Beyond barcoding : a mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae)

Members of the Calliphoridae (blowflies) are significant for medical and veterinary management, due to the ability of some species to consume living flesh as larvae, and for forensic investigations due to the ability of others to develop in corpses. Due to the difficulty of accurately identifying larval blowflies to species there is a need for DNA-based diagnostics for this family, however the widely used DNA-barcoding marker, cox1, has been shown to fail for several groups within this family. Additionally, many phylogenetic relationships within the Calliphoridae are still unresolved, particularly deeper level relationships. Sequencing whole mt genomes has been demonstrated both as an effective method for identifying the most informative diagnostic markers and for resolving phylogenetic relationships. Twenty-seven complete, or nearly so, mt genomes were sequenced representing 13 species, seven genera and four calliphorid subfamilies and a member of the related family Tachinidae. PCR and sequencing primers developed for sequencing one calliphorid species could be reused to sequence related species within the same superfamily with success rates ranging from 61% to 100%, demonstrating the speed and efficiency with which an mt genome dataset can be assembled. Comparison of molecular divergences for each of the 13 protein-coding genes and 2 ribosomal RNA genes, at a range of taxonomic scales identified novel targets for developing as diagnostic markers which were 117–200% more variable than the markers which have been used previously in calliphorids. Phylogenetic analysis of whole mt genome sequences resulted in much stronger support for family and subfamily-level relationships. The Calliphoridae are polyphyletic, with the Polleninae more closely related to the Tachinidae, and the Sarcophagidae are the sister group of the remaining calliphorids. Within the Calliphoridae, there was strong support for the monophyly of the Chrysomyinae and Luciliinae and for the sister-grouping of Luciliinae with Calliphorinae. Relationships within Chrysomya were not well resolved. Whole mt genome data, supported the previously demonstrated paraphyly of Lucilia cuprina with respect to L. sericata and allowed us to conclude that it is due to hybrid introgression prior to the last common ancestor of modern sericata populations, rather than due to recent hybridisation, nuclear pseudogenes or incomplete lineage sorting.

Preparing for portfolio careers in Australian music : setting a research agenda

In the twenty-first century, Australian musicians increasingly maintain ‘portfolio’ careers, in which they combine diverse employment arrangements and activities. Often, these incorporate industry sectors outside of music. This career pattern is widespread but not well understood, largely because of the limitations of existing research. The lack of knowledge about musicians’ work and careers means that Australia currently may not provide appropriate and effective policy, funding, initial training and continuing career support across the diverse music sector. This article discusses existing research relating to the careers and skilling needs of musicians in Australia, and outlines a targeted agenda for further research that has the potential to inform stronger alignment between the requirements of building sustainable music careers and musicians’ education and training.

Engineering across cultures : new learning resources for intercultural competency in engineering

BACKGROUND The work described in this paper has emerged from an ALTC/OLT funded project, Exploring Intercultural Competency in Engineering. The project indentified many facets of culture and intercultural competence that go beyond a culture-as-nationality paradigm. It was clear from this work that resources were needed to help engineering educators introduce students to the complex issues of culture as they relate to engineering practice. A set of learning modules focussing on intercultural competence in engineering practice were developed early on in the project. Through the OLT project, these modules have been expanded into a range of resources covering various aspects of culture in engineering. Supporting the resources, an eBook detailing the ins and outs of intercultural competency has also been developed to assist engineering educators to embed opportunities for students to develop skills in unpacking and managing cross-cultural challenges in engineering practice. PURPOSE This paper describes the key principles behind the development of the learning modules, the areas they cover and the eBook developed to support the modules. The paper is intended as an introduction to the approaches and resources and extends an invitation to the community to draw from, and contribute to this initial work. DESIGN/METHOD A key aim of this project was to go beyond the culture-as-nationality approach adopted in much of the work around intercultural competency (Deardorff, 2011). The eBook explores different dimensions of culture such as workplace culture, culture’s influence on engineering design, and culture in the classroom. The authors describe how these connect to industry practice and explore what they mean for engineering education. The packaged learning modules described here have been developed as a matrix of approaches moving from familiar known methods through complicated activities relying to some extent on expert knowledge. Some modules draw on the concept of ‘complex un-order’ as described in the ‘Cynefin domains’ proposed by Kurtz and Snowden (2003). RESULTS Several of the modules included in the eBook have already been trialled at a variety of institutions. Feedback from staff has been reassuringly positive so far. Further trials are planned for second semester 2012, and version 1 of the eBook and learning modules, Engineering Across Cultures, is due to be released in late October 2012. CONCLUSIONS The Engineering Across Cultures eBook and learning modules provide a useful and ready to employ resource to help educators tackle the complex issue of intercultural competency in engineering education. The book is by no means exhaustive, and nor are the modules, they instead provide an accessible, engineering specific guide to bringing cultural issues into the engineering classroom.

