Australian coastal catchment (Poona Creek). Total reactive Fe was abundant throughout 0e30 cm soil cores, consisting primarily of crystalline forms in well-drained sand soils and water-logged loam soils, whereas in water-logged, low clay soils, over half of total reactive Fe was present in poorly-crystalline forms due to organic and inorganic complexation, respectively. Forestry practices such as plantation clear-felling and replanting, seasonal water logging and mineral soil properties significantly impacted soil organic carbon (C), potentially-bioavailable Fe pools and densities of S-, but not Fe-, bacterial populations. Bacterial Fe(III) reduction and abiotic Fe(II) oxidation, as well as chemolithotrophic S oxidation and aerobic, heterotrophic respiration were integral to catchment terrestrial FeeC cycling. This work demonstrates bacterial involvement in terrestrial Fe cycling in a subtropical coastal circumneutral-pH ecosystem.

Iron biogeochemistry and associated greenhouse gas evolution in a forested subtropical Australian coastal catchment : Poona Creek, Southeast Queensland

Iron (Fe) is the fourth most abundant element in the Earth’s crust. Excess Fe mobilization from terrestrial into aquatic systems is of concern for deterioration of water quality via biofouling and nuisance algal blooms in coastal and marine systems. Substantial Fe dissolution and transport involve alternate Fe(II) oxidation followed by Fe(III) reduction, with a diversity of Bacteria and Archaea acting as the key catalyst. Microbially-mediated Fe cycling is of global significance with regard to cycles of carbon (C), sulfur (S) and manganese (Mn). However, knowledge regarding microbial Fe cycling in circumneutral-pH habitats that prevail on Earth has been lacking until recently. In particular, little is known regarding microbial function in Fe cycling and associated Fe mobilization and greenhouse (CO2 and CH4, GHG) evolution in subtropical Australian coastal systems where microbial response to ambient variations such as seasonal flooding and land use changes is of concern. Using the plantation-forested Poona Creek catchment on the Fraser Coast of Southeast Queensland (SEQ), this research aimed to 1) study Fe cycling-associated bacterial populations in diverse terrestrial and aquatic habitats of a representative subtropical coastal circumneutral-pH (4–7) ecosystem; and 2) assess potential impacts of Pinus plantation forestry practices on microbially-mediated Fe mobilization, organic C mineralization and associated GHG evolution in coastal SEQ. A combination of wet-chemical extraction, undisturbed core microcosm, laboratory bacterial cultivation, microscopy and 16S rRNA-based molecular phylogenetic techniques were employed. The study area consisted primarily of loamy sands, with low organic C and dissolved nutrients. Total reactive Fe was abundant and evenly distributed within soil 0–30 cm profiles. Organic complexation primarily controlled Fe bioavailability and forms in well-drained plantation soils and water-logged, native riparian soils, whereas tidal flushing exerted a strong “seawater effect” in estuarine locations and formed a large proportion of inorganic Fe(III) complexes. There was a lack of Fe(II) sources across the catchment terrestrial system. Mature, first-rotation plantation clear-felling and second-rotation replanting significantly decreased organic matter and poorly crystalline Fe in well-drained soils, although variations in labile soil organic C fractions (dissolved organic C, DOC; and microbial biomass C, MBC) were minor. Both well-drained plantation soils and water-logged, native-vegetation soils were inhabited by a variety of cultivable, chemotrophic bacterial populations capable of C, Fe, S