High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States

Replication and pathogenesis of the human immunodeficiency virus (HIV) is tightly linked to the structure of its RNA genome, but genome structure in infectious virions is poorly understood. We invent high-throughput SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) technology, which uses many of the same tools as DNA sequencing, to quantify RNA backbone flexibility at single-nucleotide resolution and from which robust structural information can be immediately derived. We analyze the structure of HIV-1 genomic RNA in four biologically instructive states, including the authentic viral genome inside native particles. Remarkably, given the large number of plausible local structures, the first 10% of the HIV-1 genome exists in a single, predominant conformation in all four states. We also discover that noncoding regions functioning in a regulatory role have significantly lower (p-value < 0.0001) SHAPE reactivities, and hence more structure, than do viral coding regions that function as the template for protein synthesis. By directly monitoring protein binding inside virions, we identify the RNA recognition motif for the viral nucleocapsid protein. Seven structurally homologous binding sites occur in a well-defined domain in the genome, consistent with a role in directing specific packaging of genomic RNA into nascent virions. In addition, we identify two distinct motifs that are targets for the duplex destabilizing activity of this same protein. The nucleocapsid protein destabilizes local HIV-1 RNA structure in ways likely to facilitate initial movement both of the retroviral reverse transcriptase from its tRNA primer and of the ribosome in coding regions. Each of the three nucleocapsid interaction motifs falls in a specific genome domain, indicating that local protein interactions can be organized by the long-range architecture of an RNA. High-throughput SHAPE reveals a comprehensive view of HIV-1 RNA genome structure, and further application of this technology will make possible newly informative analysis of any RNA in a cellular transcriptome

Radio morphology and spectral analysis of cD galaxies in rich and poor galaxy clusters

We present a radio morphological study and spectral analysis for a sample of 13 cD galaxies in rich and poor clusters of galaxies.} Our study is based on new high sensitivity Giant Metrewave Radio Telescope (GMRT) observations at 1.28 GHz, 610 MHz and 235 MHz, and on archival data. From a statistical sample of cluster cD galaxies we selected those sources with little information available in the literature and promising for the detection of aged radio emission. Beyond the high sensitivity images for all 13 radio galaxies, we present also a detailed spectral analysis for 7 of them. We found a variety of morphologies and linear sizes, as typical for radio galaxies in the radio power range sampled here (low to intermediate power radio galaxies). The spectral analysis shows that 10/13 radio galaxies have steep radio spectrum, with spectral index $\alpha \ge 1$. In general, the radiative ages and growth velocities are consistent with previous findings that the evolution of radio galaxies at the cluster centres is affected by the dense external medium (i.e. low growth velocities and old ages. We suggest that the dominant galaxies in A 2622 and MKW 03s are dying radio sources, which at present are not fed by nuclear activity. On the other hand, the spectacular source at the centre of A 2372 might be a very interesting example of restarted radio galaxy. For this source we estimated a life cycle of the order of 10$^6$ yr.Comment: Accepted by A&A, 25 pages, 28 figures, 6 tables and appendix Full version including high quality images available at http://www.ira.inaf.it/~tventuri/pap/Venturi.pd

Supersymmetry Relations Between Contributions To One-Loop Gauge Boson Amplitudes

We apply ideas motivated by string theory to improve the calculational efficiency of one-loop weak interaction processes with massive external gauge bosons. In certain cases ``supersymmetry'' relations between diagrams with a fermion loop and with a gauge boson loop hold. This is explicitly illustrated for a particular one-loop standard model process with four-external gauge bosons. The supersymmetry relations can be used to provide further significant improvements in calculational efficiency.Comment: 21 pages of plain TeX + 5 PostScript figures (compressed and uuencoded), UCLA/93/TEP/36 and DTP/93/8

Astrometry and geodesy with radio interferometry: experiments, models, results

Summarizes current status of radio interferometry at radio frequencies between Earth-based receivers, for astrometric and geodetic applications. Emphasizes theoretical models of VLBI observables that are required to extract results at the present accuracy levels of 1 cm and 1 nanoradian. Highlights the achievements of VLBI during the past two decades in reference frames, Earth orientation, atmospheric effects on microwave propagation, and relativity.Comment: 83 pages, 19 Postscript figures. To be published in Rev. Mod. Phys., Vol. 70, Oct. 199

Telephone survey of private patients' views on continuity of care and registration with general practice in Ireland

BACKGROUND: The desire of patients for personal continuity of care with a General Practitioner (GP) has been well documented, but not within non-registered private patients in Ireland. This study set out to examine the attitudes and reported behaviours of private fee-paying patients towards continuity of GP care and universal registration for patients. METHODS: Cross-sectional telephone survey of 400 randomly chosen fee-paying patients living within County Dublin. There is no formal system of registration with a GP for these patients. Main outcomes were attendance of respondents at primary health care facilities and their attitudes towards continuity of care and registration with a GP. Data was analysed using descriptive statistics and using parametric and non-parametric tests of association. Pearson correlation was used to quantify the association between the described variables and attitudes towards continuity and registration with a GP. Variables showing significance at the 5% level were entered into multiple linear regression models. RESULTS: 97% of respondents had seen a GP in the previous 5 years. The mean number of visits to the GP for respondents was 2.3 per annum. 89% of respondents had a regular GP and the mean length of time with their GP was 15.6 years. 96% preferred their personal medical care to be provided within one general practice. 16% of respondents had consulted a GP outside of their own practice in the previous year. They were more likely to be female, commute a longer distance to work or have poorer health status. 81% considered it important to be officially registered with a GP practice of their choice. CONCLUSION: Both personal and longitudinal continuity of care with a GP are important to private patients. Respondents who chose to visit GPs other than their regular GP were not easily characterised in this study and individual circumstances may lead to this behaviour. There is strong support for a system of universal patient registration within general practice

