qRT-PCR of Small RNAs

Plant small RNAs are a class of 19- to 25-nucleotide (nt) RNA molecules that are essential for genome stability, development and differentiation, disease, cellular communication, signaling, and adaptive responses to biotic and abiotic stress. Small RNAs comprise two major RNA classes, short interfering RNAs (siRNAs) and microRNAs (miRNAs). Efficient and reliable detection and quantification of small RNA expression has become an essential step in understanding their roles in specific cells and tissues. Here we provide protocols for the detection of miRNAs by stem-loop RT-PCR. This method enables fast and reliable miRNA expression profiling from as little as 20 pg of total RNA extracted from plant tissue and is suitable for high-throughput miRNA expression analysis. In addition, this method can be used to detect other classes of small RNAs, provided the sequence is known and their GC contents are similar to those specific for miRNAs.

Characterisation of red mud and seawater neutralised red mud using vibrational spectroscopic techniques

Bauxite refinery residues are derived from the Bayer process by the digestion of crushed bauxite in concentrated caustic at elevated temperatures. Chemically, it comprises, in varying amounts (depending upon the composition of the starting bauxite), oxides of iron and titanium, residual alumina, sodalite, silica, and minor quantities of other metal oxides. Bauxite residues are being neutralised by seawater in recent years to reduce the alkalinity in bauxite residue, through the precipitation of hydrotalcite-like compounds and some other Mg, Ca, and Al hydroxide and carbonate minerals. A combination of X-ray diffraction (XRD) and vibrational spectroscopy techniques, including mid-infrared (IR), Raman, near-infrared (NIR), and UV-Visible, have been used to characterise bauxite residue and seawater neutralised bauxite residue. Both the ferrous (Fe2+) and ferric (Fe3+) ions within bauxite residue can be identified by their characteristic NIR bands, where ferrous ions produce a strong absorption band at around 9000 cm-1, while ferric ions produce two strong bands at 25000 and 14300 cm-1. The presence of adsorbed carbonate and hydroxide anions can be identified at around 5200 and 7000 cm-1, respectively, attributed to the 2nd overtone of the 1st fundamental overtones observed in the mid-IR spectra. The complex bands in the Raman and mid-IR spectra around 3500 cm-1 are assigned to the OH stretching vibrations of the various oxides present in bauxite residue, and water. The combination of carbonate and hydroxyl units and their fundamental overtones give rise to many of the features of the NIR spectra.

Outback institutions : an application of the Institutional Analysis and Development (IAD) framework to four case studies in Australia’s Outback -- Part 4 : Incentives for community participation and land use decisions in Etheridge Shire, Queensland

Natural resource management planning in the Northern Gulf region of Queensland is concerned with ‘how [natural assets] and community aspirations can be protected and enhanced to provide the Northern Gulf community with the economic, social and environmental means to meet the continuing growth of the region in an ecological and economically sustainable way’ (McDonald & Dawson 2004). In the Etheridge Shire, located in the tropical savanna of the Northern Gulf region, two of the activities that influence the balance between economic growth and long-term sustainable development are: 1. the land-use decisions people in the Shire make with regards to their own enterprises. 2. their decisions to engage in civically-minded activities aimed at improving conditions in the region. Land-use decision and engagement in community development activities were chosen for detailed analysis because they are activities for which policies can be devised to improve economic and sustainable development outcomes. Changing the formal and informal rules that guide and govern these two different kinds of decisions that people can make in the Etheridge Shire – the decision to improve one’s own situation and the decision to improve the situation for others in the community – may expand the set of available options for people in the Shire to achieve their goals and aspirations. Identifying appropriate and effective changes in rules requires, first, an understanding of the ‘action arena’, in this case comprised of a diversity of ‘participants’ from both within and outside the Etheridge Shire, and secondly knowledge of ‘action situations’ (land-use decisions and engagement in community development activities) in which stakeholders are involved and/or have a stake. These discussions are presented in sections 4.1.1.1 and 4.1.1.2.

