Mobile silencing in plants: what is the signal and what defines the target

RNA-mediated silencing in plants can spread from cell to cell and over a long distance, and such mobile silencing has been extensively studied in the past decade. However, major questions remain as to what is the exact nature of the mobile silencing signals, how the components of the RNA-directed DNA methylation pathway are involved, and why systemic spread of silencing has only been observed for transgenes but not endogenous genes. In this review, we provide an overview of the current knowledge on mobile gene silencing in plants and present a model where systemic silencing involves long nuclear RNA transcripts that serve as a template to amplify primary siRNA signals.

The Enamovirus P0 protein is a silencing suppressor which inhibits local and systemic RNA silencing through AGO1 degradation

The P0 protein of poleroviruses and P1 protein of sobemoviruses suppress the plant's RNA silencing machinery. Here we identified a silencing suppressor protein (SSP), P0PE, in the Enamovirus Pea enation mosaic virus-1 (PEMV-1) and showed that it and the P0s of poleroviruses Potato leaf roll virus and Cereal yellow dwarf virus have strong local and systemic SSP activity, while the P1 of Sobemovirus Southern bean mosaic virus supresses systemic silencing. The nuclear localized P0PE has no discernable sequence conservation with known SSPs, but proved to be a strong suppressor of local silencing and a moderate suppressor of systemic silencing. Like the P0s from poleroviruses, P0PE destabilizes AGO1 and this action is mediated by an F-box-like domain. Therefore, despite the lack of any sequence similarity, the poleroviral and enamoviral SSPs have a conserved mode of action upon the RNA silencing machinery. © 2012 Elsevier Inc.

Synthesis of complementary RNA by RNA-dependent RNA polymerases in plant extracts is independent of an RNA primer

RNA-dependent RNA polymerase (RDR) activities were readily detected in extracts from cauliflower and broccoli florets, Arabidopsis thaliana (L.) Heynh callus tissue and broccoli nuclei. The synthesis of complementary RNA (cRNA) was independent of a RNA primer, whether or not the primer contained a 3′ terminal 2′-O-methyl group or was phosphorylated at the 5′ terminus. cRNA synthesis in plant extracts was not affected by loss-of-function mutations in the DICER-LIKE (DCL) proteins DCL2, DCL3, and DCL4, indicating that RDRs function independently of these DCL proteins. A loss-of-function mutation in RDR1, RDR2 or RDR6 did not significantly reduce the amount of cRNA synthesis. This indicates that these RDRs did not account for the bulk RDR activities in plant extracts, and suggest that either the individual RDRs each contribute a fraction of polymerase activity or another RDR(s) is predominant in the plant extract. © CSIRO 2008.

Posttranscriptional gene silencing is not compromised in the Arabidopsis CARPEL FACTORY (DICER-LIKE1) mutant, a homolog of dicer-1 from Drosophila

Posttranscriptional silencing (PTGS) in plants, nematodes, Drosophila, and perhaps all eukaryotes operates by sequence-specific degradation or translational inhibition of the target mRNA. These processes are mediated by duplexed RNA. In Drosophila and nematodes, double-stranded (ds)RNA or self-complementary RNA is processed into fragments of approximately 21 nt by Dicer-1 [1, 2]. These small interfering RNAs (siRNAs) serve as guides to target degradation of homologous single-stranded (ss)RNA [1, 3]. In some cases, the approximately 21 nt guide fragments derived from endogenous, imperfectly self-complementary RNAs cause translational inhibition of their target mRNAs, with which they have substantial, but not perfect sequence complementarity [4-6]. These small temporal RNAs (stRNAs) belong to a class of noncoding microRNAs (miRNAs), 20-24 nt in length, that are found in flies, plants, nematodes, and mammals [4, 6-12]. In nematodes, the Dicer-1 enzyme catalyzes the production of both siRNA and stRNA [2, 13-15]. Mutation of the Arabidopsis Dicer-1 homolog, CARPEL FACTORY (CAF), blocks miRNA production [1, 4, 16-18]. Here, we report that the same caf mutant does not block either PTGS or siRNA production induced by self-complementary hairpin RNA. This suggests either that this mutation only impairs miRNA formation or, more interestingly, that plants have two distinct dicer-like enzymes, one for miRNA and another for siRNAi production.

