Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets

tRNA-derived RNA fragments (tRFs) are 19mer small RNAs that associate with Argonaute (AGO) proteins in humans. However, in plants, it is unknown if tRFs bind with AGO proteins. Here, using public deep sequencing libraries of immunoprecipitated Argonaute proteins (AGO-IP) and bioinformatics approaches, we identified the Arabidopsis thaliana AGO-IP tRFs. Moreover, using three degradome deep sequencing libraries, we identified four putative tRF targets. The expression pattern of tRFs, based on deep sequencing data, was also analyzed under abiotic and biotic stresses. The results obtained here represent a useful starting point for future studies on tRFs in plants. © 2013 Loss-Morais et al.; licensee BioMed Central Ltd.

State of Energy Efficiency Education in Australian Technical & Further Education (TAFE) : A Report to the Australian Government Skills for the Carbon Challenge Initiative, The Natural Edge Project (TNEP), Queensland University of Technology

The Australian Government’s Skills for the Carbon Challenge (SCC) initiative aims to accelerate industry and the education sectors response to climate change. As part of the SCC initiative, the Department of Industry, Innovation, Climate Change, Science, Research and Tertiary Education (DIICCSRTE) provided funding to investigate the state of energy efficiency education in engineering-related Australian Technical and Further Education (TAFE) Programs. The following document reports on the outcomes of a multi-stage consultation project that engaged with participants from over 80% of TAFE institutions across Australia with the aim of supporting and enhancing future critical skills development in this area. Specifically, this report presents the findings of a national survey, based on a series of TAFE educator focus groups, conducted in May 2013 aimed at understanding the experiences and insights of Australian TAFE educators teaching engineering-related courses. Responses were received from 224 TAFE Educators across 50 of the 61 TAFE institutions in Australia (82% response rate).

How much information can be obtained from tracking the position of the leading edge in a scratch assay?

Moving cell fronts are an essential feature of wound healing, development and disease. The rate at which a cell front moves is driven, in part, by the cell motility, quantified in terms of the cell diffusivity $D$, and the cell proliferation rate �$\lambda$. Scratch assays are a commonly-reported procedure used to investigate the motion of cell fronts where an initial cell monolayer is scratched and the motion of the front is monitored over a short period of time, often less than 24 hours. The simplest way of quantifying a scratch assay is to monitor the progression of the leading edge. Leading edge data is very convenient since, unlike other methods, it is nondestructive and does not require labeling, tracking or counting individual cells amongst the population. In this work we study short time leading edge data in a scratch assay using a discrete mathematical model and automated image analysis with the aim of investigating whether such data allows us to reliably identify $D$ and $\lambda$�. Using a naıve calibration approach where we simply scan the relevant region of the ($D$;$\lambda$�) parameter space, we show that there are many choices of $D$ and $\lambda$� for which our model produces indistinguishable short time leading edge data. Therefore, without due care, it is impossible to estimate $D$ and $\lambda$� from this kind of data. To address this, we present a modified approach accounting for the fact that cell motility occurs over a much shorter time scale than proliferation. Using this information we divide the duration of the experiment into two periods, and we estimate $D$ using data from the first period, while we estimate �$\lambda$ using data from the second period. We confirm the accuracy of our approach using in silico data and a new set of in vitro data, which shows that our method recovers estimates of $D$ and $\lamdba$� that are consistent with previously-reported values except that that our approach is fast, inexpensive, nondestructive and avoids the need for cell labeling and cell counting.

Plasma enables edge-to-center-oriented graphene nanoarrays on Si nanograss

The formation of clearly separated vertical graphenenanosheets on silicon nanograss support is demonstrated. The plasma-enabled, two-stage mask-free process produced self-organized vertical graphenes of a few carbon layers (as confirmed by advanced microanalysis), prominently oriented in the substrate center–substrate edge direction. It is shown that the width of the alignment zone depends on the substrate conductivity, and thus the electric field in the vicinity of the growth surface is responsible for the graphene alignment. This finding is confirmed by the Monte Carlo simulations of the ion flux distribution in the silicon nanograss pattern.

Plasma-aided nanofabrication: where is the cutting edge?