Institutional response and Indigenous experiences of Cyclone Tracy

Early on Christmas morning 1974 Tropical Cyclone Tracy, a Category 4 storm, devastated the Northern Territory city of Darwin leaving only 6% of the city’s housing habitable. The extent of the disaster was largely the result of unregulated and poorly constructed buildings, predominantly housing. While the engineering and reconstruction process demonstrated a very successful response and adaptation to an existing and future risk, the impact of the cyclone of the local community and its Indigenous population in particular, had not been well recorded. NCCARF therefore commissioned a report on the Indigenous experience of Cyclone Tracy to document how Indigenous people were impacted by, responded to, and recovered from Cyclone Tracy in comparison to non-Indigenous groups. The report also considers the research literature on disasters and Indigenous people in the Northern Territory, with a specific focus on cyclones, and considers the socio-political context of Indigenous communities in Darwin prior to Cyclone Tracy.

Adaptation lessons from cyclone Tracy

This case study will review the impact of Tropical Cyclone Tracy on the city and people of Darwin, the Australian engineering and institutional responses that it invoked and the relevance of these lessons to a world threatened by global climate change. At Christmas, 1974, Tropical Cyclone Tracy laid waste the city of Darwin, an iconic episode in the history of Australian natural disasters. It provides one of the clearest and most successful examples worldwide of adaptation to a catastrophe. Following large losses in Townsville from Tropical Cyclone Althea in 1971, the level of destruction in Darwin was such that it led to new regulations mandating the use of the wind code for reconstruction, and eventually to similar regulations for new construction in other cyclone-prone areas of Australia.

Independent learning skills, self-determination theory and psychological well-being : strategies for supporting the first year university experience

The purpose of this article is to explain why the first year in higher education experience of Australian tertiary students can be improved through the explicit teaching of independent learning skills. Becoming an independent learner has many benefits, but the focus of this piece is upon the connection between independent learning and the improvement of student psychological well-being. High psychological distress levels appear to start in the first year of university education. We argue that explicitly teaching students independent learning skills is an important curriculum-based strategy that will contribute to the significant task of addressing this issue.

Loading of a very tall building in a simulated downburst wind field

Thunderstorm downbursts are important for wind engineers as they have been shown to produce the design wind speeds for mid to high return periods in many regions of Australia [1]. In structural design codes (e.g. AS/NZS1170.02-02) an atmospheric boundary layer (ABL) is assumed, and a vertical profile is interpolated from recorded 10 m wind speeds. The ABL assumption is however inaccurate when considering the complex structure of a thunderstorm outflow, and its effects on engineered structures. Several researchers have shown that the downburst, close to its point of divergence is better represented by an impinging wall jet profile than the traditional ABL. Physical modelling is the generally accepted approach to estimate wind loads on structures and it is therefore important to physically model the thunderstorm downburst so that its effects on engineered structures may be studied. An advancement on the simple impinging jet theory, addressed here is the addition of a pulsing mechanism to the jet which allows not only the divergent characteristics of a downburst to be produced, but also it allows the associated leading ring vortex to be developed. The ring vortex modelling is considered very important for structural design as it is within the horizontal vortex that the largest velocities occur [2]. This paper discusses the flow field produced by a pulsed wall jet, and also discusses the induced pressures that this type of flow has on a scaled tall building.

Discussion on full-scale internal pressure measurements

The wind loading on most structural elements is made up of both an external and internal pressure. Internal pressures are also important for the design of naturally ventilated buildings. The internal pressure is the interaction between the external pressure propagating through the building envelope and any internal plant causing building pressurization. Although the external pressure field can be well defined through a series of wind tunnel tests, modeling complexities makes accurate prediction of the internal pressure difficult. For commercial testing for the determination of design cladding pressures, an internal pressure coefficient is generally assumed from wind loading standards. Several theories regarding the propagation of internal pressures through single and multiple dominant openings have been proposed for small and large flexible buildings (Harris (1990), Holmes, (1979), Liu & Saathoff (1981 ), Vickery (1986, 1994), Vickery & Bloxham (1992), Vickery & Georgiou (1991))...