and Mn metabolism via lithotrophic or heterotrophic, (micro)aerobic or anaerobic pathways. Neutrophilic Fe(III)-reducing bacteria (FeRB) were most abundant, followed by aerobic, heterotrophic bacteria (heterotrophic plate count, HPC). Despite an abundance of FeRB, cultivable Fe(II)-oxidizing bacteria (FeOB) were absent in associated soils. A lack of links between cultivable Fe, S or Mn bacterial densities and relevant chemical measurements (except for HPC correlated with DOC) was likely due to complex biogeochemical interactions. Neither did variations in cultivable bacterial densities correlate with plantation forestry practices, despite total cultivable bacterial densities being significantly lower in estuarine soils when compared with well-drained plantation soils and water-logged, riparian native-vegetation soils. Given that bacterial Fe(III) reduction is the primary mechanism of Fe oxide dissolution in soils upon saturation, associated Fe mobilization involved several abiotic and biological processes. Abiotic oxidation of dissolved Fe(II) by Mn appeared to control Fe transport and inhibit Fe dissolution from mature, first-rotation plantation soils post-saturation. Such an effect was not observed in clear-felled and replanted soils associated with low SOM and potentially low Mn reactivity. Associated GHG evolution post-saturation mainly involved variable CO2 emissions, with low, but consistently increasing CH4 effluxes in mature, first-rotation plantation soil only. In comparison, water-logged soils in the riparian native-vegetation buffer zone functioned as an important GHG source, with high potentials for Fe mobilization and GHG, particularly CH4 emissions in riparian loam soils associated with high clay and crystalline Fe fractions. Active Fe–C cycling was unlikely to occur in lower-catchment estuarine soils associated with low cultivable bacterial densities and GHG effluxes. As a key component of bacterial Fe cycling, neutrophilic FeOB widely occurred in diverse aquatic, but not terrestrial, habitats of the catchment study area. Stalked and sheathed FeOB resembling Gallionella and Leptothrix were limited to microbial mat material deposited in surface fresh waters associated with a circumneutral-pH seep, and clay-rich soil within riparian buffer zones. Unicellular, Sideroxydans-related FeOB (96% sequence identity) were ubiquitous in surface and subsurface freshwater environments, with highest abundance in estuary-adjacent shallow coastal groundwater water associated with redox transition. The abundance of dissolved C and Fe in the groundwater-dependent system was associated with high numbers of cultivable anaerobic, heterotrophic FeRB, microaerophilic, putatively lithotrophic FeOB and aerobic, heterotrophic bacteria. This research represents the first study of microbial Fe cycling in diverse circumneutral-pH environments (terrestrial–aquatic, freshwater–estuarine, surface–subsurface) of a subtropical coastal ecosystem. It also represents the first study of its kind in the southern hemisphere. This work highlights the significance of bacterial Fe(III) reduction in terrestrial, and bacterial Fe(II) oxidation in aquatic catchment Fe cycling. Results indicate the risk of promotion of Fe mobilization due to plantation clear-felling and replanting, and GHG emissions associated with seasonal water-logging. Additional significant outcomes were also achieved. The first direct evidence for multiple biomineralization patterns of neutrophilic, microaerophilic, unicellular FeOB was presented. A putatively pure culture, which represents the first cultivable neutrophilic FeOB from the southern hemisphere, was obtained as representative FeOB ubiquitous in diverse catchment aquatic habitats.

