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.

Complete genomic sequence of a Rubus yellow net virus isolate and detection of genome-wide pararetrovirus-derived small RNAs

Rubus yellow net virus (RYNV) was cloned and sequenced from a red raspberry (Rubus idaeus L.) plant exhibiting symptoms of mosaic and mottling in the leaves. Its genomic sequence indicates that it is a distinct member of the genus Badnavirus, with 7932. bp and seven ORFs, the first three corresponding in size and location to the ORFs found in the type member Commelina yellow mottle virus. Bioinformatic analysis of the genomic sequence detected several features including nucleic acid binding motifs, multiple zinc finger-like sequences and domains associated with cellular signaling. Subsequent sequencing of the small RNAs (sRNAs) from RYNV-infected R. idaeus leaf tissue was used to determine any RYNV sequences targeted by RNA silencing and identified abundant virus-derived small RNAs (vsRNAs). The majority of the vsRNAs were 22-nt in length. We observed a highly uneven genome-wide distribution of vsRNAs with strong clustering to small defined regions distributed over both strands of the RYNV genome. Together, our data show that sequences of the aphid-transmitted pararetrovirus RYNV are targeted in red raspberry by the interfering RNA pathway, a predominant antiviral defense mechanism in plants. © 2013.

RNA silencing platforms in plants

Since the discovery of RNAi, its mechanism in plants and animals has been intensively studied, widely exploited as a research tool, and used for a number of potential commercial applications. In this article, we discuss the platforms for delivering RNAi in plants. We provide a brief background to these platforms and concentrate on discussing the more recent advances, comparing the RNAi technologies used in plants with those used in animals, and trying to predict the ways in which RNAi technologies may further develop. © 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

No sex difference in body fat in response to supervised and measured exercise

It is often reported that females lose less body weight than males do in response to exercise. These differences are suggested to be a result of females exhibiting a stronger defense of body fat and a greater compensatory appetite response to exercise than males do. Purpose This study aimed to compare the effect of a 12-wk supervised exercise program on body weight, body composition, appetite, and energy intake in males and females. Methods A total of 107 overweight and obese adults (males = 35, premenopausal females = 72, BMI = 31.4 ± 4.2 kg·m−2, age = 40.9 ± 9.2 yr) completed a supervised 12-wk exercise program expending approximately 10.5 MJ·wk−1 at 70% HRmax. Body composition, energy intake, appetite ratings, RMR, and cardiovascular fitness were measured at weeks 0 and 12. Results The 12-wk exercise program led to significant reductions in body mass (males [M] = −3.03 ± 3.4 kg and females [F] = −2.28 ± 3.1 kg), fat mass (M = −3.14 ± 3.7 kg and F = −3.01 ± 3.0 kg), and percent body fat (M = −2.45% ± 3.3% and F = −2.45% ± 2.2%; all P < 0.0001), but there were no sex-based differences (P > 0.05). There were no significant changes in daily energy intake in males or females after the exercise intervention compared with baseline (M = 199.2 ± 2418.1 kJ and F = −131.6 ± 1912.0 kJ, P > 0.05). Fasting hunger levels significantly increased after the intervention compared with baseline values (M = 11.0 ± 21.1 min and F = 14.0 ± 22.9 mm, P < 0.0001), but there were no differences between males and females (P > 0.05). The exercise also improved satiety responses to an individualized fixed-energy breakfast (P < 0.0001). This was comparable in males and females. Conclusions Males and premenopausal females did not differ in their response to a 12-wk exercise intervention and achieved similar reductions in body fat. When exercise interventions are supervised and energy expenditure is controlled, there are no sex-based differences in the measured compensatory response to exercise.

The Implications of Activity Based Funding for Emergency Departments : A Comprehensive Literature Review