High-efficiency silencing of a β-glucuronidase gene in rice is correlated with repetitive transgene structure but is independent of DNA methylation

Two transgenic callus lines of rice, stably expressing a β-glucuronidase (GUS) gene, were supertransformed with a set of constructs designed to silence the resident GUS gene. An inverted-repeat (i/r) GUS construct, designed to produce mRNA with self-complementarity, was much more effective than simple sense and antisense constructs at inducing silencing. Supertransforming rice calluses with a direct-repeat (d/r) construct, although not as effective as those with the i/r construct, was also substantially more effective in silencing the resident GUS gene than the simple sense and antisense constructs. DNA hybridisation analyses revealed that every callus line supertransformed with either simple sense or antisense constructs, and subsequently showing GUS silencing, had the silence-inducing transgenes integrated into the plant genome in inverted-repeat configurations. The silenced lines containing i/r and d/r constructs did not necessarily have inverted-repeat T-DNA insertions. There was significant methylation of the GUS sequences in most of the silenced lines but not in the unsilenced lines. However, demethylation treatment of silenced lines with 5-azacytidine did not reverse the post-transcriptional gene silencing (PTGS) of GUS. Whereas the levels of RNA specific to the resident GUS gene were uniformly low in the silenced lines, RNA specific to the inducer transgenes accumulated to a substantial level, and the majority of the i/r RNA was unpolyadenylated. Altogether, these results suggest that both sense- and antisense-mediated gene suppression share a similar molecular basis, that unpolyadenylated RNA plays an important role in PTGS, and that methylation is not essential for PTGS.

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.

Is foot ulcer simulation training (FUST) really effective? Participants’ supervisors speak out

Background Foot ulcers are a common reason for diabetes-related hospitalisation. Foot ulcer simulation training (FUST) programs have increased podiatry participants self-confidence to manage foot ulcers. However, supervisors’ perspectives on their participants attending these simulation programs have not been investigated. This mixed method (quantitative and qualitative) study aimed to investigate home clinical supervisors’ perspectives on any changes to their participants’ competence and practice following FUST. Methods Clinical supervisors of fifteen podiatrists, who participated in a two-day Foot Ulcer Simulation Training (FUST) course, were recruited. Supervisors completed quantitative surveys evaluating their participants’ foot ulcer competence pre-FUST and 6-months post-FUST, via a purposed designed 21-item survey using a five-point Likert scale (1=Very limited, 5=Highly competent). Supervisors also attended a semi-structured qualitative group interview to investigate supervisors’ perspectives on FUST. Results Supervisors surveys returned were pre-FUST (n=10) and post-FUST (n=12). Significant competence improvements were observed at the 6-month survey (mean scores 2.84 cf. 3.72, p < 0.05). Five supervisors attended the group interview. Five sub-themes emerged: i) FUST provided a good foundation for future learning, ii) FUST modelled good clinical behaviour, iii) clinical practice improvement was evident in most participants, iv) clinical improvements were dependent on participant’s willingness to change and existing workplace culture, v) FUST needs to be reinforced back in the home clinic. Conclusion Overall, supervisors of FUST participants indicated that the course improved their participants’ competence and clinical practice. However, the degree of improvement appears dependant on the participants’ home workplace culture and willingness to embrace change.

Queensland diabetic foot hospitalisations (2005-10) : in what state is our foot hospital problem?

Background Diabetes foot complications are a leading cause of overall avoidable hospital admissions. Since 2006, the Queensland Diabetes Clinical Network has implemented programs aimed at reducing diabetes-related hospitalisation. The aim of this retrospective observational study was to determine the incidence of diabetes foot-related hospital admissions in Queensland from 2005 to 2010. Methods Data on all primary diabetes foot-related admissions in Queensland from 2005-2010 was obtained using diabetes foot-related ICD-10-AM (hospital discharge) codes. Queensland diabetes foot-related admission incidences were calculated using general population data from the Australian Bureau of Statistics. Furthermore, diabetes foot-related sub-group admissions were analysed. Chi-squared tests were used to assess changes in admissions over time. Results Overall, 24,917 diabetes foot-related admissions occurred, resulting in the use of 260,085 bed days or 1.4% of all available Queensland hospital bed days (18,352,152). The primary reasons for these admissions were foot ulcers (49.8%), cellulitis (20.7%), peripheral vascular disease (17.8%) and osteomyelitis (3.8%). The diabetes foot-related admission incidence among the general population (per 100,000) reduced by 22% (103.0 in 2005, to 80.7 in 2010, p < 0.001); bed days decreased by 18% (1,099 to 904, p < 0.001). Conclusion Diabetes foot complications appear to be the primary reason for 1.4 out of every 100 hospital beds used in Queensland. There has been a significant reduction in the incidence of diabetes foot-related admissions in Queensland between 2005 and 2010. This decrease has coincided with a corresponding decrease in amputations and the implementation of several diabetes foot clinical programs throughout Queensland.

