miRPlant : an integrated tool for identification of plant miRNA from RNA sequencing data

Background Small RNA sequencing is commonly used to identify novel miRNAs and to determine their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep*. miRDeep-P was developed to identify plant miRNA using miRDeep’s probabilistic model of miRNA biogenesis, but it depends on several third party tools and lacks a user-friendly interface. The objective of our miRPlant program is to predict novel plant miRNA, while providing a user-friendly interface with improved accuracy of prediction. Result We have developed a user-friendly plant miRNA prediction tool called miRPlant. We show using 16 plant miRNA datasets from four different plant species that miRPlant has at least a 10% improvement in accuracy compared to miRDeep-P, which is the most popular plant miRNA prediction tool. Furthermore, miRPlant uses a Graphical User Interface for data input and output, and identified miRNA are shown with all RNAseq reads in a hairpin diagram. Conclusions We have developed miRPlant which extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants. miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. miRPlant is also the first plant miRNA prediction tool that dynamically plots miRNA hairpin structure with small reads for identified novel miRNAs. This feature will enable biologists to visualize novel pre-miRNA structure and the location of small RNA reads relative to the hairpin. Moreover, miRPlant can be easily used by biologists with limited bioinformatics skills.

First results of a major study on safety at Queensland roadworks

The Centre for Accident Research and Road Safety – Queensland (CARRS-Q) is conducting a 3-year program of research, titled Integrating Technological and Organisational Approaches to Enhance the Safety of Roadworkers. The program is funded by the Australian Research Council (ARC), with support from industry partners Leighton Contractors, GHD, Queensland Transport and Main Roads (TMR), and the Australian Workers Union (AWU). This multidisciplinary project involves working together to enhance roadworker safety by: • Investigating the real and perceived dangers at roadworks. • Strengthening organisational policies and practices for roadworker safety. • Testing innovative initiatives to improve driver behaviour at roadworks. • Developing safety management models spanning different regulatory frameworks. The project outcomes will include the following benefits: • Practical and theoretical contributions at industry and academic levels for developing effective interventions/strategies to improve safety in road construction. • Development of new measures to evaluate effectiveness of policy and organisational interventions to produce behavioural change among organisations involved in roadworks. • Improved safety and productivity in urban and rural areas of Australia as a result of facilitating the delivery of road improvements. This paper presents an overview of the research conducted to date as part of the overall program. The paper concentrates on issues relevant to moving vehicles, although the research recognises the importance of other hazards and risks associated with roadworks and construction projects generally.

Transition Pedagogy Handbook : A Good Practice Guide for Policy and Practice in the First Year Experience at QUT

This Handbook has been specifically designed for academic and professional staff responsible for managing first year students and curriculum and co-curricular programs at QUT. As well as presenting examples of good practice, the handbook provides a brief overview of QUT’s First Year Experience Program, a summary of QUT’s First Year Experience and Retention Policy and the Transition Pedagogy that frames both curricular and co-curricular activities. We hope you find this resource both useful and informative.

Visions and values : the Children’s Book Council of Australia’s prizing of picture books in the twenty-first century

The Children’s Book Council of Australia (CBCA) administers the oldest national prize for children’s literature in Australia. Each year, the CBCA confers “Book of the Year” awards to literature for young people in five categories. In 2001, the establishment of an “Early Childhood” category opened up the venerable “Picture Book” category (first awarded in 1955) to books with an implied readership up to 18 years of age. As a result, this category has emerged in recent years as a highly visible space within which the CBCA can contest discourses of cultural marginalisation insofar as Australian (“colonial”) literature is constructed as inferior or adjunct to the major Anglophone literary traditions, and the consistent identification of children’s literature (and, indeed, of children) as lesser than its ‘adult’ counterparts. The CBCA is engaged in defining, evaluating, and legitimising a tradition of Australian children’s literature which is underpinned by a canonical impulse, and is a reflexive practice of self-definition, self-evaluation and self-legitimisation for the CBCA itself. While it is obviously problematic to identify award winners as a canon, it is equally obvious that literary prizing is a cultural practice derived from the logic of canonicity. In his discussion of the United States’s Newbery Medal, Kenneth Kidd notes that “Medal books are instant classics, the selection process an ostensible simulation of the test of time” (169) and that “the Medal is part of the canonical architecture of children's literature” (169). Thus, it is instructive to consider the visions and values of the national, of the social, and of the literary-aesthetic, in the picture books chosen by the Children’s Book Council of Australia (CBCA) as the “best” of the early twenty-first century. These books not only constitute a kind of canon for contemporary Australian children’s literature, but may well come to define what contemporary Australian children’s literature means in the wider literary field. The Book of the Year: Picture Book awards given by the CBCA since 2001 demonstrate that it is not only true of the Booker Prize that, “The choices of winning books reflect not only on the books themselves, then, but also back on the Prize, affecting its reputation and creating journalistic capital which is vital for the Prize to achieve its prominence and impact.” (81). Many of the twenty-first century CBCA award-winning picture books complicate traditional or comfortable understanding of Australianness, children’s literature, or “appropriate” modes of form and content, reminding us that “moments when texts resist or complicate recuperation into national discourses offer fruitful points for exploring the relationships between text and celebratory context” (Roberts 6). The CBCA has taken the opportunities offered by the liberation of the Picture Book category from an implied readership to challenge dominant constructions of children’s literature in Australia, and in so doing, are engaged in overt practices of canonicity with potentially long-lasting effects. Works Cited: Kidd, Kenneth. “Prizing Children’s Literature: The Case of Newbery Gold.” Children's Literature 35 (2007): 166-190. Roberts, Gillian. Prizing Literature: The Celebration and Circulation of National Culture. Toronto: U Toronto P, 2011. Squires, Claire. “Book Marketing and the Booker Prize.” Judging a Book by Its Cover: Fans, Publishers, Designers, and the Marketing of Fiction. Eds. Nicole Matthews and Nickianne Moody. Aldershot: Ashgate, 2007. 71-82.