Executive Summary Emergency Departments (EDs) locally, nationally and internationally are becoming increasingly busy. Within this context, it can be challenging to deliver a health service that is safe, of high quality and cost-effective. Whilst various models are described within the literature that aim to measure ED ‘work’ or ‘activity’, they are often not linked to a measure of costs to provide such activity. It is important for hospital and ED managers to understand and apply this link so that optimal staffing and financial resourcing can be justifiably sought. This research is timely given that Australia has moved towards a national Activity Based Funding (ABF) model for ED activity. ABF is believed to increase transparency of care and fairness (i.e. equal work receives equal pay). ABF involves a person-, performance- or activity-based payment system, and thus a move away from historical “block payment” models that do not incentivise efficiency and quality. The aim of the Statewide Workforce and Activity-Based Funding Modelling Project in Queensland Emergency Departments (SWAMPED) is to identify and describe best practice Emergency Department (ED) workforce models within the current context of ED funding that operates under an ABF model. The study is comprised of five distinct phases. This monograph (Phase 1) comprises a systematic review of the literature that was completed in June 2013. The remaining phases include a detailed survey of Queensland hospital EDs’ resource levels, activity and operational models of care, development of new resource models, development of a user-friendly modelling interface for ED mangers, and production of a final report that identifies policy implications. The anticipated deliverable outcome of this research is the development of an ABF based Emergency Workforce Modelling Tool that will enable ED managers to profile both their workforce and operational models of care. Additionally, the tool will assist with the ability to more accurately inform adequate staffing numbers required in the future, inform planning of expected expenditures and be used for standardisation and benchmarking across similar EDs. Summary of the Findings Within the remit of this review of the literature, the main findings include: 1. EDs are becoming busier and more congested Rising demand, barriers to ED throughput and transitions of care all contribute to ED congestion. In addition requests by organisational managers and the community require continued broadening of the scope of services required of the ED and further increases in demand. As the population live longer with more lifestyle diseases their propensity to require ED care continues to grow. 2. Various models of care within EDs exist Models often vary to account for site specific characteritics to suit staffing profile, ED geographical location (e.g. metropolitan or rural site), and patient demographic profile (e.g. paediatrics, older persons, ethnicity). Existing and new models implemented within EDs often depend on the target outcome requiring change. Generally this is focussed on addressing issues at the input, throughput or output areas of the ED. Even with models targeting similar demographic or illness, the structure and process elements underpinning the model can vary, which can impact on outcomes and variance to the patient and carer experience between and within EDs. Major models of care to manage throughput inefficiencies include: A. Workforce Models of Care focus on the appropriate level of staffing for a given workload to provide prompt, timely and clinically effective patient care within an emergency care setting. The studies reviewed suggest that the early involvement of senior medical decision maker and/or specialised nursing roles such as Emergency Nurse Practitioners and Clinical Initiatives Nurse, primary contact or extended scope Allied Health Practitioners can facilitate patient flow and improve key indicators such as length of stay and reducing the number of those who did not wait to be seen amongst others. B. Operational Models of Care within EDs focus on mechanisms for streaming (e.g. fast-tracking) or otherwise grouping patient care based on acuity and complexity to assist with minimising any throughput inefficiencies. While studies support the positive impact of these models in general, it appears that they are most effective when they are adequately resourced. 3. Various methods of measuring ED activity exist Measuring ED activity requires careful consideration of models of care and staffing profile. Measuring activity requires the ability to account for factors including: patient census, acuity, LOS, intensity of intervention, department skill-mix plus an adjustment for non-patient care time. 4. Gaps in the literature Continued ED growth calls for new and innovative care delivery models that are safe, clinically effective and cost effective. New roles and stand-alone service delivery models are often evaluated in isolation without considering the global and economic impact on staffing profiles. Whilst various models of accounting for and measuring health care activity exist, costing studies and cost effectiveness studies are lacking for EDs making accurate and reliable assessments of care models difficult. There is a necessity to further understand, refine and account for measures of ED complexity that define a workload upon which resources and appropriate staffing determinations can be made into the future. There is also a need for continued monitoring and comprehensive evaluation of newly implemented workforce modelling tools. This research acknowledges those gaps and aims to: • Undertake a comprehensive and integrated whole of department workforce profiling exercise relative to resources in the context of ABF. • Inform workforce requirements based on traditional quantitative markers (e.g. volume and acuity) combined with qualitative elements of ED models of care; • Develop a comprehensive and validated workforce calculation tool that can be used to better inform or at least guide workforce requirements in a more transparent manner.

Socio-technological phishing prevention

Phishing is deceptive collection of personal information leading to embezzlement, identity theft, and so on. Preventive and combative measures have been taken by banking institutions, software vendors, and network authorities to fight phishing. At the forefront of this resilience are consortiums such as APWG (Anti-Phishing Working Group) and PhishTank, the latter being a collaborative platform where everyone can submit potentially phishing web-pages and classify web-pages as either phish or genuine. PhishTank also has an API that the browsers use to notify users when she tries to load a phishing page. There are some organizations and individuals who are very active and highly accurate in classifying web-pages on PhishTank. In this paper, we propose a defense model that uses these experts to fight phishing.

Strategies for improving safety performance of repair, maintenance, minor alteration and addition (RMAA) works

Purpose Managing and maintaining infrastructure assets are one of the indispensible tasks for many government agencies to preserve the nations' economic viability and social welfare. To reduce the expenditures over the life-cycle of an infrastructure asset and extend the period for which the asset performs effectively, proper repair and maintenance are essential. While repair, maintenance, minor alteration and addition (RMAA) sector is expanding in many developed cities, occurrences of fatalities and injuries in this sector are also soaring. The purposes of this paper are to identify and then evaluate the various strategies for improving the safety performance of RMAA works. Design/methodology/approach Semi-structured interviews and two rounds of Delphi survey were conducted for data collection. Findings Raising safety awareness of RMAA workers and selecting contractors with a good record of safety performance are the two most important strategies to improve the safety performance in this sector. Technology innovations and a pay-for-safety scheme are regarded as the two least important strategies. Originality/value The paper highlights possible ways to enhance safety of the rather under-explored RMAA sector in the construction industry.