A new approach to determining whole viral genomic sequences including termini using a single deep sequencing run

Next-generation sequencing is now commonly used for a variety of applications in virology including virus discovery, investigation of quasispecies, viral evolution, metagenomics, and analyses of antiviral resistance. However, there are limitations with the current sample preparation methods used for deep sequencing of viral genomes, especially during de novo sequencing. For example, current methods are unable to capture the terminal sequences of viral genomes in an efficient and effective manner; data representing the 3' and 5' ends are typically insufficient. Methods such as Rapid Amplification of cDNA Ends address this issue but these methods can be time consuming, may require some prior knowledge of the viral sequence, and require multiple independent procedures. The current study outlines a sample preparation technique that overcomes some of these shortcomings. The method relied on random fragmentation with divalent cations and subsequent adapter ligation directly to RNA, rather than cDNA, to maximize the quality and quantity of terminal reads. The technique was tested on RNA samples from two different RNA viruses, Ebola virus and hepatitis C virus. This method permits rapid preparation of samples for deep sequencing while eliminating the use of sequence specific primers and captures the entire genome sequence, including the 5' and 3' ends. This could improve the efficiency of virus discovery projects where the terminal ends are unknown.

Enhanced factor VIIIa stability of A2 domain interface variants results from an increased apparent affinity for the A2 subunit. Results from an increased apparent affinity for the A2 subunit

Factor (F)VIIIa, a heterotrimer comprised of A1, A2, and A3C1C2 subunits, is labile due to the tendency of the A2 subunit to dissociate from the A1/A3C1C2 dimer. As dissociation of the A2 subunit inactivates FVIIIa activity, retention of A2 defines FVIIIa stability and thus, FXase activity. Earlier results showed that replacing residues D519, E665, and E1984 at the A2 domain interface with Ala or Val reduced rates of FVIIIa decay, increasing FXa and thrombin generation. We now show the enhanced FVIIIa stability of these variants results from increases in inter-A2 subunit affinity. Using a FVIIIa reconstitution assay to monitor inter-subunit affinity by activity regeneration, the apparent Kd value for the interaction of wild-type (WT) A2 subunit with WT A1/A3C1C2 dimer (43 ± 2 nM) was significantly higher than values observed for the A2 point mutants D519A/V, E665A/V, and E1984A/V which ranged from ~5 to ~19 nM. Val was determined to be the optimal hydrophobic residue at position 665 (apparent Kd = 5.1 ± 0.7 nM) as substitutions with Ile or Leu at this position increased the apparent Kd value by ~3- and ~7-fold, respectively. Furthermore, the double mutant (D519V/E665V) showed an ~47-fold lower apparent Kd value (0.9 ± 0.6 nM) than WT. Thus these hydrophobic mutations at the A2 subunit interfaces result in high binding affinities for the A2 subunit and correlate well with previously observed reductions in rates in FVIIIa decay.

The cost effectiveness of ivabradine in the treatment of chronic heart failure from the U.K. National Health Service perspective

Objective

Ivabradine, a specific heart rate lowering therapy, has been shown in a randomised placebo-controlled study, Systolic HF Treatment with the I_f Inhibitor Ivabradine Trial (SHI_fT), to significantly reduce the composite end point of cardiovascular death and hospitalisation for worsening heart failure (HF) in patients with systolic HF who are in sinus rhythm and with a heart rate ≥70 bpm, when added to optimised medical therapy (HR: 0.82, 95% CI 0.75 to 0.90, p<0.0001). We assessed the cost effectiveness of ivabradine, from a UK National Health Service perspective, based on the results of SHI_fT.

Methods

A Markov model estimated the cost effectiveness of ivabradine compared with standard care for two cohorts of patients with HF (heart rate ≥75 bpm in line with the EU labelled indication; and heart rate ≥70 bpm in line with the SHI_fT study population). Modelled outcomes included death, hospitalisation, quality of life and New York Heart Association class. Total costs and quality adjusted life years (QALYs) for ivabradine and standard care were estimated over a lifetime horizon.

Results

The incremental cost per additional QALY for ivabradine plus standard care versus standard care has been estimated as £8498 for heart rate ≥75 bpm and £13 764 for heart rate ≥70 bpm. Ivabradine is expected to have a 95% chance of being cost-effective in the EU licensed population using the current National Institute for Health and Care Excellence cost effectiveness threshold of £20 000 per QALY. These results were robust in sensitivity analyses.