Is the clinical Queensland High Risk Foot Form valid or reliable for research?

Background High-risk foot complications such as neuropathy, ischaemia, deformity, infections, ulcers and amputations consume considerable health care resources and typically result from chronic diseases. This study aimed to develop and test the validity and reliability of a Queensland High Risk Foot Form (QHRFF) tool. Methods Phase one involved developing a QHRFF using an existing diabetes high-risk foot tool, literature search, expert panel and several state-wide stakeholder groups. Phase two tested the criterion-related validity along with inter- and intra-rater reliability of the final QHRFF. Three cohorts of patients (n = 94) and four clinicians, representing different levels of expertise, were recruited. Validity was determined by calculating sensitivity, specificity and positive predictive values (PPV). Kappa and intra-class correlation (ICC) statistics were used to establish reliability. Results A QHRFF tool containing 46-items across seven domains was developed and endorsed. The majority of QHRFF items achieved moderate-to-perfect validity (PPV = 0.71 – 1) and reliability (Kappa/ICC = 0.41 – 1). Items with weak validity and/or reliability included those identifying health professionals previously attending the patient, other (non-listed) co-morbidity, previous foot ulcer, foot deformity, optimum offloading and optimum footwear. Conclusions The QHRFF had moderate-to-perfect validity and reliability across the majority of items, particularly identifying individual co-morbidities and foot complications. Items with weak validity or reliability need to be re-defined or removed. Overall, the QHRFF appears to be a valid and reliable tool to assess, collect and measure clinical data pertaining to high-risk foot complications for clinical or research purposes.

Offer to settle in an originating application : is it an offer under the UCPR?

Sheryl Jackson looks at the decision of Justice McMeekin in Northbound Property Group Pty Ltd v Carosi (No.2) [2013] QSC 189.

Copyright and computer generated materials : is it time to reboot the discussion about authorship?

Computer generated materials are ubiquitous and we encounter them on a daily basis, even though most people are unaware that this is the case. Blockbuster movies, television weather reports and telephone directories all include material that is produced by utilising computer technologies. Copyright protection for materials generated by a programmed computer was considered by the Federal Court and Full Court of the Federal Court in Telstra Corporation Limited v Phone Directories Company Pty Ltd. The court held that the White and Yellow pages telephone directories produced by Telstra and its subsidiary, Sensis, were not protected by copyright because they were computer-generated works which lacked the requisite human authorship. The Copyright Act 1968 (Cth) does not contain specific provisions on the subsistence of copyright in computer-generated materials. Although the issue of copyright protection for computer-generated materials has been examined in Australia on two separate occasions by independently-constituted Copyright Law Review Committees over a period of 10 years (1988 to 1998), the Committees’ recommendations for legislative clarification by the enactment of specific amendments to the Copyright Act have not yet been implemented and the legal position remains unclear. In the light of the decision of the Full Federal Court in Telstra v Phone Directories it is timely to consider whether specific provisions should be enacted to clarify the position of computer-generated works under copyright law and, in particular, whether the requirement of human authorship for original works protected under Part III of the Copyright Act should now be reconceptualised to align with the realities of how copyright materials are created in the digital era.

A conceptualization of complexity in IS-driven organizational transformations

Organizational transformations reliant on successful ICT system developments (continue to) fail to deliver projected benefits even when contemporary governance models are applied rigorously. Modifications to traditional program, project and systems development management methods have produced little material improvement to successful transformation as they are unable to routinely address the complexity and uncertainty of dynamic alignment of IS investments and innovation. Complexity theory provides insight into why this phenomenon occurs and is used to develop a conceptualization of complexity in IS-driven organizational transformations. This research-in-progress aims to identify complexity formulations relevant to organizational transformation. Political/power based influences, interrelated business rules, socio-technical innovation, impacts on stakeholders and emergent behaviors are commonly considered as characterizing complexity while the proposed conceptualization accommodates these as connectivity, irreducibility, entropy and/or information gain in hierarchically approximation and scaling, number of states in a finite automata and/or dimension of attractor, and information and/or variety.

