De Novo Transcriptome Sequence Assembly and Analysis of RNA Silencing Genes of Nicotiana benthamiana

Background: Nicotiana benthamiana has been widely used for transient gene expression assays and as a model plant in the study of plant-microbe interactions, lipid engineering and RNA silencing pathways. Assembling the sequence of its transcriptome provides information that, in conjunction with the genome sequence, will facilitate gaining insight into the plant's capacity for high-level transient transgene expression, generation of mobile gene silencing signals, and hyper-susceptibility to viral infection. Methodology/Results: RNA-seq libraries from 9 different tissues were deep sequenced and assembled, de novo, into a representation of the transcriptome. The assembly, of16GB of sequence, yielded 237,340 contigs, clustering into 119,014 transcripts (unigenes). Between 80 and 85% of reads from all tissues could be mapped back to the full transcriptome. Approximately 63% of the unigenes exhibited a match to the Solgenomics tomato predicted proteins database. Approximately 94% of the Solgenomics N. benthamiana unigene set (16,024 sequences) matched our unigene set (119,014 sequences). Using homology searches we identified 31 homologues that are involved in RNAi-associated pathways in Arabidopsis thaliana, and show that they possess the domains characteristic of these proteins. Of these genes, the RNA dependent RNA polymerase gene, Rdr1, is transcribed but has a 72 nt insertion in exon1 that would cause premature termination of translation. Dicer-like 3 (DCL3) appears to lack both the DEAD helicase motif and second dsRNA binding motif, and DCL2 and AGO4b have unexpectedly high levels of transcription. Conclusions: The assembled and annotated representation of the transcriptome and list of RNAi-associated sequences are accessible at www.benthgenome.com alongside a draft genome assembly. These genomic resources will be very useful for further study of the developmental, metabolic and defense pathways of N. benthamiana and in understanding the mechanisms behind the features which have made it such a well-used model plant. © 2013 Nakasugi et al.

Creating efficiencies in teaching : where are the right resources when you need them?

Early career engineering academics are encouraged to join and contribute to established research groups at the leading edge of their discipline. This is often facilitated by various staff development and support programs. Given that academics are often appointed primarily on the basis of their research skills and outputs, such an approach is justified and is likely to result in advancing the individual academic’s career. It also enhances their capacity to attract competitive research funding, while contributing to the overall research performance of their institution, with further potential for an increased share of government funding. In contrast, there is much less clarity of direction or availability of support mechanisms for those academics in their role as teachers. Following a general induction to teaching and learning at their institution, they would commonly think about preparing some lecture materials, whether for delivery in a face-to-face or on-line modality. Typically they would look for new references and textbooks to act as a guide for preparing the content. They would probably find out how the course has been taught before, and what laboratory facilities and experiments have been used. In all of these and other related tasks, the majority of newly appointed academics are guided strongly by their own experiences as students, rather than any firm knowledge of pedagogical principles. At a time of increased demands on academics’ time, and high expectations of performance and productivity in both research and teaching, it is essential to examine possible actions to support academics in enhancing their teaching performance in effective and efficient ways. Many resources have been produced over the years in engineering schools around the world, with very high intellectual and monetary costs. In Australia, the last few years have seen a surge in the number of ALTC/OLT projects and fellowships addressing a range of engineering education issues and providing many resources. There are concerns however regarding the extent to which these resources are being effectively utilised. Why are academics still re-inventing the wheel and creating their own version of teaching resources and pedagogical practice? Why do they spend so much of their precious time in such an inefficient way? A symposium examining the above issues was conducted at the AAEE2012 conference, and some pointers to possible responses to the above questions were obtained. These are explored in this paper and supplemented by the responses to a survey of a group of engineering education leaders on some of the aspects of these research questions. The outcomes of the workshop and survey results have been analysed in view of the literature and the ALTC/OLT sponsored learning and teaching projects and resources. Other factors are discussed, including how such resources can be found, how their quality might be evaluated, and how assessment may be appropriately incorporated, again using readily available resources. This study found a strong resonance between resources reuse with work on technology acceptance (Davis, 1989), suggesting that technology adoption models could be used to encourage resource sharing. Efficient use of outstanding learning materials is an enabling approach. The paper provides some insights on the factors affecting the re-use of available resources, and makes some recommendations and suggestions on how the issue of resources re-use might be incorporated in the process of applying and completing engineering education projects.

