Construct design for efficient, effective and high-throughput gene silencing in plants

Post-transcriptional silencing of plant genes using anti-sense or co-suppression constructs usually results in only a modest proportion of silenced individuals. Recent work has demonstrated the potential for constructs encoding self-complementary 'hairpin' RNA (hpRNA) to efficiently silence genes. In this study we examine design rules for efficient gene silencing, in terms of both the proportion of independent transgenic plants showing silencing, and the degree of silencing. Using hpRNA constructs containing sense/anti-sense arms ranging from 98 to 853 nt gave efficient silencing in a wide range of plant species, and inclusion of an intron in these constructs had a consistently enhancing effect. Intron-containing constructs (ihpRNA) generally gave 90-100% of independent transgenic plants showing silencing. The degree of silencing with these constructs was much greater than that obtained using either co-suppression or anti-sense constructs. We have made a generic vector, pHANNIBAL, that allows a simple, single PCR product from a gene of interest to be easily converted into a highly effective ihpRNA silencing construct. We have also created a high-throughput vector, pHELLSGATE, that should facilitate the cloning of gene libraries or large numbers of defined genes, such as those in EST collections, using an in vitro recombinase system. This system may facilitate the large-scale determination and discovery of plant gene functions in the same way as RNAi is being used to examine gene function in Caenorhabditis elegans.

Marker gene elimination from transgenic barley, using co-transformation with adjacent 'twin T-DNAs' on a standard Agrobacterium transformation vector

We have tested a methodology for the elimination of the selectable marker gene after Agrobacterium-mediated transformation of barley. This involves segregation of the selectable marker gene away from the gene of interest following co-transformation using a plasmid carrying two T-DNAs, which were located adjacent to each other with no intervening region. A standard binary transformation vector was modified by insertion of a small section composed of an additional left and right T-DNA border, so that the selectable marker gene and the site for insertion of the gene of interest (GOI) were each flanked by a left and right border. Using this vector three different GOIs were transformed into barley. Analysis of transgene inheritance was facilitated by a novel and rapid assay utilizing PCR amplification from macerated leaf tissue. Co-insertion was observed in two thirds of transformants, and among these approximately one quarter had transgene inserts which segregated in the next generation to yield selectable marker-free transgenic plants. Insertion of non-T-DNA plasmid sequences was observed in only one of fourteen SMF lines tested. This technique thus provides a workable system for generating transgenic barley free from selectable marker genes, thereby obviating public concerns regarding proliferation of these genes.

The M(r) 43K major capsid protein of rice ragged stunt oryzavirus is a post-translationally processed product of a M(r) 67 348 polypeptide encoded by genome segment 8

The nucleotide sequence of DNA complementary to rice ragged stunt oryzavirus (RRSV) genome segment 8 (S8) of an isolate from Thailand was determined. RRSV S8 is 1 914 bp in size and contains a single large open reading frame (ORF) spanning nucleotides 23 to 1 810 which is capable of encoding a protein of M(r) 67 348. The N-terminal amino acid sequence of a ~43K virion polypeptide matched to that inferred for an internal region of the S8 coding sequence. These data suggest that the 43K protein is encoded by S8 and is derived by a proteolytic cleavage. Predicted polypeptide sizes from this possible cleavage of S8 protein are 26K and 42K. Polyclonal antibodies raised against a maltose binding protein (MBP)-S8 fusion polypeptide (expressed in Escherichia coli) recognised four RRSV particle associated polypeptides of M(r) 67K, 46K, 43K and 26K and all except the 26K polypeptide were also highly immunoreactive to polyclonal antibodies raised against purified RRSV particles. Cleavage of the MBP-S8 fusion polypeptide with protease Factor X produced the expected 40K MBP and two polypeptides of apparent M(r) 46K and 26K. Antibodies to purified RRSV particles reacted strongly with the intact fusion protein and the 46K cleavage product but weakly to the 26K product. Furthermore, in vitro transcription and translation of the S8 coding region revealed a post-translational self cleavage of the 67K polypeptide to 46K and 26K products. These data indicate that S8 encodes a structural polypeptide, the majority of which is auto- catalytically cleaved to 26K and 46K proteins. The data also suggest that the 26K protein is the self cleaving protease and that the 46K product is further processed or undergoes stable conformational changes to a ~43K major capsid protein.