Evidence for CRHR1 in multiple sclerosis using supervised machine learning and meta-analysis in 12 566 individuals

The primary genetic risk factor in multiple sclerosis (MS) is the HLA-DRB1*1501 allele; however, much of the remaining genetic contribution to MS has yet to be elucidated. Several lines of evidence support a role for neuroendocrine system involvement in autoimmunity which may, in part, be genetically determined. Here, we comprehensively investigated variation within eight candidate hypothalamic-pituitary-adrenal (HPA) axis genes and susceptibility to MS. A total of 326 SNPs were investigated in a discovery dataset of 1343 MS cases and 1379 healthy controls of European ancestry using a multi-analytical strategy. Random Forests, a supervised machine-learning algorithm, identified eight intronic SNPs within the corticotrophin-releasing hormone receptor 1 or CRHR1 locus on 17q21.31 as important predictors of MS. On the basis of univariate analyses, six CRHR1 variants were associated with decreased risk for disease following a conservative correction for multiple tests. Independent replication was observed for CRHR1 in a large meta-analysis comprising 2624 MS cases and 7220 healthy controls of European ancestry. Results from a combined meta-analysis of all 3967 MS cases and 8599 controls provide strong evidence for the involvement of CRHR1 in MS. The strongest association was observed for rs242936 (OR = 0.82, 95% CI = 0.74-0.90, P = 9.7 × 10-5). Replicated CRHR1 variants appear to exist on a single associated haplotype. Further investigation of mechanisms involved in HPA axis regulation and response to stress in MS pathogenesis is warranted. © The Author 2010. Published by Oxford University Press. All rights reserved.

