Rapid genome wide mapping of phosphine resistance loci by a simple regional averaging analysis in the red flour beetle, Tribolium castaneum

Background Next-generation sequencing technology is an important tool for the rapid, genome-wide identification of genetic variations. However, it is difficult to resolve the ‘signal’ of variations of interest and the ‘noise’ of stochastic sequencing and bioinformatic errors in the large datasets that are generated. We report a simple approach to identify regional linkage to a trait that requires only two pools of DNA to be sequenced from progeny of a defined genetic cross (i.e. bulk segregant analysis) at low coverage (<10×) and without parentage assignment of individual SNPs. The analysis relies on regional averaging of pooled SNP frequencies to rapidly scan polymorphisms across the genome for differential regional homozygosity, which is then displayed graphically. Results Progeny from defined genetic crosses of Tribolium castaneum (F4 and F19) segregating for the phosphine resistance trait were exposed to phosphine to select for the resistance trait while the remainders were left unexposed. Next generation sequencing was then carried out on the genomic DNA from each pool of selected and unselected insects from each generation. The reads were mapped against the annotated T. castaneum genome from NCBI (v3.0) and analysed for SNP variations. Since it is difficult to accurately call individual SNP frequencies when the depth of sequence coverage is low, variant frequencies were averaged across larger regions. Results from regional SNP frequency averaging identified two loci, tc_rph1 on chromosome 8 and tc_rph2 on chromosome 9, which together are responsible for high level resistance. Identification of the two loci was possible with only 5-7× average coverage of the genome per dataset. These loci were subsequently confirmed by direct SNP marker analysis and fine-scale mapping. Individually, homozygosity of tc_rph1 or tc_rph2 results in only weak resistance to phosphine (estimated at up to 1.5-2.5× and 3-5× respectively), whereas in combination they interact synergistically to provide a high-level resistance >200×. The tc_rph2 resistance allele resulted in a significant fitness cost relative to the wild type allele in unselected beetles over eighteen generations. Conclusion We have validated the technique of linkage mapping by low-coverage sequencing of progeny from a simple genetic cross. The approach relied on regional averaging of SNP frequencies and was used to successfully identify candidate gene loci for phosphine resistance in T. castaneum. This is a relatively simple and rapid approach to identifying genomic regions associated with traits in defined genetic crosses that does not require any specialised statistical analysis.

Modelling interactions between farm-level structural adjustment and a regional economy: A case of the Australian rice industry

Climate change and on-going water policy reforms will likely contribute to on-farm and regional structural adjustment in Australia. This paper gathers empirical evidence of farm-level structural adjustments and integrates these with a regional equilibrium model to investigate sectoral and regional impacts of climate change and recent water use policy on rice industry. We find strong evidence of adjustments to the farming system, enabled by existing diversity in on-farm production. A further loss of water with additional pressures to adopt less intensive and larger-scale farming, will however reduce the net number of farm businesses, which may affect regional rice production. The results from a regional CGE model show impacts on the regional economy over and above the direct cost of the environmental water, although a net reduction in real economic output and real income is partially offset by gains in rest of the Australia through the reallocation or resources. There is some interest within the industry and from potential new corporate entrants in the relocation of some rice production to the north. However, strong government support would be crucial to implement such relocation.

Drink driving among Indigenous Australians in outer regional and remote communities and development of a drink driving program: A summary of findings and recommendations

Drink driving is a leading cause of criminal justice system contact for Indigenous Australians. National and state strategies recommend Indigenous road safety initiatives are warranted. However, there is sparse evidence to inform drink driving-related preventive and treatment measures. Using quantitative and qualitative methods, the study examines the profile of Queensland’s Indigenous drink drivers using court convictions and identifies the contributing psycho-social, cultural and contextual factors through qualitative interviews.

Challenges in developing a new regional road safety strategy for ASEAN

In 2011, more than 75,000 people died in road crashes in the ten member countries of the Association of South East Asian Nations (ASEAN) and many times this number sustained long term injuries. Improving road safety outcomes in ASEAN is not only important for the welfare and economic benefit of these countries, but given that a significant proportion of the world's population lives in ASEAN, it will strongly influence whether the aims of the United Nations Decade of Action for Road Safety and the Sustainable Development Goals are reached. Following the ASEAN Senior Transport Officials Meeting in May 2011, the Secretariat requested the Asian Development Bank (ADB) to provide assistance to improve road safety in ASEAN. In response, ADB, funded by the Japan Fund for Poverty Reduction, has funded a package of action to improve road safety in ASEAN, including the development of a new regional road safety strategy. The diversity of the member nations of ASEAN poses significant challenges for the development of the strategy. For example, the road fatality rates per 100,000 population in Malaysia and Thailand are about 5 times greater than in Singapore. In addition, the importance of particular road safety issues varies across the ASEAN countries and for countries which are undergoing rapid motorization, the order of importance may change over the life of the strategy. The development of the ASEAN Regional Road Safety Strategy has adopted the five pillars of road safety of the UN Decade of Action but focused on those aspects which are most relevant at the regional level and where a regional approach will support and facilitate actions taken by individual countries. A draft ASEAN Regional Road Safety Strategy document has been prepared and consultation will further refine its directions and contents. The paper will describe the processes undertaken to identify issues and solutions, the measurement of road safety maturity and behavioural risk factors, and the overall structure and themes of the strategy.