Co-creating knowledge online : approaches for community artists

Forming peer alliances to share and build knowledge is an important aspect of community arts practice, and these co-creation processes are increasingly being mediated by the internet. This paper offers guidance for practitioners who are interested in better utilising the internet to connect, share, and make new knowledge. It argues that new approaches are required to foster the organising activities that underpin online co-creation, building from the premise that people have become increasingly networked as individuals rather than in groups (Rainie and Wellman 2012: 6), and that these new ways of connecting enable new modes of peer-to-peer production and exchange. This position advocates that practitioners move beyond situating the internet as a platform for dissemination and a tool for co-creating media, to embrace its knowledge collaboration potential. Drawing on a design experiment I developed to promote online knowledge co-creation, this paper suggests three development phases – developing connections, developing ideas, and developing agility – to ground six methods. They are: switching and routing, engaging in small trades of ideas with networked individuals; organising, co-ordinating networked individuals and their data; beta-release, offering ‘beta’ artifacts as knowledge trades; beta-testing, trialing and modifying other peoples ‘beta’ ideas; adapting, responding to technological disruption; and, reconfiguring, embracing opportunities offered by technological disruption. These approaches position knowledge co-creation as another capability of the community artist, along with co-creating art and media.

Back to basics: Informing the public of co-morbid physical health problems in those with mental illness

Abstract OBJECTIVE: Those with mental illness are at increased risk of physical health problems. The current study aimed to examine the information available online to the Australian public about the increased risk and consequences of physical illness in those with mental health problems and the services available to address these co-morbidities. METHODS: A structured online search was conducted with the search engine Google Australia (www.google.com.au) using generic search terms 'mental health information Australia', 'mental illness information Australia', 'depression', 'anxiety', and 'psychosis'. The direct content of websites was examined for information on the physical co-morbidities of mental illness. All external links on high-profile websites [the first five websites retrieved under each search term (n = 25)] were examined for information pertaining to physical health. RESULTS: Only 4.2% of websites informing the public about mental health contained direct content information about the increased risk of physical co-morbidities. The Australian Government's Department of Health and Ageing site did not contain any information. Of the high-profile websites, 62% had external links to resources about physical health and 55% had recommendations or resources for physical health. Most recommendations were generic. CONCLUSIONS: Relative to the seriousness of this problem, there is a paucity of information available to the public about the increased physical health risks associated with mental illness. Improved public awareness is the starting point of addressing this health inequity.

The Effective and The Evocative : A Spectrum of Creative Practice Research

In the expanding literature on creative practice research, art and design are often described as a unified field. They are bracketed together (art-and-design), referred to as interchangeable terms (art/design), and nested together, as if the practices of one domain encompass the other. However it is possible to establish substantial differences in research approaches. In this chapter we argue that core distinctions arise out of the goals of the research, intentions invested in the resulting “artefacts” (creative works, products, events), and the knowledge claims made for the research outcomes. Moreover, these fundamental differences give rise to a number of contingent attributes of the research such as the forming contexts, methodological approaches, and ways of evidencing and reporting new knowledge. We do not strictly ascribe these differences to disciplinary contexts. Rather, we use the terms effective practice research and evocative practice research to describe the spirit of the two distinctive research paradigms we identify. In short, effective practice research (often pursued in design fields) seeks a solution (or resolution) to a problem identified with a particular community, and it produces an artefact that addresses this problem by effecting change (making a situation, product or process more efficient or effective in some way). On the other hand, evocative practice research (often pursued by creative arts fields) is driven by individual pre-occupations, cultural concerns or human experience more broadly. It produces artefacts that evoke affect and resonance, and are poetically irreducible in meaning. We cite recent examples of creative research projects that illustrate the distinctions we identify. We then go on to describe projects that integrate these modes of research. In this way, we map out a creative research spectrum, with distinct poles as well as multiple hybrid possibilities. The hybrid projects we reference are not presented as evidence an undifferentiated field. Instead, we argue that they integrate research modes in deliberate, purposeful and distinctive ways: employing effective practice research methods in the production of evocative artefacts or harnessing evocative (as well as effective) research paradigms to effect change.

Anticipated user experience in the early stages of product development

This research investigates users' anticipation of their future experiences with interactive products to support design for experience in the early stages of product development. This research generates new knowledge of anticipated user experience (AUX), which reveals users' tendency to perceive the pragmatic quality of products as the main determinant of their positive future experiences. The AUX Framework has been an important outcome of this study. The exploration of the components of this framework allows a better prediction and understanding of users' underlying needs and potential usage contexts valuable for the early design phases.

Networked identity work as project development among co-creative communities

Networked identity work is the conscious negotiation or co-creation of identity, enacted by speaking and listening across differences among multiple publics, including those real and imagined, familiar and unknown, on and offline, present and future. It is a concept I explore extensively in research with queer Digital Storytellers who share their personal stories in public places to catalyse social change (Vivienne 2013). In this article I consider distinctions between ‘story’ and ‘identity’; ‘networking’ and ‘networked identity work’ and argue that the two concepts may be usefully employed in development of co-creative community projects. Finally I consider how variable definitions of co-creativity influence project development.

How to guarantee compliance between workflows and product lifecycles?