Discussion on the wind climate of Kuwait and Dubai

Historical wind data for Kuwait and Dubai have been analysed to determine the design wind speed for the region. Kuwait and Dubai are located near the northern and southern end of the Persian Gulf respectively. The winds in this region just north of the Tropic of Capricorn are dominated by the Shamal, literally 'north' in Arabic. The winds have traditional Bedouin names such as Al-Haffar (the driller), and Barih Thorayya (morning star). The Al-Dabaran is generally the strongest Shamal in late summer, and can last up to 40 days bringing sand and duststorms.

Priority threat management of invasive plant species in the Lake Eyre Basin

This project is led by scientists in conservation decision appraisal and brings together a group of experts working across the Lake Eyre Basin (LEB). The LEB covers a sixth of Australia, with an array of globally significant natural values that are threatened by invasive plants, among other things. Managers at various levels are investing in attempts to control, contain and eradicate these invasive plant species, under severe time and resources limitations. To date there has been no basin-wide assessment of which weed management strategies and locations provide the best investments for maximising outcomes for biodiversity per unit cost. Further, there has been no assessment of the extent of ecosystem intactness that may be lost without effective invasive plant species management strategies. Given that there are insufficient resources to manage all invasive plant species everywhere, this information has the potential to improve current investment decisions. Here, we provide a prioritisation of invasive plant management strategies in the LEB. Prioritisation was based on cost-effectiveness for biodiversity benefits. We identify the key invasive plant species to target to protect ecosystem intactness across the bioregions of the LEB, the level of investment required and the likely reduction in invasive species dominance gained per dollar spent on each strategy. Our focus is on strategies that are technically and socially feasible and reduce the likelihood that high impact invasive plant species will dominate native ecosystems, and therefore change their form and function. The outputs of this work are designed to help guide decision-making and further planning and investment in weed management for the Basin. Experts in weed management, policy-making, community engagement, biodiversity and natural values of the Basin, attended a workshop and agreed upon 12 strategies to manage invasive plants. The strategies focused primarily on 10 weeds which were considered to have a high potential for broad, significant impacts on natural ecosystems in the next 50 years and for which feasible management strategies could be defined. Each strategy consisted of one or more supporting actions, many of which were spatially linked to IBRA (Interim Biogeographical Regionalisation of Australia) bioregions. The first strategy was an over-arching recommendation for improved mapping, information sharing, education and extension efforts in order to facilitate the more specific weed management strategies. The 10 more specific weed management strategies targeted the control and/or eradication of the following high-impact exotic plants: mesquite, parkinsonia, rubber vine, bellyache bush, cacti, mother of millions, chinee apple, athel pine and prickly acacia, as well as a separate strategy for eradicating all invasive plants from one key threatened ecological community, the GAB (Great Artesian Basin dependant) mound springs. Experts estimated the expected biodiversity benefit of each strategy as the reduction in area that an invasive plant species is likely to dominate in over a 50-year period, where dominance was defined as more than 30% coverage at a site. Costs were estimated in present day terms over 50 years largely during follow up discussions post workshop. Cost-effectiveness was then calculated for each strategy in each bioregion by dividing the average expected benefit by the average annual costs. Overall, the total cost of managing 12 invasive plant strategies over the next 50 years was estimated at $1.7 billion. It was estimated that implementation of these strategies would result in a reduction of invasive plant dominance by 17 million ha (a potential 32% reduction), roughly 14% of the LEB. If only targeting Weeds of National Significance (WONS), the total cost was estimated to be $113 million over the next 50 years. Over the next 50 years, $2.3 million was estimated to eradicate all invasive plant species from the Great Artesian Basin Mound Springs threatened ecological community. Prevention and