Plasma-aided nanofabrication is a rapidly expanding area of research spanning disciplines ranging from physics and chemistry of plasmas and gas discharges to solid state physics, materials science, surface science, nanoscience and nanotechnology and related engineering subjects. The current status of the research field is discussed and examples of superior performance and competitive advantage of plasma processes and techniques are given. These examples are selected to represent a range of applications of two major types of plasmas suitable for nanoscale synthesis and processing, namely thermally non-equilibrium and thermal plasmas. Major concepts and terminology used in the field are introduced. The paper also pinpoints the major challenges facing plasma-aided nanofabrication and identifies some emerging topics for future research. © 2007 IOP Publishing Ltd.

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

Urban Form at the Edge : Proceedings from ISUF 2013 [Volume 1]

Urban morphology as a field of study has developed primarily in Europe and North America, and more recently emerging as a recurrent topic in China and South America. As a counterpoint to this centric view, the ISUF 2013 conference explored aspects of ‘urban form at the edge’. In particular the conference examined ‘off centre areas’ such as India, Africa, Middle East, Central Asia and Australasia which require innovative approaches to the study of traditional, as well as post-colonial and contemporary, morphologies. Broader interpretations of urban form at the edge focus on minor centres and suburbia, with their developing and transilient character; edge cities and regional centres; and new technologies and approaches that are developing alongside established methods, tools and theories of urban morphology...

Extinction risk in cloud forest fragments under climate change and habitat loss

Aim: To quantify the consequences of major threats to biodiversity, such as climate and land-use change, it is important to use explicit measures of species persistence, such as extinction risk. The extinction risk of metapopulations can be approximated through simple models, providing a regional snapshot of the extinction probability of a species. We evaluated the extinction risk of three species under different climate change scenarios in three different regions of the Mexican cloud forest, a highly fragmented habitat that is particularly vulnerable to climate change. Location: Cloud forests in Mexico. Methods: Using Maxent, we estimated the potential distribution of cloud forest for three different time horizons (2030, 2050 and 2080) and their overlap with protected areas. Then, we calculated the extinction risk of three contrasting vertebrate species for two scenarios: (1) climate change only (all suitable areas of cloud forest through time) and (2) climate and land-use change (only suitable areas within a currently protected area), using an explicit patch-occupancy approximation model and calculating the joint probability of all populations becoming extinct when the number of remaining patches was less than five. Results: Our results show that the extent of environmentally suitable areas for cloud forest in Mexico will sharply decline in the next 70 years. We discovered that if all habitat outside protected areas is transformed, then only species with small area requirements are likely to persist. With habitat loss through climate change only, high dispersal rates are sufficient for persistence, but this requires protection of all remaining cloud forest areas. Main conclusions: Even if high dispersal rates mitigate the extinction risk of species due to climate change, the synergistic impacts of changing climate and land use further threaten the persistence of species with higher area requirements. Our approach for assessing the impacts of threats on biodiversity is particularly useful when there is little time or data for detailed population viability analyses. © 2013 John Wiley & Sons Ltd.

The edge of glory: the relationship between metacritic scores and player experience

This study sought to examine how measures of player experience used in videogame research relate to Metacritic Professional and User scores. In total, 573 participants completed an online survey, where they responded the Player Experience of Need Satisfaction (PENS) and the Game Experience Questionnaire (GEQ) in relation to their current favourite videogame. Correlations among the data indicate an overlap between the player experience constructs and the factors informing Metacritic scores. Additionally, differences emerged in the ways professionals and users appear to allocate game ratings. However, the data also provide clear evidence that Metacritic scores do not reflect the full complexity of player experience and may be misleading in some cases.