Without an Alibi

The project is a book collection of 65 poems, primarily with an environmental focus. This practice-led project draws on eco-critical theory (Wilson, 1992; and Bate, 2000) and Darwinian literary theory (Carroll, 2004) to explore ideas of ecology, the ‘natural’, and conservation. The poems explore a proposal of synthesis: that nature is for us both a construction of language/culture (as argued by post structuralism/ cultural studies) and also a pragmatic, empirical entity that can be experienced through the senses as well as through culture. For example, individual poems describe genres of ‘forest’ (‘Literary Forests’, ‘The Conservative Forest’, ‘The Imperial Forest’) which demonstrate how ‘nature’ can be culturally constructed, but also remain an empirical entity with which we experience a more immediate, physical connection, as posited by Bate (following Heidegger’s ‘being-in-the-world’) . The work also explores through satire the concept of evolutionary adaptation, for example the integration of machine into forest (‘The Black Forest’), animals adopting human characteristics (‘In Praise of Bears’), and ‘nature’ as a damaged or absent ‘other’. Without an Alibi makes various strands of theoretical thinking concrete and manifest by ‘showing not telling’, in creative practice. The work has been high positively reviewed in the prestigious Australian Book Review, and by Professor Peter Pierce in the Canberra Times. Several of the poems have since been reproduced in national anthologies including The Penguin Anthology of Australian Poetry (2000) and Australian Poetry Since 1988 (Uni of NSW Press).

Multicultural melting pot : painting for the planet

This brief paper gives an outline of a series of painting workshops held over a two year period (2010 and 2011) with the principal aim of raising the awareness of University students to human impact on the planet and on its biodiversity. The workshops were part of a Post-graduate research students' network engagement programme instigated and supported by a number of staff in Counselling Services and International Student Services. Two of the United Nations International years were celebrated and student engagement in practical painting workshops had many benefits that are discussed in the body of the paper.

A genealogy of calculations at an early Queensland sugar mill

This study of a unique historic situation is sociologically framed and politically contextualized. It examines the technical and persuasive rhetorical dimensions of calculations employed at a nineteenth-century Queensland sugar plantation and mill in relation to the employment of indentured labour. Historical archival data is interpreted through the lens of the rhetoric of rationality. Queensland legislation permitted the employment of indentured Pacific islanders to assist in the development of its sugar industry. Accounting practices employed at the Colonial Sugar Refinery (CSR) Company’s Goondi Plantation and Mill focused on recording and controlling labour costs to maximize profits and maintain a healthy dividend to shareholders. The use of this single perspective, while it provides a restricted interpretation of events, nevertheless enables some unique insights about the practice of accounting in this historic context.

Offsetting greenhouse gas emissions through biological carbon sequestration in North Eastern Australia

The Kyoto Protocol recognises trees as a sink of carbon and a valid means to offset greenhouse gas emissions and meet internationally agreed emissions targets. This study details biological carbon sequestration rates for common plantation species Araucaria cunninghamii (hoop pine), Eucalyptus cloeziana, Eucalyptus argophloia, Pinus elliottii and Pinus caribaea var hondurensis and individual land areas required in north-eastern Australia to offset greenhouse gas emissions of 1000tCO 2e. The 3PG simulation model was used to predict above and below-ground estimates of biomass carbon for a range of soil productivity conditions for six representative locations in agricultural regions of north-eastern Australia. The total area required to offset 1000tCO 2e ranges from 1ha of E. cloeziana under high productivity conditions in coastal North Queensland to 45ha of hoop pine in low productivity conditions of inland Central Queensland. These areas must remain planted for a minimum of 30years to meet the offset of 1000tCO 2e.