awareness programs were another key strategy targeted across the Basin and estimated at $17.5 million in total over 50 years. The cost of controlling, eradicating and containing buffel grass were the most expensive, over $1.5 billion over 50 years; this strategy was estimated to result in a reduction in buffel grass dominance of a million ha in areas where this species is identified as an environmental problem. Buffel grass has been deliberately planted across the Basin for pasture production and is by far the most widely distributed exotic species. Its management is contentious, having economic value to many graziers while posing serious threats to biodiversity and sites of high cultural and conservation interest. The strategy for containing and locally eradicating buffel grass was a challenge to cost based on expert knowledge, possibly because of the dual nature of this species as a valued pastoral grass and environmental weed. Based on our conversations with experts, it appears that control and eradication programs for this species, in conservation areas, are growing rapidly and that information on the most cost-effective strategies for this species will continue to develop over time. The top five most cost-effective strategies for the entire LEB were for the management of: 1) parkinsonia, 2) chinee apple, 3) mesquite, 4) rubber vine and 5) bellyache bush. Chinee apple and mother of millions are not WONS and have comparatively small populations within the semi-arid bioregions of Queensland. Experts felt that there was an opportunity to eradicate these species before they had the chance to develop into high-impact species within the LEB. Prickly acacia was estimated to have one of the highest benefits, but the costs of this strategy were high, therefore it was ranked 7th overall. The buffel grass strategy was ranked the lowest (10th) in terms of cost effectiveness. The top five most cost-effective strategies within and across the bioregions were the management of: 1) parkinsonia in the Channel Country, 2) parkinsonia in the Desert Uplands, 3) mesquite in the Mitchell Grass Downs, 4) parkinsonia in the Mitchell Grass Downs, and 5) mother of millions in the Desert Uplands. Although actions for several invasive plant species like parkinsonia and prickly acacia were concentrated in the Queensland part of the LEB, the actions involved investing in containment zones to prevent the spread of these species into other states. In the NT and SA bioregions of the LEB, the management of athel pine, parkinsonia and cacti were the main strategies. While outside the scientific research goals of study, this work highlighted a number of important incidental findings that led us to make the following recommendations for future research and implementation of weed management in the Basin: • Ongoing stakeholder engagement, extension and participation is required to ensure this prioritisation effort has a positive impact in affecting on-ground decision making and planning. • Short term funding for weed management was identified as a major reason for failure of current efforts, hence future funding needs to be secure and ongoing. • Improved mapping and information sharing is essential to implement effective weed management. • Due to uncertainties in the outcomes and impacts of management options, strategies should be implemented as part of an adaptive management program. The information provided in this report can be used to guide investment for controlling high-impact invasive plant species for the benefits of biodiversity conservation. We do not present a final prioritisation of invasive plant strategies for the LEB, and we have not addressed the cultural, socio-economic or spatial components necessary for an implementation plan. Cost-effectiveness depends on the objectives used; in our case we used the intactness of ecosystems as a surrogate for expected biodiversity benefits, measured by the extent that each invasive plant species is likely to dominate in a bioregion. When other relevant factors for implementation are considered the priorities may change and some actions may not be appropriate in some locations. We present the costs, ecological benefits and cost-effectiveness of preventing, containing, reducing and eradicating the dominance of high impact invasive plants through realistic management actions over the next 50 years. In doing so, we are able to estimate the size of the weed management problem in the LEB and provide expert-based estimates of the likely outcomes and benefits of implementing weed management strategies. The priorities resulting from this work provide a prospectus for guiding further investment in management and in improving information availability.