Edge-weighting of gene expression graphs

In recent years, considerable research efforts have been directed to micro-array technologies and their role in providing simultaneous information on expression profiles for thousands of genes. These data, when subjected to clustering and classification procedures, can assist in identifying patterns and providing insight on biological processes. To understand the properties of complex gene expression datasets, graphical representations can be used. Intuitively, the data can be represented in terms of a bipartite graph, with weighted edges corresponding to gene-sample node couples in the dataset. Biologically meaningful subgraphs can be sought, but performance can be influenced both by the search algorithm, and, by the graph-weighting scheme and both merit rigorous investigation. In this paper, we focus on edge-weighting schemes for bipartite graphical representation of gene expression. Two novel methods are presented: the first is based on empirical evidence; the second on a geometric distribution. The schemes are compared for several real datasets, assessing efficiency of performance based on four essential properties: robustness to noise and missing values, discrimination, parameter influence on scheme efficiency and reusability. Recommendations and limitations are briefly discussed. Keywords: Edge-weighting; weighted graphs; gene expression; bi-clustering

Working on the edge : Exploring the creative tensions experienced by practitioners facilitating participatory media projects with refugees and asylum seekers in Australia

This paper aims to provide a contextualised and embedded exploration of how the notions of "practice" and "participation", key concepts in the study of culture and media, are manifest in an example of a complex creative project. This project aimed to engage with refugees and asylum seekers through the co-creation of cultural material and is an outcome of an? ethnographic action research (Tacchi et al. 2003) partnership involving a community development worker in a settlement support agency and a storytelling/community media researcher (the author), along with other project collaborators. The discussion of this project focuses on the role of the facilitator and illustrates the processes of orchestrating a complex project involving a series of linked stages with cumulative effect. As practitioners at this site we are working in the space where personal narratives, participatory arts and media, and the staging of intercultural, civic dialogue events, intersect. Co-creative media facilitation in these contexts involves both managing hybrid communicative spaces and (re)combining the "integrative practices" (Schatzki 1996) of a range of professional approaches and creative roles. This is liminal work, located on the boundaries of several disciplines and practices. Drawing on reflections gathered from collaborative ethnographic descriptions (Bhattacharya 2008), this paper traces moments of practitioner uncertainty that can be linked to the way "practice" and “participation” is problematised within the community cultural development field in a way that is at times an uneasy fit with conventional ways of operating in social service roles. These moments of tension also indicate where this project pushed practitioners into spaces of improvisation and new learning. Keywords: Youth, refugees, community cultural development, co-creative media facilitation, ethnographic action research, intercultural dialogue.

Mitochondrial DNA sequence analysis from multiple gene fragments reveals genetic heterogeneity of Crassostrea ariakensis in East Asia

The native Asian oyster, Crassostrea ariakensis is one of the most common and important Crassostrea species that occur naturally along the coast of East Asia. Molecular species diagnosis is a prerequisite for population genetic analysis of wild oyster populations because oyster species cannot be discriminated reliably using external morphological characters alone due to character ambiguity. To date there have been few phylogeographic studies of natural edible oyster populations in East Asia, in particular this is true of the common species in Korea C. ariakensis. We therefore assessed the levels and patterns of molecular genetic variation in East Asian wild populations of C. ariakensis from Korea, Japan, and China using DNA sequence analysis of five concatenated mtDNA regions namely; 16S rRNA, cytochrome oxidase I, cytochrome oxidase II, cytochrome oxidase III, and cytochrome b. Two divergent C. ariakensis clades were identified between southern China and remaining sites from the northern region. In addition, hierarchical AMOVA and pairwise UST analyses showed that genetic diversity was discontinuous among wild populations of C. ariakensis in East Asia. Biogeographical and historical sea level changes are discussed as potential factors that may have influenced the genetic heterogeneity of wild C. ariakensis stocks across this region.

Fresh thinking in services marketing: Contemporary, cutting-edge and creative thoughts

Purpose The purpose of this paper is to highlight and promote fresh thinking in services marketing research. Design/methodology/approach The topic of the special issue was deliberately chosen to encourage fresh ideas and concepts that will move the discipline forward. The accepted papers have been categorised for ease and convenience of reading by scholars and practitioners, with a short commentary on each category. Findings There is a wealth of forward-thinking by service(s) marketing researchers that bodes well for the future of the sub-discipline. Research limitations/implications The special issue does not address fresh thinking in all areas of services marketing research. Other potential areas for fresh thinking are identified. Originality/value New thinking in a scholarly field is necessary to propel the discipline forward.