Towards local cultures of sustainability : facilitating community created environment education centres through design

Ecological sustainability has been proposed to address the problem of human impacts increasingly degrading planetary resources and ecosystems, threatening biodiversity, eco-services and human survival. Ecological sustainability is an imperative, with Australia having one of the highest eco-footprints per person worldwide. While significant progress has been made via implementation of ecologically sustainable design in urban communities, relatively little has been undertaken in small, disparate regional communities in Australia. Regional communities are disadvantaged by rural economic decline associated with structural change and inequities of resource transfer. The ecologically sustainable solution is holistic, so all settlements need to be globally wise, richly biodiverse yet locally specific. As a regional solution to this global problem, this research offers the practical means by which a small regional community can contribute. It focuses on the design and implementation of a community centre and the fostering of transformative community learning through an integrated ‘learning community’ awareness of ecologically sustainable best practice. Lessons learned are documented by the participant researcher who as a designer, facilitator, local resident and social narrator has been deeply connected with the Tweed-Caldera region over a period since 1980. The collective action of the local community of Chillingham has been diligently recorded over a decade of design and development. Over this period, several positive elements emerged in terms of improvements to the natural and built environment, greater social cohesion and co-operative learning along with a shift towards a greener local economy. Behavioural changes in the community were noted as residents strived to embrace ecological ideals and reduce fossil fuel dependency. They found attractive local solutions to sourcing of food and using local employment opportunities to up skill their residents via transformative learning as a community in transition. Finally, the catalytic impact of external partnering has also been documented. How well the region as a whole has achieved its ecologically sustainable objectives is measured in terms of the delivered success of private and public partnering with the community, the creation of a community centre cum environment education centre, the restoration of local heritage buildings, the repair of riparian forests and improved water conditions in local river systems, better roads and road safety, local skills and knowledge transfer, support of local food and local/regional growers markets to attract tourists via the integrated trails network. In aggregate, each and every element contributes to a measure of eco-positive development for the built environment, its social organisation and its economy that has guided the local community to find its own pathway to sustainability. Within the Tweed-Caldera bioregion in northern New South Wales, there has been a lack of strategic planning, ecologically sustainable knowledge and facilities in isolated communities that could support the development of a local sustained green economy, provide a hub for socio-cultural activities and ecology based education. The first challenge in this research was to model a whole systems approach to eco-positive development in Chillingham, NSW, a small community where Nature and humanity know no specific boundary. The net result was the creation of a community environment education centre featuring best-affordable ecological practice and regionally distinctive, educational building form from a disused heritage building (cow bale). This development, implemented over a decade, resonated with the later regional wide programs that were linked in the Caldera region by the common purpose of extending the reach of local and state government assistance to regional NSW in economic transition coupled with sustainability. The lessons learned from these linked projects reveal that subsequent programs have been significantly easier to initiate, manage, develop and deliver results. In particular, pursuing collaborative networks with all levels of government and external private partners has been economically effective. Each community’s uniqueness has been celebrated and through drawing out these distinctions, has highlighted local vision, strategic planning, sense of belonging and connection of people with place. This step has significantly reduced the level of friction between communities that comes from natural competition for the finite pool of funds. Following the pilot Tweed-Caldera study, several other NSW regional communities are now undertaking a Community Economic Transition Program based on the processes, trials and positive experiences witnessed in the Tweed-Caldera region where it has been demonstrated that regional community transition programs can provide an opportunity to plan and implement effective long term strategies for sustainability, empowering communities to participate in eco-governance. This thesis includes the design and development of a framework for community created environment education centres to provide an equal access place for community to participate to meet their essential needs locally. An environment centre that facilitates community transition based on easily accessible environmental education, skills and infrastructure is necessary to develop local cultures of sustainability. This research draws upon the literatures of ecologically sustainable development, environmental education and community development in the context of regional community transition towards ‘strong sustainability’. The research approach adapted is best described as a four stage collaborative action research cycle where the participant researcher (me) has a significant involvement in the process to foster local cultures of sustainability by empowering its citizens to act locally and in doing so, become more self reliant and socially resilient. This research also draws upon the many fine working exemplars, such as the resilience of the Cuban people, the transition town initiative in Totnes, U.K. and the models of Australian Community Gardens, such as CERES (Melbourne) and Northey Street (Brisbane). The objectives of this study are to research and evaluate exemplars of ecologically sustainable environment education centres, to facilitate the design and development of an environment education centre created by a small regional community as an ecologically sustainable learning environment; to facilitate a framework for community transition based on environmental education, skills and infrastructure necessary to develop local cultures of sustainability. The research was undertaken as action research in the Tweed Caldera in Northern NSW. This involved the author as participant researcher, designer and volunteer in two interconnected initiatives: the Chillingham Community Centre development and the Caldera Economic Transition Program (CETP). Both initiatives involved a series of design-led participatory community workshops that were externally facilitated with the support of government agency partnerships, steering committees and local volunteers. Together the Caldera research programs involved communities participating in developing their own strategic planning process and outcomes. The Chillingham Community Centre was developed as a sustainable community centre/hub using a participatory design process. The Caldera Economic Transition Program (CETP) prioritised Caldera region projects: the Caldera farmer’s market; community gardens and community kitchens; community renewable energy systems and an integrated trails network. The significant findings were: the CETP projects were capable of moving towards an eco-positive design benchmark through transformative learning. Community transition to sustainability programs need to be underpinned by sustainability and environmental education based frameworks and practical on ground experience in local needs based projects through transformative learning. The actioned projects were successfully undertaken through community participation and teamwork. Ecological footprint surveys were undertaken to guide and assess the ongoing community transition process, however the paucity of responses needs to be revisited. The concept of ecologically sustainable development has been adopted internationally, however existing design and planning strategies do not assure future generations continued access to healthy natural life support systems. Sustainable design research has usually been urban focussed, with little attention paid to regional communities. This study seeks to redress this paucity through the design of ecologically sustainable (deep green) learning environments for small regional communities. Through a design-led process of environmental education, this study investigates how regional communities can be facilitated to model the principles of eco-positive development to support transition to local cultures of sustainability. This research shows how community transition processes and projects can incorporate sustainable community development as transformative learning through design. Regional community transition programs can provide an opportunity to plan long term strategies for sustainability, empowering people to participate in eco-governance. A framework is developed for a community created environment education centre to provide an equal access place for the local community to participate in implementing ways to meet their essential needs locally. A community environment education centre that facilitates community transition based on holistic environmental education, skills and infrastructure is necessary to develop local cultures of sustainability.