Prevalence of risk factors for undiagnosed obstructive sleep apnoea is high in truck drivers on UK roads

Objectives To determine the prevalence of symptoms and risk factors of obstructive sleep apnoea (OSA) in truck drivers at a UK large truck stop. Methods Over a 5 day period, truck drivers completed a short questionnaire at a major UK ‘truck stop’. The questionnaire asked about OSA rist factors and symptoms, and included the Epworth Sleepiness Scale (ESS). Additionally, measurements of height, weight and collar size were taken. 148 truck drivers participated and within this random group the risk factors of OSA that were looked for were:men age over 40 y, obesity, parge neck circumference, smoking, high ESS and bed partner reporting snoring with witnessed apnoeas. Results Our sample were all men, with 82% aged over 40 y. 47% were obese (compared with 23% for UK men in general) and average neck circumference was 42 cm (compared with 38 cm for UK men in general – Martin et al 1997). 31% smoked (vs 21% for general population), and ESS averaged 2.1 points higher than expected for a healthy population (Johns et al 1997). Snoring was quite evident at 57% (compared wth 40% for men in general) and witnessed apnoeas were almost double (7%) compared with 3.8% given by Ohayon et al (1997) generally for men. Conclusion 8 key symptoms and risk factors of OSA have been found to be prevalent in a sample of truck drivers on UK roads, and to greater extent that for estimates in the general male population. Bed partners of truck drivers reporting witnessed apnoeas strongly suggests this group has a high potential for undiagnosed OSA. OSA sufferers are known to be at high risk of causing road traffi c accidents. This, together with the large size of trucks, then the potential for serious road crashes is great. Truck drivers, especially those who are obese, ought to be a high priority population for OSA screening.

Is the two hour recommended maximum driving time appropriate for both healthy older and treated obstructive sleep apnoea drivers?

Objectives The UK Department for Transport recommends taking a break from driving every 2 h. This study investigated: (i) if a 2 h drive time on a monotonous road is appropriate for OSA patients treated with CPAP, compared with healthy age matched controls, (ii) the impact of a night’s sleep restriction (with CPAP) and (iii) what happens if these patients miss one nights’ CPAP treatment. Methods About 19 healthy men aged 52–74 y (m = 66.2 y) and 19 OSA participants aged 50–75 y (m = 64.4 y) drove an interactive car simulator under monotonous motorway conditions for 2 h on two afternoons, in a counterbalanced design; (1) following a normal night’s sleep (8 h). (2) following a restricted night’s sleep (5 h), with normal CPAP use (3) following a night without CPAP treatment. (n = 11) Lane drifting incidents, indicative of falling asleep, were recorded for up to 2 h depending on competence to continue driving. Results Normal sleep: Controls drove for an average of 95.9 min (s.d. 37 min) and treated OSA drivers for 89.6 min (s.d. 29 min) without incident. 63.2% of controls and 42.1% of OSA drivers successfully completed the drive without an incident. Sleep restriction: 47.4% of controls and 26.3% OSA drivers finished without incident. Overall: controls drove for an average of 89.5 min (s.d. 39 min) and treated OSA drivers 65 min (s.d. 42 min) without incident. The effect of condition was significant [F(1.36) = 9.237, P < 0.05, eta2 = 0.204]. Stopping CPAP: 18.2% of drivers successfully completed the drive. Overall, participants drove for an average of 50.1 min (s.d. 38 min) without incident. The effect of condition was significant [F(2) = 8.8, P < 0.05, eta2 = 0.468]. Conclusion 52.6% of all drivers were able to complete a 2 hour drive under monotonous conditions after a full night’s sleep. Sleep restriction significantly affected both control and OSA drivers. We find evidence that treated OSA drivers are more impaired by sleep restriction than healthy control, as they were less able to sustain safely the 2 h drive without incidents. OSA drivers should be aware that non-compliance with CPAP can significantly impair driving performance. It may be appropriate to recommend older drivers take a break from driving every 90 min especially when undertaking a monotonous drive, as was the case here.

Countermeasures to driver sleepiness : is the message getting through?

The most effective countermeasures to driver sleepiness (caffeine and a nap, ideally in combination) are not the most popular choice for UK drivers. Groups susceptible to driver sleepiness (OSA patients and truck drivers) do not favour effective countermeasures to driver sleepiness. Prior experience of driver sleepiness does not promote an effective choice of countermeasure.