The local library across the digital and physical city : opportunities for economic development

This paper considers the role of the public library as a community hub, engagement space, and entrepreneurial incubator in the context of the city, city governance, and local government planning. It considers this role from the perspective of library experts and their future visions for libraries in a networked knowledge economy. Public libraries (often operated by or on behalf of local governments) potentially play a pivotal role for local governments in positioning communities within the global digital network. Fourteen qualitative interviews with library experts informed the study which investigates how the relationship between digital technology and the physical library space can potentially support the community to develop innovative, collaborative environments for transitioning to a digital future. The study found that libraries can capitalise on their position as community hubs for two purposes: first, to build vibrant community networks and forge economic links across urban localities; and second, to cross the digital divide and act as places of innovation and lifelong learning. Libraries provide a specific combination of community and technology spaces and have significant tangible connection points in the digital age. The paper further discusses the potential benefits for libraries in using ICT networks and infrastructure, such as the National Broadband Network in Australia. These networks could facilitate greater use of library assets and community knowledge, which, in turn, could assist knowledge economies and regional prosperity.

Experience of being an advanced practice nurse within Australian acute care settings : a systematic review of qualitative evidence

Background Nationally and internationally, advanced practice nurses are working under various titles and in different contexts to address gaps within healthcare systems. Analysis of advanced practice roles in different countries has been undertaken, but due to variations in cultural, geographical and professional factors, it is difficult and perhaps ineffectual to compare roles between countries. Contextual factors may also affect the actual experience of being an advanced practice nurse. A systematic review was therefore undertaken of qualitative evidence on the experience of being an advanced practice nurse in Australia, to provide deeper understanding of the role in the defined context. Methods The review followed the method for qualitative synthesis as per the Joanna Briggs Institute. An extensive search was undertaken of databases and online resources to find published and unpublished studies. Papers from 1990 to October 2011 which met specified inclusion criteria were appraised using the Joanna Briggs Institute Qualitative Assessment and Review Instrument. Results Three published studies and one unpublished dissertation were included in the review. From these studies, 216 findings were extracted and these were formed into 18 categories. Six meta-syntheses grouped under the headings of expert knowledge, confidence, education, relationships, negative experiences and patient-centred experience were created. Organisational factors impact greatly on the experience, professionally and personally. Conclusions Heterogeneity of role titles makes synthesis a difficult process, but contextualising the population provides a pragmatic approach to informing the status of the advanced practice nurse discourse. The review identifies positive and negative experiences of being an advanced practice nurse in Australian acute care settings with overlapping and intertwining findings that reinforce the complexity of the role.

Biobanking of blood and bone marrow : emerging challenges for custodians of public resources

The Australian Bone Marrow Donor Registry (ABMDR) is a publicly funded company that is part of an international network that facilitates unrelated bone marrow transplantation. This role means that the ABMDR has access to a large biospecimen repository, therefore making it a highly valuable research resource. Recognising the potential value of these biospecimens for research purposes, the ABMDR is in the process of determining whether, and how, to share its biospecimens with other biobanks. While this would undoubtedly be of value to the scientific community, and ultimately to the wider community, it would also inevitably transform the role of an institution whose primary role is therapeutic, and would compromise the degree of control that a custodian has over donated material. This article describe the challenges confronting the ABMDR, and organisations like it, in balancing their duties to donors, patients, researchers and the general public. These problems have led inevitably to the use of "property" rights language in the discussion of these issues but notions of gift, ownership, trusteeship and transfer might also be considered.