CO2 emissions from the combustion of native Australian trees

Carbon dioxide (CO2), as a primary product of combustion, is a known factor affecting climate change and global warming. In Australia, CO2 emissions from biomass burning are a significant contributor to total carbon in the atmosphere and therefore, it is important to quantify the CO2 emission factors from biomass burning in order to estimate their magnitude and impact on the Australian atmosphere. This paper presents the quantification of CO2 emission factors for five common tree species found in South East Queensland forests, as well as several grasses taken from savannah lands in the Northern Territory of Australia, under controlled ‘fast burning’ and ‘slow burning’ laboratory conditions. The results showed that CO2 emission factors varied according to the type of vegetation and burning conditions, with emission factors for fast burning being 2574 ± 254 g/kg for wood, 394 ± 40 g/kg for branches and leaves, and 2181 ± 120 g/kg for grass. Under slow burning conditions, the CO2 emission factors were 218 ± 20 g/kg for wood, 392± 80 g/kg for branches and leaves, and 2027 ± 809 g/kg for grass.

Deforestation, REDD and international law

International environmental law governing conservation and management of forests has been largely limited to soft-law instruments. Nevertheless, increasing attention has been given to forest issues, most recently in the context of the climate change regime and the reducing emissions from deforestation and degradation (REDD) mechanism. The current law impacting upon the protection of forests and the contribution of emissions from deforestation will be considered in this chapter. The way forward will be explored, including the current options being considered for the post-Kyoto period.

Extreme architecture : can architects future proof us against fire and flood.

In the face of Australia’s disaster-prone environment, architects Ian Weir and James Davidson are reconceptualising how our residential buildings might become more resilient to fire, flood and cyclone. With their first-hand experience of natural disasters, James, director of Emergency Architects Australia (EAA), and Ian, one of Australia’s few ‘bushfire architects’, discuss the ways we can design with disaster in mind. Dr Ian Weir is one of Australia’s few ‘bushfire architects’. Exploring a holistic ‘ground up’ approach to bushfire where landscape, building design and habitation patterns are orchestrated to respond to site-specific fire characteristics. Ian’s research is developed through design studio teaching at QUT and through built works in Western Australia’s fire prone forests and heathlands.

Opportunities for forest finance under the International climate change regime

The international climate change regime has the potential to increase revenue available for forest restoration projects in Commonwealth nations. There are three mechanisms which could be used to fund forest projects aimed at forest conservation, forest restoration and sustainable forest management. The first forest funding opportunity arises under the clean development mechanism, a flexibility mechanism of the Kyoto Protocol. The clean development mechanism allows Annex I parties (industrialised nations) to invest in emission reduction activities in non-Annex 1 (developing countries) and the establishment of forest sinks is an eligible clean development mechanism activity. Secondly, parties to the Kyoto Protocol are able to include sustainable forest management activities in their national carbon accounting. The international rules concerning this are called the Land-Use, Land-Use Change and Forestry Guidelines. Thirdly, it is anticipated that at the upcoming Copenhagen negotiations that a Reduced Emissions from Deforestation and Degradation (REDD) instrument will be created. This will provide a direct funding mechanism for those developing countries with tropical forests. Payments made under a REDD arrangement will be based upon the developing country with tropical forest cover agreeing to protect and conserve a designated forest estate. These three funding options available under the international climate change regime demonstrate that there is potential for forest finance within the regime. These opportunities are however hindered by a number of technical and policy barriers which prevent the ability of the regime to significantly increase funding for forest projects. There are two types of carbon markets, compliance carbon markets (Kyoto based) and voluntary carbon markets. Voluntary carbon markets are more flexible then compliance markets and as such offer potential to increase revenue available for sustainable forest projects.

Issues in negotiating a Carbon Sequestration Agreement for a Biosequestration Offsets Project

Biosequestration of carbon in trees, forests and vegetation is a key method for offsetting greenhouse gas emissions. To facilitate it, the Commonwealth has introduced the Carbon Farming Initiative, a scheme whereby carbon credits can be earned for biosequestration offsets projects. The project proponent must acquire under state law a ‘carbon sequestration right’ which confers the benefit of the sequestered carbon on the land. Each State provides for an agreement associated with the carbon sequestration right between the landowner and the holder of the right (‘carbon sequestration agreement’). This article identifies some key risks and issues that must be considered in the drafting of a carbon sequestration agreement to support the successful operation of a biosequestration offsets project.

Cryptic diversity and evolutionary relationships among Australian closed-forest Melomys (Rodentia: Muridae) and related Australo-Papuan mosaic-tailed rats

This thesis investigates patterns of evolution in a group of native Australo-Papuan rodents. Past climatic change and associated sea level fluctuations, and fragmentation of wet forests in eastern Australia has facilitated rapid radiation, diversification and speciation in this group. This study adds to our understanding of the evolution of Australia’s rainforest fauna and describes the evolutionary relationships of a new genus of Australian rodent.