Direct effects of diazepam on emotional processing in healthy volunteers

RATIONALE: Pharmacological agents used in the treatment of anxiety have been reported to decrease threat relevant processing in patients and healthy controls, suggesting a potentially relevant mechanism of action. However, the effects of the anxiolytic diazepam have typically been examined at sedative doses, which do not allow the direct actions on emotional processing to be fully separated from global effects of the drug on cognition and alertness. OBJECTIVES: The aim of this study was to investigate the effect of a lower, but still clinically effective, dose of diazepam on emotional processing in healthy volunteers. MATERIALS AND METHODS: Twenty-four participants were randomised to receive a single dose of diazepam (5 mg) or placebo. Sixty minutes later, participants completed a battery of psychological tests, including measures of non-emotional cognitive performance (reaction time and sustained attention) and emotional processing (affective modulation of the startle reflex, attentional dot probe, facial expression recognition, and emotional memory). Mood and subjective experience were also measured. RESULTS: Diazepam significantly modulated attentional vigilance to masked emotional faces and significantly decreased overall startle reactivity. Diazepam did not significantly affect mood, alertness, response times, facial expression recognition, or sustained attention. CONCLUSIONS: At non-sedating doses, diazepam produces effects on attentional vigilance and startle responsivity that are consistent with its anxiolytic action. This may be an underlying mechanism through which benzodiazepines exert their therapeutic effects in clinical anxiety

Transat—A Method for Detecting the Conserved Helices of Functional RNA Structures, Including Transient, Pseudo-Knotted and Alternative Structures

The prediction of functional RNA structures has attracted increased interest, as it allows us to study the potential functional roles of many genes. RNA structure prediction methods, however, assume that there is a unique functional RNA structure and also do not predict functional features required for in vivo folding. In order to understand how functional RNA structures form in vivo, we require sophisticated experiments or reliable prediction methods. So far, there exist only a few, experimentally validated transient RNA structures. On the computational side, there exist several computer programs which aim to predict the co-transcriptional folding pathway in vivo, but these make a range of simplifying assumptions and do not capture all features known to influence RNA folding in vivo. We want to investigate if evolutionarily related RNA genes fold in a similar way in vivo. To this end, we have developed a new computational method, Transat, which detects conserved helices of high statistical significance. We introduce the method, present a comprehensive performance evaluation and show that Transat is able to predict the structural features of known reference structures including pseudo-knotted ones as well as those of known alternative structural configurations. Transat can also identify unstructured sub-sequences bound by other molecules and provides evidence for new helices which may define folding pathways, supporting the notion that homologous RNA sequence not only assume a similar reference RNA structure, but also fold similarly. Finally, we show that the structural features predicted by Transat differ from those assuming thermodynamic equilibrium. Unlike the existing methods for predicting folding pathways, our method works in a comparative way. This has the disadvantage of not being able to predict features as function of time, but has the considerable advantage of highlighting conserved features and of not requiring a detailed knowledge of the cellular environment

The effects of juvenile stress on anxiety, cognitive bias and decision making in adulthood:a rat model

Stress experienced in childhood is associated with an increased risk of developing psychiatric disorders in adulthood. These disorders are particularly characterized by disturbances to emotional and cognitive processes, which are not currently fully modeled in animals. Assays of cognitive bias have recently been used with animals to give an indication of their emotional/cognitive state. We used a cognitive bias test, alongside a traditional measure of anxiety (elevated plus maze), to investigate the effects of juvenile stress (JS) on adulthood behaviour using a rodent model. During the cognitive bias test, animals were trained to discriminate between two reward bowls based on a stimulus (rough/smooth sandpaper) encountered before they reached the bowls. One stimulus (e.g. rough) was associated with a lower value reward than the other (e.g. smooth). Once rats were trained, their cognitive bias was explored through the presentation of an ambiguous stimulus (intermediate grade sandpaper): a rat was classed as optimistic if it chose the bowl ordinarily associated with the high value reward. JS animals were lighter than controls, exhibited increased anxiety-like behaviour in the elevated plus maze and were more optimistic in the cognitive bias test. This increased optimism may represent an optimal foraging strategy for these underweight animals. JS animals were also faster than controls to make a decision when presented with an ambiguous stimulus, suggesting altered decision making. These results demonstrate that stress in the juvenile phase can increase anxiety-like behaviour and alter cognitive bias and decision making in adulthood in a rat model

Teaching psychology to student nurses: the use of talking heads videos

Psychology is a central part of undergraduate nursing curricula in the UK.However, student nurses report difficulties recognising the relevance and value of psychology. We sought to strengthen first-year student nurses’ application of psychology by developing a set of digital stories based around ‘Talking Head’video clips where authentic patients relate their experiences of illness and nursing care. The aim of this article is to discuss the technological, organisational and pedagogical challenges, student and staff evaluations and our recommendations for the future of Talking Heads. First-year student nurses were shown a video clip of a patient talking about their illness experiences followed by a group learning situation linking main themes to psychology and nursing. Students and staff valued the authenticity of patient’s narrative, found the video clip easy to follow,reported a raised awareness of psychological concepts and improved empathetic understanding of chronic illness. Negative evaluations were related to a sanitised, untypical representation and limited internet access. This small-scale study highlighted how patient narrative may enhance students understanding of illness experience. It chronicles the development and evaluation of a Talking Head in a specific context but which may be useful across disciplines