Years lived with disability (YLDs) for 1160 sequelae of 289 diseases and injuries 1990–2010 : a systematic analysis for the Global Burden of Disease Study 2010

Background Non-fatal health outcomes from diseases and injuries are a crucial consideration in the promotion and monitoring of individual and population health. The Global Burden of Disease (GBD) studies done in 1990 and 2000 have been the only studies to quantify non-fatal health outcomes across an exhaustive set of disorders at the global and regional level. Neither effort quantified uncertainty in prevalence or years lived with disability (YLDs). Methods Of the 291 diseases and injuries in the GBD cause list, 289 cause disability. For 1160 sequelae of the 289 diseases and injuries, we undertook a systematic analysis of prevalence, incidence, remission, duration, and excess mortality. Sources included published studies, case notification, population-based cancer registries, other disease registries, antenatal clinic serosurveillance, hospital discharge data, ambulatory care data, household surveys, other surveys, and cohort studies. For most sequelae, we used a Bayesian meta-regression method, DisMod-MR, designed to address key limitations in descriptive epidemiological data, including missing data, inconsistency, and large methodological variation between data sources. For some disorders, we used natural history models, geospatial models, back-calculation models (models calculating incidence from population mortality rates and case fatality), or registration completeness models (models adjusting for incomplete registration with health-system access and other covariates). Disability weights for 220 unique health states were used to capture the severity of health loss. YLDs by cause at age, sex, country, and year levels were adjusted for comorbidity with simulation methods. We included uncertainty estimates at all stages of the analysis. Findings Global prevalence for all ages combined in 2010 across the 1160 sequelae ranged from fewer than one case per 1 million people to 350 000 cases per 1 million people. Prevalence and severity of health loss were weakly correlated (correlation coefficient −0·37). In 2010, there were 777 million YLDs from all causes, up from 583 million in 1990. The main contributors to global YLDs were mental and behavioural disorders, musculoskeletal disorders, and diabetes or endocrine diseases. The leading specific causes of YLDs were much the same in 2010 as they were in 1990: low back pain, major depressive disorder, iron-deficiency anaemia, neck pain, chronic obstructive pulmonary disease, anxiety disorders, migraine, diabetes, and falls. Age-specific prevalence of YLDs increased with age in all regions and has decreased slightly from 1990 to 2010. Regional patterns of the leading causes of YLDs were more similar compared with years of life lost due to premature mortality. Neglected tropical diseases, HIV/AIDS, tuberculosis, malaria, and anaemia were important causes of YLDs in sub-Saharan Africa. Interpretation Rates of YLDs per 100 000 people have remained largely constant over time but rise steadily with age. Population growth and ageing have increased YLD numbers and crude rates over the past two decades. Prevalences of the most common causes of YLDs, such as mental and behavioural disorders and musculoskeletal disorders, have not decreased. Health systems will need to address the needs of the rising numbers of individuals with a range of disorders that largely cause disability but not mortality. Quantification of the burden of non-fatal health outcomes will be crucial to understand how well health systems are responding to these challenges. Effective and affordable strategies to deal with this rising burden are an urgent priority for health systems in most parts of the world. Funding Bill & Melinda Gates Foundation.

The complete mitochondrial genome of the flesh fly, Sarcophaga impatiens Walker (Diptera: Sarcophagidae)

Approximately 2500 fly species comprise the Sarcophagidae family worldwide. The complete mitochondrial genome of the carrion-breeding, forensically important Sarcophaga impatiens Walker (Diptera: Sarcophagidae) from Australia was sequenced. The 15,169 bp circular genome contains the 37 genes found in a typical Metazoan genome: 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. It also contains one non-coding A+T-rich region. The arrangement of the genes was the same as that found in the ancestral insect. All the protein initiation codons are ATN, except for cox1 that begins with TCG (encoding S). The 22 tRNA anticodons of S. impatiens are consistent with those observed in Drosophila yakuba, and all form the typical cloverleaf structure, except for tRNA-Ser(AGN) that lacks the DHU arm. The mitochondrial genome of Sarcophaga presented will be valuable for resolving phylogenetic relationships within the family Sarcophagidae and the order Diptera, and could be used to identify favourable genetic markers for species identifications for forensic purposes.