Straminipilan protists : a study of their taxonomic position, morphology and abiotic stress-mediated gene expression

Thraustochytrids have become of considerable industrial and scientific interest in the past decade due to their health benefits. They have been proven to be the principle source in marine and estuarine fish diets with high percentage of long chain (LC) or polyunsaturated fatty acids (PUFA). Therefore, the oil extracted from fish for human document.forms[0].elements[13].select();consumption is rich in PUFA with high omega-3 fatty acid content. Docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) of all of the omega-3 fatty acids, are considered beneficial essential oils for humans with a wide range of health benefits. These include brain and neural development in infants, general wellbeing of adults and drug delivery through precursor molecules. They have become one of the most extensively studied organisms for industrial oil preparations as PUFA extraction from fish becomes less profitable. Many forms of these Thraustochytrid oils are being trialled for human consumption all over the world. In Australia, there has been little research performed on these organisms in the past ten years. A few Australian studies have been conducted in the form of comparative studies related to PUFA production within the related genera, but not focussed on their identification or cellular and genomic characterisation. Therefore, the main aim of this study was to investigate the morphological and genetic characteristics of Australian Thraustochytrids in order to aid in their identification and characterisation, as well as to better understand the effect of environmental conditions in the regulation of PUFA production. It was also noted that there was a knowledge gap in the preservation and total genomic DNA extraction of these organisms for the purposes of scientific research. The cryopreservation of these organisms for studies around the world follows existing generic methods. However, it is well understood that many of these generic methods attract not only high costs for chemicals, but also uses considerable storage space and other resources, all of which can be improved with new or modified approaches. In this context, a simple and inexpensive bead preservation method is described, without compromising the storage shelf life. We also describe, for the first time, the effects of culture age on the successful cryopreservation of Thraustochytrids. It was evident in the literature that DNA and RNA extractions for molecular and genetic studies of Thraustochytrids follow the classical phenol-chloroform extraction methods. It was also observed that modern protocols failed to avoid the use of phenol-chloroform rather than improving preparation and cell disruption. In order to provide a high quantity and quality DNA extraction, a modified protocol has been introduced that employs the use of modern commercial extraction kits and standard laboratory equipment. Thraustochytrids have been shown to be highly conserved in their 18S rDNA gene sequences, which is used as the current standard for identification. It was demonstrated that the 18S rDNA gene sequence limits the recognition of closely related genera or within the genera from each member. Therefore, it was proposed that another profile, such as a randomly amplified polymorphic DNA (RAPD) based profiling system, be tested for use in the characterisation of Thraustochytrids. The RAPD profiles were shown to provide a unique DNA fingerprint for each isolate and small variations in their genome were able to be detected. This method involved the use of a minimum number of standard arbitrary primers and with an increase in the number of different primers used, a very high discrimination between organisms could be achieved. However, the method was not suitable for taxonomic purposes because the results did not correlate with other taxonomic features such as morphology. Another knowledge gap was found with respect to Australian Thraustochytrid growth characteristics, in that these had not been recorded and published. In order to rectify this, a record of colony and microscopic features of 12 selected isolates was performed. The results of preliminary studies indicated that further microbiological and biochemical studies are needed for full characterisation of these organisms. This information is of great importance to bio-prospecting of new Thraustochytrids from Australian ecosystems and would allow for their accurate identification, and so permit the prediction of their PUFA capability by comparison with related genera/species. It was well recognized that environmental stress plays a role in the PUFA production and is mainly due to the reactive oxygen species as abiotic stress (Chiou et al., 2001; Okuyama et al., 2008; Shabala et al., 2009; Shabala et al., 2001). In this aspect, this study makes the first attempt towards better understanding of this phenomenon by way of the use of real-time PCR for the detection of environmental effects on the regulation of PUFA production. Three main environmental conditions including temperature, pH and oxygen availability were monitored as stress inducers. In summary, this study provides novel approaches for the preservation and handling of Thraustochytrids, their molecular biological features, taxonomy, characterisation and responses to environmental factors with respect to their oil production enzymes. The information produced from this study will prove to be vital for both industrial and scientific investigations in the future.

Experience indigenous culture in Arnhem Land, NT

A travel article about a journey to the Cobourg Peninsula, Arnhem Land. "NOW I know I'm back,'' says our guide David McMahon as the scent of wood smoke makes its way into the 4WD. For McMahon, being back means Kakadu and Arnhem Land, and ultimately our final destination in the Northern Territory's Cobourg Peninsula. In the north, one of the first things you need to adjust is your attitude to fire. The indigenous people have long worked with it. The rangers perform controlled burns. The animals have adapted and know how to escape the flames. The smoke trail leads us down the old Jim Jim Rd, our first stretch of dirt track since leaving Darwin. Our destination is the Venture North campsite at Garig Gunak Barlu National Park...

Exploring the effect of achievements on students attending university orientation

University orientation is a key event for new students that aids in the transition from a school to a university environment. A smartphone orientation application was built to aid students attending the event. Achievements were added to the application in an attempt to engage students further with the orientation activities and application. An exploratory field study was undertaken to evaluate the effect of the achievement system on participants attending orientation. Forty-six new students were recruited to test the orientation application. Twenty-six participants used a gamified version of the orientation application and twenty participants used a non-gamified version. While the gamification was generally well received, no impact on user experience was evident. Some effect on engagement with orientation activities was shown. Participants who used the gamified system reported the game elements as fun, but some negative issues arose, such as cheating.