Predictive modelling to aid the regional-scale management of a vertebrate pest

Extensive resources are allocated to managing vertebrate pests, yet spatial understanding of pest threats, and how they respond to management, is limited at the regional scale where much decision-making is undertaken. We provide regional-scale spatial models and management guidance for European rabbits (Oryctolagus cuniculus) in a 260,791 km(2) region in Australia by determining habitat suitability, habitat susceptibility and the effects of the primary rabbit management options (barrier fence, shooting and baiting and warren ripping) or changing predation or disease control levels. A participatory modelling approach was used to develop a Bayesian network which captured the main drivers of suitability and spread, which in turn was linked spatially to develop high resolution risk maps. Policy-makers, rabbit managers and technical experts were responsible for defining the questions the model needed to address, and for subsequently developing and parameterising the model. Habitat suitability was determined by conditions required for warren-building and by above-ground requirements, such as food and harbour, and habitat susceptibility by the distance from current distributions, habitat suitability, and the costs of traversing habitats of different quality. At least one-third of the region had a high probability of being highly suitable (support high rabbit densities), with the model supported by validation. Habitat susceptibility was largely restricted by the current known rabbit distribution. Warren ripping was the most effective control option as warrens were considered essential for rabbit persistence. The anticipated increase in disease resistance was predicted to increase the probability of moderately suitable habitat becoming highly suitable, but not increase the at-risk area. We demonstrate that it is possible to build spatial models to guide regional-level management of vertebrate pests which use the best available knowledge and capture fine spatial-scale processes.

Science, ICT and Mathematics Education in Rural and Regional Australia: The SiMERR National Survey

The SiMERR National Survey was one of the first priorities of the National Centre of Science, Information and Communication Technology and Mathematics Education for Rural and Regional Australia (SiMERR Australia), established at the University of New England in July 2004 through a federal government grant. With university based ‘hubs’ in each state and territory, SiMERR Australia aims to support rural and regional teachers, students and communities in improving educational outcomes in these subject areas. The purpose of the survey was to identify the key issues affecting these outcomes. The National Survey makes six substantial contributions to our understanding of issues in rural education. First, it focuses specifically on school science, ICT and mathematics education, rather than on education more generally. Second, it compares the different circumstances and needs of teachers across a nationally agreed geographical framework, and quantifies these differences. Third, it compares the circumstances and needs of teachers in schools with different proportions of Indigenous students. Fourth, it provides greater detail than previous studies on the specific needs of schools and teachers in these subject areas. Fifth, the analyses of teacher ‘needs’ have been controlled for the socio-economic background of school locations, resulting in findings that are more tightly associated with geographic location than with economic circumstances. Finally, most previous reports on rural education in Australia were based upon focus interviews, public submissions or secondary analyses of available data. In contrast, the National Survey has generated a sizable body of original quantitative and qualitative data.

Livelihood, land use and environment interactions in the highlands of East Africa

This study aims at improving understanding of the interactions of livelihoods and the environment focusing on both socio-economic and biodiversity implications of land use change in the context of population pressure, global and local markets, climate change, cultural and regional historical factors in the highlands of East Africa. The study is based on three components (1) two extensive livelihood surveys, one on Mt. Kilimanjaro in Tanzania and the other in the Taita Hills of Kenya, (2) a land use change study of the southern slopes of Mt. Kilimanjaro focusing on land use trends between 1960s and 1980s and 1980s and 2000 and (3) a bird diversity study focusing on the potential impacts of the future land use change on birds in the main land use types on the slopes and the adjacent plains of Mt. Kilimanjaro. In addition, information on the highlands in Embu and the adjacent lowlands in Mbeere of Kenya are added to the discussion. Some general patterns of livelihood, land use and environment interactions can be found in the three sites. However, the linkages are very complex. Various external factors at different times in history have influenced most of the major turning points. Farmers continually make small adaptations to their farming practices, but the locally conceived alternatives are too few. Farmers lack specific information and knowledge on the most suitable crops, market opportunities and the quality requirements for growing the crops for markets. Population growth emerges as the most forceful driver of land use and environmental change. The higher altitudes have become extremely crowded with population densities in some areas higher than typical urban population densities. Natural vegetation has almost totally been replaced by farmland. Decreasing farm size due to population pressure is currently threatening the viability of whole farming systems. In addition, capital-poor intensification has lead to soil fertility depletion. Agricultural expansion to the agriculturally marginal lowlands has created a new and distinct group of farmers struggling constantly with climate variability causing frequent crop failures. Extensification to the fragile drylands is the major cause of fragmentation and loss of wildlife habitat. The linkages between livelihoods, land use and the environment generally point to degradation of the environment leading to reduced environmental services and ecosystem functions. There is no indication that the system is self-regulating in this respect. Positive interventions will be needed to maintain ecosystem integrity.