Peer assisted learning, skills development and Generation Y : a case study of a first year undergraduate law unit

The majority of current first year university students belong to Generation Y. Consequently, research suggests that, in order to more effectively engage them, their particular learning preferences should be acknowledged in the organisation of their learning environments and in the support provided. These preferences are reflected in the Torts Student Peer Mentor Program, which, as part of the undergraduate law degree at the Queensland University of Technology, utilises active learning, structured sessions and teamwork to supplement student understanding of the substantive law of Torts with the development of life-long skills. This article outlines the Program, and its relevance to the learning styles and experiences of Generation Y first year law students transitioning to university, in order to investigate student perceptions of its effectiveness – both generally and, more specifically, in terms of the Program’s capacity to assist students to develop academic and work-related skills.

Legal practitioners’ negligence liability for claim investigation and advice

Nigam v Harm (No 2) [2011] WASCA 221, Western Australia Court of Appeal, 18 October 2011

Second Skin 2012 Workshop

The Second Skin 2012 Workshop Program consisted of a full-day intensive design immersion workshop run on Saturday 14 July 2012, at the QUT Faculty of Creative Industries Fashion Studios at Kelvin Grove Brisbane, Australia, for 30? self-selected high-achieving junior and middle school (year 5-9) students, as part of the Queensland Academies ‘Young Scholars’ Program. Inspired by a scientist researching the impact of sun on skin, and mentored by tertiary fashion design and interior design educators, and six tertiary fashion design and interior design students, the workshop explored science and design-inspired prototype solutions for sun-safety. This action research study aimed to facilitate an acute awareness in young people of the sun safety message (alternative to a scare campaign), the role of design in society and the value of design thinking skills in solving complex challenges, and to inspire the generation of strategies to address a systemic health issue. It also aimed to investigate the value of collaboration between junior and middle school students, tertiary design educators and students and industry professionals in targeting youth sun safety, and inspiring post-secondary pathways and idea generation for education. During the workshop, students developed sketching, making, communication, presentation and collaboration skills to improve their design process, while considering social, cultural and environmental opportunities. Through a series of hands-on collaborative design experiments, participants explored in teams of five, ways in which a ‘second skin’ can mirror elements of our skin – the ability to protect, divide, enclose, stretch, scar, pattern, peel and reveal – inspiring both functional and aesthetic design solutions. Underpinned by the State Library of Queensland Design Minds Website ‘inquire, ideate and implement’ model of design thinking, the experiments culminated in the development of a detailed client brief, the design and fabrication of a fashionable sun safe clothing range and then a team presentation and modelling of prototypes in a fashion parade, viewed also by parents. The final collections were judged by three prominent judges: Louise Baldwin - Executive Manager Public Health QLD Cancer Council, Shane Thompson - Architect and 2012 Queensland Smart Design Fellow, and Leigh Buchanan – Fashion designer and Project Runway Australia finalist. The workshop was filmed for Queensland television program ‘Totally Wild’ for dissemination of the value of design, the Design Minds model and the sun safety message to a wider target youth audience.

Brave new green world : consequences of a carbon economy for the conservation of Australian biodiversity

Pricing greenhouse gas emissions is a burgeoning and possibly lucrative financial means for climate change mitigation. Emissions pricing is being used to fund emissions-abatement technologies and to modify land management to improve carbon sequestration and retention. Here we discuss the principal land-management options under existing and realistic future emissions-price legislation in Australia, and examine them with respect to their anticipated direct and indirect effects on biodiversity. The main ways in which emissions price-driven changes to land management can affect biodiversity are through policies and practices for (1) environmental plantings for carbon sequestration, (2) native regrowth, (3) fire management, (4) forestry, (5) agricultural practices (including cropping and grazing), and (6) feral animal control. While most land-management options available to reduce net greenhouse gas emissions offer clear advantages to increase the viability of native biodiversity, we describe several caveats regarding potentially negative outcomes, and outline components that need to be considered if biodiversity is also to benefit from the new carbon economy. Carbon plantings will only have real biodiversity value if they comprise appropriate native tree species and provide suitable habitats and resources for valued fauna. Such plantings also risk severely altering local hydrology and reducing water availability. Management of regrowth post-agricultural abandonment requires setting appropriate baselines and allowing for thinning in certain circumstances, and improvements to forestry rotation lengths would likely increase carbon-retention capacity and biodiversity value. Prescribed burning to reduce the frequency of high-intensity wildfires in northern Australia is being used as a tool to increase carbon retention. Fire management in southern Australia is not readily amenable for maximising carbon storage potential, but will become increasingly important for biodiversity conservation as the climate warms. Carbon price-based modifications to agriculture that would benefit biodiversity include reductions in tillage frequency and livestock densities, reductions in fertiliser use, and retention and regeneration of native shrubs; however, anticipated shifts to exotic perennial grass species such as buffel grass and kikuyu could have net negative implications for native biodiversity. Finally, it is unlikely that major reductions in greenhouse gas emissions arising from feral animal control are possible, even though reduced densities of feral herbivores will benefit Australian biodiversity greatly.