English in the urban environment : resources for 21st century readers

Where teachers of English as a foreign language (EFL) once observed a paucity of authentic language input, public displays of written English are now proliferating. Ideas for capitalising on this abundance can be drawn from two strands of pedagogic thought: a psycholinguistic approach to conventional literacy long established in foreign, second and first language education (e.g., Teng, 2009), and a more recent and critical approach informed by diverse theoretical understandings of the ‘linguistic landscape’ (e.g., Rowland, 2013). In this paper I draw from these two approaches to suggest ways of helping EFL learners use environmental print to develop knowledge and skills required of English readers in the twenty-first century: (1) fluency in breaking the codes of English and other languages of publicly displayed text; (2) facility with making meaning as the English of these texts becomes ever more diverse in cultural, historical and contextual implication; (3) use of environmental English in contexts that range from the local to the transnational; and (4) critique of the presence of English and attendant worldviews in the urban environment (Chern & Dooley, forthcoming). The psychological concept of motivation and the complementary sociological concept of investment are at the heart of my deliberations here: realisation of the pedagogic potential of environmental print to develop literate resources requires consideration of sources of motivation in the classroom learning situation (Dörnyei & Ushioda, 2011), as well as learner investment in literate practices in English (Norton, 2010).

Design, synthesis and spectroscopic characterisation of a focused library based on the polyandrocarpamine natural product scaffold

A focused library based on the marine natural products polyandrocarpamines A (1) and B (2) has been designed and synthesised using parallel solution-phase chemistry. In silico physicochemical property calculations were performed on synthetic candidates in order to optimise the library for drug discovery and chemical biology. A library of ten 2-aminoimidazolone products (3–12) was prepared by coupling glycocyamidine and a variety of aldehydes using a one-step stereoselective aldol condensation reaction under microwave conditions. All analogues were characterised by NMR, UV, IR and MS. The library was evaluated for cytotoxicity towards the prostate cancer cell lines, LNCaP, PC-3 and 22Rv1.

Queensland small towns Documentary project

This photographic documentary project explores diverse stories of Queensland mining towns. Images compare the interplay between communities, commerce and natural resources. The project is a collaboration between three Brisbane universities (Queensland University of Technology, Griffith University and University of Queensland) and is supported by the Brisbane Powerhouse and the State Library of Queensland. Funded by a $50,000 Arts Queensland grant.

Using cost-effective multimedia to create engaging learning experiences : Resources Manual

A guide to utilising multi-media for teaching and learning.

Spatial prediction of N2O emissions in pasture : a Bayesian model averaging analysis

Nitrous oxide (N2O) is one of the greenhouse gases that can contribute to global warming. Spatial variability of N2O can lead to large uncertainties in prediction. However, previous studies have often ignored the spatial dependency to quantify the N2O - environmental factors relationships. Few researches have examined the impacts of various spatial correlation structures (e.g. independence, distance-based and neighbourhood based) on spatial prediction of N2O emissions. This study aimed to assess the impact of three spatial correlation structures on spatial predictions and calibrate the spatial prediction using Bayesian model averaging (BMA) based on replicated, irregular point-referenced data. The data were measured in 17 chambers randomly placed across a 271 m(2) field between October 2007 and September 2008 in the southeast of Australia. We used a Bayesian geostatistical model and a Bayesian spatial conditional autoregressive (CAR) model to investigate and accommodate spatial dependency, and to estimate the effects of environmental variables on N2O emissions across the study site. We compared these with a Bayesian regression model with independent errors. The three approaches resulted in different derived maps of spatial prediction of N2O emissions. We found that incorporating spatial dependency in the model not only substantially improved predictions of N2O emission from soil, but also better quantified uncertainties of soil parameters in the study. The hybrid model structure obtained by BMA improved the accuracy of spatial prediction of N2O emissions across this study region.

Primary control level of parallel distributed energy resources converters in system of multiple interconnected autonomous microgrids within self-healing networks

To minimise the number of load sheddings in a microgrid (MG) during autonomous operation, islanded neighbour MGs can be interconnected if they are on a self-healing network and an extra generation capacity is available in the distributed energy resources (DER) of one of the MGs. In this way, the total load in the system of interconnected MGs can be shared by all the DERs within those MGs. However, for this purpose, carefully designed self-healing and supply restoration control algorithm, protection systems and communication infrastructure are required at the network and MG levels. In this study, first, a hierarchical control structure is discussed for interconnecting the neighbour autonomous MGs where the introduced primary control level is the main focus of this study. Through the developed primary control level, this study demonstrates how the parallel DERs in the system of multiple interconnected autonomous MGs can properly share the load of the system. This controller is designed such that the converter-interfaced DERs operate in a voltage-controlled mode following a decentralised power sharing algorithm based on droop control. DER converters are controlled based on a per-phase technique instead of a conventional direct-quadratic transformation technique. In addition, linear quadratic regulator-based state feedback controllers, which are more stable than conventional proportional integrator controllers, are utilised to prevent instability and weak dynamic performances of the DERs when autonomous MGs are interconnected. The efficacy of the primary control level of the DERs in the system of multiple interconnected autonomous MGs is validated through the PSCAD/EMTDC simulations considering detailed dynamic models of DERs and converters.