Mathematical Aspects of Financial Markets with Frictions

Frictions are factors that hinder trading of securities in financial markets. Typical frictions include limited market depth, transaction costs, lack of infinite divisibility of securities, and taxes. Conventional models used in mathematical finance often gloss over these issues, which affect almost all financial markets, by arguing that the impact of frictions is negligible and, consequently, the frictionless models are valid approximations. This dissertation consists of three research papers, which are related to the study of the validity of such approximations in two distinct modeling problems. Models of price dynamics that are based on diffusion processes, i.e., continuous strong Markov processes, are widely used in the frictionless scenario. The first paper establishes that diffusion models can indeed be understood as approximations of price dynamics in markets with frictions. This is achieved by introducing an agent-based model of a financial market where finitely many agents trade a financial security, the price of which evolves according to price impacts generated by trades. It is shown that, if the number of agents is large, then under certain assumptions the price process of security, which is a pure-jump process, can be approximated by a one-dimensional diffusion process. In a slightly extended model, in which agents may exhibit herd behavior, the approximating diffusion model turns out to be a stochastic volatility model. Finally, it is shown that when agents' tendency to herd is strong, logarithmic returns in the approximating stochastic volatility model are heavy-tailed. The remaining papers are related to no-arbitrage criteria and superhedging in continuous-time option pricing models under small-transaction-cost asymptotics. Guasoni, Rásonyi, and Schachermayer have recently shown that, in such a setting, any financial security admits no arbitrage opportunities and there exist no feasible superhedging strategies for European call and put options written on it, as long as its price process is continuous and has the so-called conditional full support (CFS) property. Motivated by this result, CFS is established for certain stochastic integrals and a subclass of Brownian semistationary processes in the two papers. As a consequence, a wide range of possibly non-Markovian local and stochastic volatility models have the CFS property.

A generic method of engagement to elicit regional coastal management options

Stakeholder engagement is important for successful management of natural resources, both to make effective decisions and to obtain support. However, in the context of coastal management, questions remain unanswered on how to effectively link decisions made at the catchment level with objectives for marine biodiversity and fisheries productivity. Moreover, there is much uncertainty on how to best elicit community input in a rigorous manner that supports management decisions. A decision support process is described that uses the adaptive management loop as its basis to elicit management objectives, priorities and management options using two case studies in the Great Barrier Reef, Australia. The approach described is then generalised for international interest. A hierarchical engagement model of local stakeholders, regional and senior managers is used. The result is a semi-quantitative generic elicitation framework that ultimately provides a prioritised list of management options in the context of clearly articulated management objectives that has widespread application for coastal communities worldwide. The case studies show that demand for local input and regional management is high, but local influences affect the relative success of both engagement processes and uptake by managers. Differences between case study outcomes highlight the importance of discussing objectives prior to suggesting management actions, and avoiding or minimising conflicts at the early stages of the process. Strong contributors to success are a) the provision of local information to the community group, and b) the early inclusion of senior managers and influencers in the group to ensure the intellectual and time investment is not compromised at the final stages of the process. The project has uncovered a conundrum in the significant gap between the way managers perceive their management actions and outcomes, and community's perception of the effectiveness (and wisdom) of these same management actions.