Aerosol mass spectrometric analysis of the chemical composition of non- refractory PM1 samples from school environments in Brisbane, Australia

Long term exposure to vehicle emissions has been associated with harmful health effects. Children are amongst the most susceptible group and schools represent an environment where they can experience significant exposure to vehicle emissions. However, there are limited studies on children’s exposure to vehicle emissions in schools. The aim of this study was to quantify the concentration of organic aerosol and in particular, vehicle emissions that children are exposed to during school hours. Therefore an Aerodyne compact time-of-flight aerosol mass spectrometer (TOF-AMS) was deployed at five urban schools in Brisbane, Australia. The TOF-AMS enabled the chemical composition of the non- refractory (NR-PM1) to be analysed with a high temporal resolution to assess the concentration of vehicle emissions and other organic aerosols during school hours. At each school the organic fraction comprised the majority of NR-PM1 with secondary organic aerosols as the main constitute. At two of the schools, a significant source of the organic aerosol (OA) was slightly aged vehicle emissions from nearby highways. More aged and oxidised OA was observed at the other three schools, which also recorded strong biomass burning influences. Primary emissions were found to dominate the OA at only one school which had an O:C ratio of 0.17, due to fuel powered gardening equipment used near the TOF-AMS. The diurnal cycle of OA concentration varied between schools and was found to be at a minimum during school hours. The major organic component that school children were exposed to during school hours was secondary OA. Peak exposure of school children to HOA occurred during school drop off and pick up times. Unless a school is located near major roads, children are exposed predominately to regional secondary OA as opposed to local emissions during schools hours in urban environments.

Spatial variation of particle number concentration in school microscale environments and its impact on exposure assessment

It has not yet been established whether the spatial variation of particle number concentration (PNC) within a microscale environment can have an effect on exposure estimation results. In general, the degree of spatial variation within microscale environments remains unclear, since previous studies have only focused on spatial variation within macroscale environments. The aims of this study were to determine the spatial variation of PNC within microscale school environments, in order to assess the importance of the number of monitoring sites on exposure estimation. Furthermore, this paper aims to identify which parameters have the largest influence on spatial variation, as well as the relationship between those parameters and spatial variation. Air quality measurements were conducted for two consecutive weeks at each of the 25 schools across Brisbane, Australia. PNC was measured at three sites within the grounds of each school, along with the measurement of meteorological and several other air quality parameters. Traffic density was recorded for the busiest road adjacent to the school. Spatial variation at each school was quantified using coefficient of variation (CV). The portion of CV associated with instrument uncertainty was found to be 0.3 and therefore, CV was corrected so that only non-instrument uncertainty was analysed in the data. The median corrected CV (CVc) ranged from 0 to 0.35 across the schools, with 12 schools found to exhibit spatial variation. The study determined the number of required monitoring sites at schools with spatial variability and tested the deviation in exposure estimation arising from using only a single site. Nine schools required two measurement sites and three schools required three sites. Overall, the deviation in exposure estimation from using only one monitoring site was as much as one order of magnitude. The study also tested the association of spatial variation with wind speed/direction and traffic density, using partial correlation coefficients to identify sources of variation and non-parametric function estimation to quantify the level of variability. Traffic density and road to school wind direction were found to have a positive effect on CVc, and therefore, also on spatial variation. Wind speed was found to have a decreasing effect on spatial variation when it exceeded a threshold of 1.5 (m/s), while it had no effect below this threshold. Traffic density had a positive effect on spatial variation and its effect increased until it reached a density of 70 vehicles per five minutes, at which point its effect plateaued and did not increase further as a result of increasing traffic density.