Conclusions

This economic evaluation suggests that the use of ivabradine is likely to be cost-effective in eligible patients with HF from a UK National Health Service perspective.

High-intensity focused ultrasound in obstetrics and gynecology: the birth of a new era of noninvasive surgery?

Although ultrasound is an essential investigative modality in obstetrics and gynecology, the potential for therapeutic high-intensity focused ultrasound (HIFU) (also referred to as focused ultrasound surgery, FUS) to offer an alternative to invasive surgery is less well known. The ability of HIFU to create discrete regions of tissue necrosis only in precisely targeted positions by careful placement of the focus, without the need for any surgical intervention, has made HIFU of interest to those seeking noninvasive alternatives to conventional abdominal surgery. This article reviews the current experimental and clinical experience with HIFU in obstetrics and gynecology, and outlines potential future applications in fetal medicine and the challenges faced in their development.

The population ecology of two tropical trees, Brachychiton diversifolius (Malvaceae) and Bombax ceiba (Bombaceae), harvested by Indigenous woodcarvers in Arnhem Land, Australia

We describe the population ecology of two tropical deciduous trees, Bombax ceiba leiocarpum A. Robyns and Brachychiton diversifolius R. Br., which are in high demand for Indigenous sculpture production in Arnhem Land, Australia. We monitored tagged populations of both species at two locations for 2 years to examine their reproduction, growth, and survival rates and their response to harvest. Both species have similar life histories: they reproduce during the dry season (June-November) producing a high seed load, seed predation was high, seeds did not survive in the soil past the following wet season to form a seed bank, and germination rates were low and variable for both species. Average annual circumference growth rates were 1.07 cm year(-1) for B. ceiba and 0.98 cm year(-1) for B. diversifolius, with most of the growth occurring during the early wet season. Most (65-88 %) of the harvested B. ceiba and B. diversifolius stems coppiced. Coppice and stem size class were the main factors influencing tree growth rates with coppice stems growing up to six times faster than similar sized non-coppice stems. The survival of B. ceiba and B. diversifolius stems was size class dependent and affected by local site factors (e.g. fire and other disturbances) so that the smaller size classes had a low probability of survival. Given the resprouting potential of both species, their wild harvest is likely to have only minimal local impact on wild populations. However, further population modelling is required to determine whether the small and disjunct B. ceiba populations can sustain harvesting at current levels.

Emergency capnography monitoring: comparing ergonomic design of intensive care unit ventilator interfaces and specific training of staff in reducing time to activation

Modern ventilators provide capnography monitoring in patients with tracheal tubes, in compliance with national and international recommendations. This technology is often not used when patients' lungs are non-invasively ventilated; however, it should be accessed immediately following tracheal intubation to confirm tube placement. This study assessed the effect of ventilation interface design on the speed with which capnography can be activated by comparing the Dräger Evita 4 and Dräger V500 before and after a specific training episode. We configured the V500 to have a capnography activation button on the front screen in contrast to the Evita 4 which requires a sequence of actions to access capnography monitoring. We used a randomised crossover design, measuring time to monitoring activation, and repeated the study after 3 months. Survival analysis showed significantly quicker activation associated with ventilator choice (V500, p < 0.0001) and training (p = 0.0058). The training improved activation speed with both machines, though this was only significant for the Evita 4 (p = 0.0097).

Slipping and sliding: frameshift mutations in herpes simplex virus thymidine kinase and drug-resistance

Some of the most successful antiviral agents currently available are effective against herpes simplex virus. However, resistance to these drugs is frequently associated with significant morbidity, particularly in immunocompromised patients. In addition to the clinical implications of drug resistance, the range of biological processes exploited by the virus to attain resistance while maintaining pathogenicity is proving to be surprising. These mechanisms, which include ribosomal frameshifting, induced infidelity of the DNA polymerase, and internal ribosome entry, are discussed.

Packaging of Non-Coding RNAs into Herpesvirus Virions: Comparisons to Coding RNAs

The herpesviruses are a family of large DNA viruses capable of establishing lifelong infections. Recent reports have shown that herpesviruses package non-coding RNA into virions; this follows earlier observations showing that coding RNAs are detected in virions. Packaging RNAs allows for their function immediately after virus entry and in the absence of de novo transcription. Despite the collective understanding that RNAs are packaged into herpesvirus virions, many questions remain. This review will highlight what is known regarding packaged coding and non-coding RNAs and discuss their potential impact to virus biology.