Product Lifecycle Management (PLM) systems are widely used in the manufacturing industry. A core feature of such systems is to provide support for versioning of product data. As workflow functionality is increasingly used in PLM systems, the possibility emerges that the versioning transitions for product objects as encapsulated in process models do not comply with the valid version control policies mandated in the objects’ actual lifecycles. In this paper we propose a solution to tackle the (non-)compliance issues between processes and object version control policies. We formally define the notion of compliance between these two artifacts in product lifecycle management and then develop a compliance checking method which employs a well-established workflow analysis technique. This forms the basis of a tool which offers automated support to the proposed approach. By applying the approach to a collection of real-life specifications in a main PLM system, we demonstrate the practical applicability of our solution to the field.

The art of co-creative media : an Australian survey

This article describes how - in the processes of responding to participatory storytelling practices - community, public service, and to a lesser extent, commercial media institutions are themselves negotiated and changed. Although there are significant variations in the conditions, durability, extent, motivations and quality of these developments and their impacts, they nonetheless increase the possibilities and pathways of participatory media culture. This description first frames digital storytelling as a ‘co-creative’ media practice. It then discusses the role of community arts and cultural development (CACD) practitioners and networks as co-creative media intermediaries, and then considers their influence in Australian broadcast and Internet media. It looks at how participatory storytelling methods are evolving in the Australian context and explores some of the implications for cultural inclusion arising from a shared interest in ‘co-creative’ media methods and approaches.

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.

Too many cooks? Co-creating and co-teaching studio courses in the creative media context : a career-focussed approach

This Case Study relates to the creation and implementation of career‐focussed courses in Creative Media for film, television, animation, broadcast and web contexts. The paper examines the advantages and disadvantages of co‐teaching, and how different professional and academic backgrounds and disciplines can productively inform curriculum design and delivery in the academic/professional context. The authors, as co‐creators and co‐lecturers, have developed a number of courses which represent current working models for intermediate to advanced level academic/professional study, and attract students from across the creative disciplines; including theatre, media, visual arts and music. These courses are structured to develop in students a wide range of aesthetic and technical skills, as well as their ability to apply those skills professionally within and across the creative media industries. Issues regarding the balance between academic rigour, practical hands‐on skill development, assessment, logistics, resources, teamwork and other issues, are examined in the paper.

Ontology-based product's reputation model

Different reputation models are used in the web in order to generate reputation values for products using uses' review data. Most of the current reputation models use review ratings and neglect users' textual reviews, because it is more difficult to process. However, we argue that the overall reputation score for an item does not reflect the actual reputation for all of its features. And that's why the use of users' textual reviews is necessary. In our work we introduce a new reputation model that defines a new aggregation method for users' extracted opinions about products' features from users' text. Our model uses features ontology in order to define general features and sub-features of a product. It also reflects the frequencies of positive and negative opinions. We provide a case study to show how our results compare with other reputation models.

Product feature taxonomy learning based on user reviews

In recent years, the Web 2.0 has provided considerable facilities for people to create, share and exchange information and ideas. Upon this, the user generated content, such as reviews, has exploded. Such data provide a rich source to exploit in order to identify the information associated with specific reviewed items. Opinion mining has been widely used to identify the significant features of items (e.g., cameras) based upon user reviews. Feature extraction is the most critical step to identify useful information from texts. Most existing approaches only find individual features about a product without revealing the structural relationships between the features which usually exist. In this paper, we propose an approach to extract features and feature relationships, represented as a tree structure called feature taxonomy, based on frequent patterns and associations between patterns derived from user reviews. The generated feature taxonomy profiles the product at multiple levels and provides more detailed information about the product. Our experiment results based on some popularly used review datasets show that our proposed approach is able to capture the product features and relations effectively.

Randomized controlled trial of MICBT for co-existing alcohol misuse and depression : outcomes to 36-months

Integrated psychological treatment addressing co-existing alcohol misuse and depression has not been compared with single-focused treatment. This trial evaluates changes over 36 months following randomization of 284 outpatients to one of four motivational interviewing and cognitive-behavior therapy (MICBT) based interventions: (1) brief integrated intervention (BI); or BI plus 9 further sessions with (2) an integrated-, (3) alcohol-, or (4) depression-focus. Outcome measures included changes in alcohol consumption, depression (BDI-II: Beck Depression Inventory) and functioning (GAF: Global Assessment of Functioning), with average improvements from baseline of 21.8 drinks per week, 12.6 BDI-II units and 8.2 GAF units. Longer interventions tended to be more effective in reducing depression and improving functioning in the long-term, and in improving alcohol consumption in the short-term. Integrated treatment was at least as good as single-focused MICBT. Alcohol-focused treatment was as effective as depression-focused treatment at reducing depression and more effective in reducing alcohol misuse. The best approach seems to be an initial focus on both conditions followed by additional integrated- or alcohol-focused sessions.