Connecting theory, practice and place in today’s landscape : an education initiative

Since the establishment of Australia’s earliest formal studies in landscape architecture, landscape planning has been a traditional focus within post-graduate studies at QUT. Study in this area has evolved from an earlier emphasis on applied physical geography through to traditional techniques and processes in visual assessment and management. The emphasis on these techniques has shifted again to a more complex exploration of natural, economic, social and cultural landscapes. Recently, the School has explored more innovative and complex dimensions of human and natural landscapes. This has involved a focus on particular regions under pressure from local social and economic change. These have included the under-threat ‘picturesque’ landscapes of the Blackall Range and the Tweed Valley. Attempts to bridge the institution and the landscape have unearthed, through a studio focus, strong connections with notions of sustainable villages, roadside interpretation, way finding, local economic initiatives, special area creation, cultural heritage brokering and ecological enhancements. These initiatives have spanned both local practice interests and academic pursuits. Central to this exploration is the concept of problem solving through the investigation of the concept of ‘multiple scales’. An open, yet intensive program is being developed with a team of ‘futurist’ practitioners offering a range of experiences and perspectives to students. The program is being increasingly linked to design studios so that landscape planning and landscape design form a fabric of inquiry that works towards reclaiming complex landscapes.

A multidisciplinary review of the teaching and assessment of prescribing : how do professions perform?

Aim To investigate the methods employed to teach and assess the principles of effective prescribing across five non-medical professions in a tertiary institution. Methods The National Prescribing Service MedicineWise Prescribing Competencies Framework was employed as the prescribing standard. A curriculum mapping exercise was undertaken to determine whether the prescribing articulated in the competency standards were addressed within the following courses: Master of Nursing Science (Nurse Practitioner), Bachelor of Vision Science, Master of Optometry, Bachelor of Pharmacy, Bachelor of Podiatry, Bachelor of Paramedic Science. The methods employed to teach and assess prescribing principles were documented. For each profession, identified gaps in teaching and/or assessment were noted.

Circulating fragments of N-Terminal Pro-B-Type Natriuretic Peptides in plasma of heart failure patients

BACKGROUND: The use of nonstandardized N-terminal pro-B-type natriuretic peptide (NT-proBNP) assays can contribute to the misdiagnosis of heart failure (HF). Moreover, there is yet to be established a common consensus regarding the circulating forms of NT-proBNP being used in current assays. We aimed to characterize and quantify the various forms of NT-proBNP in the circulation of HF patients. METHODS: Plasma samples were collected from HF patients (n = 20) at rest and stored at -80 degrees C. NT-proBNP was enriched from HF patient plasma by use of immunoprecipitation followed by mass spectrometric analysis. Customized homogeneous sandwich AlphaLISA (R) immunoassays were developed and validated to quantify 6 fragments of NT-proBNP. RESULTS: Mass spectrometry identified the presence of several N- and C-terminally processed forms of circulating NT-proBNP, with physiological proteolysis between Pro2-Leu3, Leu3-Gly4, Pro6-Gly7, and Pro75-Arg76. Consistent with this result, AlphaLISA immunoassays demonstrated that antibodies targeting the extreme N or C termini measured a low apparent concentration of circulating NT-proBNP. The apparent circulating NT-proBNP concentration was increased with antibodies targeting nonglycosylated and nonterminal epitopes (P < 0.05). CONCLUSIONS: In plasma collected from HF patients, immunoreactive NT-proBNP was present as multiple N- and C-terminally truncated fragments of the full length NT-proBNP molecule. Immunodetection of NT-proBNP was significantly improved with the use of antibodies that did not target these terminal regions. These findings support the development of a next generation NT-proBNP assay targeting nonterminal epitopes as well as avoiding the central glycosylated region of this molecule. (c) 2013 American Association for Clinical Chemistry

miRNAs in head and neck cancer revisited

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cause of cancer mortality in the world and the 5th most commonly occurring cancer. Tobacco smoking, alcohol consumption and human papilloma virus (HPV) infections have been associated with the occurrence of HNSCC. Despite advances that have been made in HNSCC treatment, smoking-associated HNSCC patients still exhibit a poor 5 year survival rate (30-50 %) and a concomitant poor quality of life. The major clinical challenge to date lies in the early detection of dysplastic lesions,which can progress to malignancy. In addition, there are currently no tools available to monitor HNSCC patients for early stages of local recurrences or distant metastases. In the recent past, micro-RNAs (miRNA) have been assessed for their role in cancer initiation and progression, including HNSCC. It is now well-established that deregulation of these single stranded, small non-coding, 19-25 nt RNAs can e.g. enhance the expression of oncogenes or subdue the expression of tumor suppressor genes. The aims of this review are three-fold: first to retrieve from the literature miRNAs that have specifically been associated with HNSCC, second to group these miRNAs into those regulating tumor initiation, progression and metastasis, and third to discern miRNAs related to smoking-associated HNSCC versus HPV-associated HNSCC development. This review gives an overview on the miRNAs regulating the development of head and neck cancers. The ultimate establishment of miRNA expression profiles that are HNSCC specific, and miRNAs that orchestrate altered gene and protein expression levels in HNSCC, could pave the way for a better understanding of the mechanism underlying its pathogenesis and the development of novel, targeted therapies.