Integrated genomic characterization of endometrial carcinoma

We performed an integrated genomic, transcriptomic and proteomic characterization of 373 endometrial carcinomas using array- and sequencing-based technologies. Uterine serous tumours and ∼25% of high-grade endometrioid tumours had extensive copy number alterations, few DNA methylation changes, low oestrogen receptor/progesterone receptor levels, and frequent TP53 mutations. Most endometrioid tumours had few copy number alterations or TP53 mutations, but frequent mutations in PTEN, CTNNB1, PIK3CA, ARID1A and KRAS and novel mutations in the SWI/SNF chromatin remodelling complex gene ARID5B. A subset of endometrioid tumours that we identified had a markedly increased transversion mutation frequency and newly identified hotspot mutations in POLE. Our results classified endometrial cancers into four categories: POLE ultramutated, microsatellite instability hypermutated, copy-number low, and copy-number high. Uterine serous carcinomas share genomic features with ovarian serous and basal-like breast carcinomas. We demonstrated that the genomic features of endometrial carcinomas permit a reclassification that may affect post-surgical adjuvant treatment for women with aggressive tumours.

School libraries, teacher-librarians and their contribution to student literacy development in Gold Coast schools

This is the first research focusing on Gold Coast school libraries and teacher- librarians. It presents a detailed picture of library provision and staffing at a representative group of 27 government and non-government schools at the Gold Coast. It shows links between employment of a teacher-librarian and higher NAPLAN reading and writing scores. And it presents the principals’ generally positive views about teacher-librarians’ contribution to reading and literacy at their schools. The findings respond in part to the recent government inquiry’s call (House of Representatives, 2011) for research about the current staffing of school libraries in Australia, and the influence of school libraries and teacher-librarians on students’ literacy and learning outcomes. While the study has focused on a relatively small group of school libraries, it has produced a range of significant outcomes: • An extensive review of international and Australian research showing impacts of school libraries and teacher-librarians on students’ literacy and learning outcomes • Findings consistent with international research showing: - An inverse relationship between lower student to EFT library staff ratio and higher school NAPLAN scores for reading and writing - Schools that employ a teacher-librarian tend to achieve school NAPLAN scores for respective year levels that are higher than the national mean It is anticipated that the study’s findings will be of interest to education authorities, school leadership teams, teacher-librarians, teachers and researchers. The findings provide evidence to: • inform policy development and strategic planning for school libraries that respond to the literacy development needs of 21st century learners • inform school-based management of school libraries • inform curriculum development and teacher-librarian practice • support further collaborative research on a State or national level • enhance conceptual understandings about relationship(s) between school libraries, teacher-librarians and literacy/information literacy development • support advocacy about school libraries, teacher-librarians and their contribution to literacy development and student learning in Australian schools SLAQ President Toni Leigh comments: “It is heartening to see findings which validate the critical role teacher-librarians play in student literacy development and the positive correlation of higher NAPLAN scores and schools with a qualified teacher-librarian. Also encouraging is the high percentage of school principals who recognise the necessity of a well resourced school library and the positive influence of these libraries on student literacy”. This research arises from a research partnership between School Library Association of Queensland (SLAQ) and Children and Youth Research Centre, QUT. Lead researcher: Dr Hilary Hughes, Children and Youth Research Centre, QUT Research assistants: Dr Hossein Bozorgian, Dr Cherie Allan, Dr Michelle Dicinoski, QUT SLAQ Research Reference Group: Toni Leigh, Marj Osborne, Sally Fraser, Chris Kahl and Helen Reynolds Reference: House of Representatives. (2011). School libraries and teacher librarians in 21st century Australia. Canberra: Commonwealth of Australia. http://www.aph.gov.au/Parliamentary_Business/Committees/House_of_Representatives_Committees?url=ee/schoollibraries/report.htm

Valuing student and community voices in the university : action research as a framework for community service-learning

The Community Service-learning Lab (the Lab) was initiated as a university-wide service-learning experience at an Australian university. The Lab engages students, academics, and key community organisations in interdisciplinary action research projects to support student learning and to explore complex and ongoing problems nominated by the community partners. The current study uses feedback from the first offering of the Lab and focuses on exploring student experiences of the service learning project using an action research framework. Student reflections on this experience have revealed some positive outcomes of the Lab such as an appreciation for positive and strengths-based change. These outcomes are corroborated by collected reflections from community partners and academics. The students also identified challenges balancing the requirements for assessment and their goals to serve the community partner’s needs. This feedback has provided vital information for the academic team, highlighting the difficulties in balancing the agenda of the academic framework and the desire to give students authentic experiences.