A comparison of methods of post-operative analgesia in children undergoing limb reconstruction with circular frames

This retrospective study compared post-operative epidural analgesia (E), continuous peripheral nerve blocks (CPNB) and morphine infusion (M) in 68 children undergoing limb reconstruction with circular frames. The data collected included episodes of severe pain, post-operative duration of analgesia, requirement for top-up analgesia, number of osteotomies, side effects and complications. There was a significant difference between the number of episodes of severe pain in patients receiving a morphine infusion and those receiving epidurals or CPNB (M vs E, p < 0.0001; M vs CPNB, p = 0.018). The CPNB group was associated with the lowest incidence of episodes of severe pain and top-up analgesia. Epidural analgesia was associated with significantly more nausea and vomiting than morphine infusion (p = 0.053) and CPNB (p = 0.023). It also had a significantly higher incidence of motor blockade than CPNB (p < 0.01). We found that the most effective method of post-operative analgesia for children undergoing lower limb reconstruction was sciatic nerve catheterisation and continuous infusion.

Mammalian alphaherpesvirus miRNAs

Mammalian alphaherpesviruses are major causes of human and veterinary disease. During productive infection, these viruses exhibit complex and robust patterns of gene expression. These viruses also form latent infections in neurons of sensory ganglia in which productive cycle gene expression is highly repressed. Both modes of infection provide advantageous opportunities for regulation by microRNAs. Thus far, published data regarding microRNAs are available for six mammalian alphaherpesviruses. No microRNAs have yet been detected from varicella zoster virus. The five other viruses-herpes simplex viruses-1 and -2, herpes B virus, bovine herpesvirus-1, and pseudorabies virus-representing both genera of mammalian alphaherpesviruses have been shown to express microRNAs. In this article, we discuss these microRNAs in terms of where they are encoded in the viral genome relative to other viral transcripts; whether they are expressed during productive or latent infection; their potential targets; what little is known about their actual targets and functions during viral infection; and what little is known about the interactions of these viruses with the host microRNA machinery. This article is part of a Special Issue entitled: "MicroRNAs in viral gene regulation".

Work-related stress case definitions and prevalence rates in national surveys

BACKGROUND

There is concern about lack of consistency in the design of case definitions used to measure work-related stress in national workforce surveys and the implications of this for the reliability and validity of prevalence estimates as well as for developments in policy and practice on tackling work-related stress.

AIMS

To examine associations between case definitions used for the measurement of work-related stress in nationally representative workforce surveys and the prevalence rates generated.

METHODS

The study focused on 18 nationally representative workforce surveys conducted between 1995 and 2008 that involved British samples. The published report from each survey was scrutinized for evidence of the case definition used to measure work-related stress and the associated prevalence rate.

RESULTS

Several types of case definition were identified that differed in terms of their theoretical basis, structure, and content. Each was associated with a unique range of prevalence rates.

CONCLUSIONS

The results illustrate the challenge presented to the production of valid and reliable estimates of the scale of work-related stress by inconsistent case definition design. The imperative for theory-based consistency in the design of case definitions used for the measurement of work-related stress in national workforce surveys is highlighted.

Drug-herb interaction: database of medicinal plants of the Caribbean, their indications, toxicities and possible interactions with conventional medication

OBJECTIVE

Healthcare professionals in the Caribbean today know very little about these drug-herb interactions of the popular West Indian medicinal herb practices linked to the immigrants from West Africa and India, and to the indigenous Amerindians. It is the intent of this project to produce a database which comprehensively summarizes indications and possible drug-herb interactions of these plants.

METHOD

Using the database programme Epi Info 3.5.1, one hundred and eighty-three herbs used in the Caribbean as medicine by locals have been entered into the West Indian Drug Herb Interaction Database version 0.06 (WIDHID 0.06).

RESULTS

A range of one to three common names have been entered with the family and scientific name of each herb, in addition to a range of one to six conditions/illnesses for which a particular plant was to be used as a medicinal herb. One to four bioactive compounds have been made to correlate with the typical herbal preparation methods and toxicity. Thirty of the most common and popular herbs have been researched for their drug herb interactions.

CONCLUSION

West Indian Drug Herb Interaction Database version 0.06 for the first time allows easy access to Caribbean ethno-medicinal plant cures with their possible drug-herb interactions reference sources, a feature often absent although so important. In addition, WIDHID 0.06 will support pharmaco-epidemiological studies in the field. It will also ensure future public access to ethno-medicinal information through developed web pages or programmes.