Early post-operative mortality after major lower limb amputation: A systematic review of population and regional based studies

OBJECTIVE: Lower limb amputation is often associated with a high risk of early post-operative mortality. Mortality rates are also increasingly being put forward as a possible benchmark for surgical performance. The primary aim of this systematic review is to investigate early post-operative mortality following a major lower limb amputation in population/regional based studies, and reported factors that might influence these mortality outcomes. METHODS: Embase, PubMed, Cinahl and Psycinfo were searched for publications in any language on 30 day or in hospital mortality after major lower limb amputation in population/regional based studies. PRISMA guidelines were followed. A self developed checklist was used to assess quality and susceptibility to bias. Summary data were extracted for the percentage of the population who died; pooling of quantitative results was not possible because of methodological differences between studies. RESULTS: Of the 9,082 publications identified, results were included from 21. The percentage of the population undergoing amputation who died within 30 days ranged from 7% to 22%, the in hospital equivalent was 4-20%. Transfemoral amputation and older age were found to have a higher proportion of early post-operative mortality, compared with transtibial and younger age, respectively. Other patient factors or surgical treatment choices related to increased early post-operative mortality varied between studies. CONCLUSIONS: Early post-operative mortality rates vary from 4% to 22%. There are very limited data presented for patient related factors (age, comorbidities) that influence mortality. Even less is known about factors related to surgical treatment choices, being limited to amputation level. More information is needed to allow comparison across studies or for any benchmarking of acceptable mortality rates. Agreement is needed on key factors to be reported.

How social preferences shape incentives in (experimental) markets for credence goods

Credence goods markets suffer from inefficiencies caused by superior information of sellers about the surplus-maximising quality. While standard theory predicts that equal mark-up prices solve the credence goods problem if customers can verify the quality received, experimental evidence indicates the opposite. We identify a lack of robustness with respect to heterogeneity in social preferences as a possible cause of this and conduct new experiments that allow for parsimonious identification of sellers’ social preference types. Our results confirm the assumed heterogeneity in social preferences and provide strong support for our explanation of the failure of verifiability to increase efficiency.

HR-MAS NMR spectroscopy shows regional metabolite variation in bovine articular cartilage

Mechanical stress is an important external factor effecting the development and maintenance of articular cartilage. The metabolite profile of diseased cartilage has been well studied but there is limited information about the variation in metabolite profile of healthy cartilage. With the importance of load in maintaining healthy cartilage, regional differences in metabolite profile associated with differences in load may provide information on how load contributes to the maintenance of healthy cartilage. HR-MAS NMR spectroscopy allows the assessment of tissue samples without modification and was used for assessing the difference in metabolic profile between the load bearing and non-load bearing regions of the bovine articular cartilage. In this preliminary study, we examined cartilage from tibia and femur of four knee joints. Sixteen pairs of 1D-NOESY spectra were acquired. Principle component analysis (PCA) identified chemical shifts responsible for variance. SBASE (AMIX) and the Human Metabolome Database were used in conjunction with previous reported cartilage data for identifying metabolites associated with the PCA results. The major contributors to load-related differences in metabolite profile were N-acetyl groups, lactate and phosphocholine peaks. Integrals of these regions were further analysed using a Student's t-test. In load bearing cartilage regions. N-acetyl groups and phosphocholine were found at significantly higher concentration (p < 0.05 and p < 0.005, respectively) in both femur and tibia, while lactate was reduced in load bearing cartilage (p < 0.005). The results of this pilot HR-MAS NMR study demonstrate its ability to provide useful metabolite information for healthy cartilage.

Connecting and collaborating in regional, rural and remote Western Australia

Teachers working in regional, rural and remote areas of Western Australia often experience a strong sense of geographic and social isolation from peers, colleagues and appropriate support mechanisms due to the huge distances between towns and communities. The projects described here have focused on the use of technology to enhance both teacher and student learning; and assist with Indigenous education and teacher professional learning. Connecting and collaborating through technologies is emerging as a powerful tool for motivating and engaging both teachers and learners within schools. Coupled with the direction of the current Federal Government with the Digital Education Revolution and the Digital Regions initiatives, opportunities for better serving regional, rural and remote communities are discussed, as are some of the current issues and needs related to these schools in Western Australia. The scope of these projects has been such that three guiding principles have been implemented through contextual lenses of varying foci - at the level of an individual, a school, and a community.

Engaging in online postgraduate education as means of professional learning

With enrolments in higher education becoming a competitive market, through the removal of caps in 2012, the equitable access to postgraduate education is raised. Postgraduate education, provided through higher education institutions, is an important aspect of career development for professionals. Professionals working outside of the metropolitan area are increasingly seeking postgraduate education opportunities that will be delivered online, at a distance. In this research study, data collected from the teaching profession, has culminated in a model that will ultimately improve access to professional learning. This research paper aims to highlight the important role that higher education providers play in the delivery of postgraduate education to professionals working in regional and remote areas of Australia. Although this paper focuses on the realm of education, the model of connectedness, where synchronous and asynchronous technologies are used, can be adapted and applied to any profession that requires equitable access to professional learning.