QUT Library advances the use of open public tools to navigate genetic inventions and builds research networks

Many emerging economies are dangling the patent system to stimulate bio-technological innovations with the ultimate premise that these will improve their economic and social growth. The patent system mandates full disclosure of the patented invention in exchange of a temporary exclusive patent right. Recently, however, patent offices have fallen short of complying with such a mandate, especially for genetic inventions. Most patent offices provide only static information about disclosed patent sequences and even some do not keep track of the sequence listing data in their own database. The successful partnership of QUT Library and Cambia exemplifies advocacy in Open Access, Open Innovation and User Participation. The library extends its services to various departments within the university, builds and encourages research networks to complement skills needed to make a contribution in the real world.

An examination of the critical resources and internet capabilities for leveraging global performance in international entrepreneurial firms

This PhD research investigates the critical resources and Internet capabilities utilized by firms for leveraging global performance in entrepreneurial firms. Firm resources have been identified as important firm assets, which contribute to the firm's competitive global position. The Internet is a critical resource for a new generation of small and medium sized enterprise (SME) in pursuing international opportunities. By facilitating international business, the Internet has the ability to increase the quality and speed of communications, lower transaction costs, and facilitate the development of networks. Despite the increasing numbers of firms utilizing the Internet to pursue international opportunities, limited research remains. Adopting multiple case study methodology and structural equation modelling, the research identified the firm-level resources, which coincide with capabilities in a model predicting how international performance in firms is achieved.

Genomic resources notes accepted 1 December 2013 - 31 January 2014

This article documents the public availability of (i) transcriptome sequence data, assembled and annotated contigs and unigenes, and BLAST hits from the Queensland fruit fly, Bactrocera tryoni; (ii) 75 single-nucleotide variants (SNVs) from 454 sequencing of reduced representation libraries for Phalangiidae harvestmen, Megabunus armatus, Megabunus vignai, Megabunus lesserti, and Rilaena triangularis; and (iii) expressed sequence tags from 454 sequencing of the lepidopterans Lymantria dispar and Lymantria monacha.

Mechanism‐based selection of a potent kallikrein‐related peptidase 7 inhibitor from a versatile library based on the sunflower trypsin inhibitor SFTI‐1

Potent and specific enzyme inhibition is a key goal in the development of therapeutic inhibitors targeting proteolytic activity. The backbone-cyclized peptide, Sunflower Trypsin Inhibitor (SFTI-1) affords a scaffold that can be engineered to achieve both these aims. SFTI-1's mechanism of inhibition is unusual in that it shows fast-on/slow-off kinetics driven by cleavage and religation of a scissile bond. This phenomenon was used to select a nanomolar inhibitor of kallikrein-related peptidase 7 (KLK7) from a versatile library of SFTI variants with diversity tailored to exploit distinctive surfaces present in the active site of serine proteases. Inhibitor selection was achieved through the use of size exclusion chromatography to separate protease/inhibitor complexes from unbound inhibitors followed by inhibitor identification according to molecular mass ascertained by mass spectrometry. This approach identified a single dominant inhibitor species with molecular weight of 1562.4 Da, which is consistent with the SFTI variant SFTI-WCTF. Once synthesized individually this inhibitor showed an IC50 of 173.9 ± 7.6 nM against chromogenic substrates and could block protein proteolysis. Molecular modeling analysis suggested that selection of SFTI-WCTF was driven by specific aromatic interactions and stabilized by an enhanced internal hydrogen bonding network. This approach provides a robust and rapid route to inhibitor selection and design.