Tempering hope with realism. Induced pluripotent stem cells in regenerative medicine

• Since their discovery in 2007, human induced pluripotent stem (iPS) cells have been widely championed as the future for regenerative medicine. • By differentiating iPS cells into specialised cells for transplantation, it may be possible to replace diseased cells and “cure” patients of various chronic degenerative conditions, including Parkinson’s disease. • Such putative iPS cell-based therapies would avoid the need to procure transplantable cells from (and in the process, destroy) human embryos, and could be administered to patients without immunosuppressive therapy. • In reality, however, the optimism surrounding iPS cell research has outpaced progress to date and likely emanates, in part, from the “moral panic” surrounding human embryo research. • At such an early stage of development, questions remain about whether iPS cells are strictly equivalent to human embryonic stem cells as a source of transplantable cells. The Heerey Committee considered this point in its recent review of the Commonwealth legislation governing embryo research and human cloning and its Report (tabled in federal Parliament in July 2011) recommended that embryonic stem cell research should continue in Australia. • In addition, there are many ethical issues which will need to be considered when enrolling vulnerable patients in trials of iPS cell therapy given the uncertain benefits and risks involved. • In the rush to embrace iPS cell therapy, there is a real risk that the public may overrate the benefits and expect imminent translation to the clinic

EpiCompare: R package for the comparison and quality control of epigenomic peak files

Summary EpiCompare combines a variety of downstream analysis tools to compare, quality control and benchmark different epigenomic datasets. The package requires minimal input from users, can be run with just one line of code and provides all results of the analysis in a single interactive HTML report. EpiCompare thus enables downstream analysis of multiple epigenomic datasets in a simple, effective and user-friendly manner. Availability and Implementation EpiCompare is available on Bioconductor (≥ v3.15): https://bioconductor.org/packages/release/bioc/html/EpiCompare.html All source code is publically available via GitHub: https://github.com/neurogenomics/EpiCompare Documentation website https://neurogenomics.github.io/EpiCompare EpiCompare DockerHub repository: https://hub.docker.com/repository/docker/neurogenomicslab/epicompare Competing Interest Statement The authors have declared no competing interest

Evaluation of mRNA markers for estimating blood deposition time : towards alibi testing from human forensic stains with rhythmic biomarkers

This study was supported by grant 27.011.001 by the Netherlands Organization for Scientific Research (NWO) Forensic Science Program, Erasmus MC University Medical Center Rotterdam, by the EU 6th Framework project EUCLOCK (018741), UK Biotechnology and Biological Sciences Research Council (BBSRC) Grant BB/I019405/1, and by a previous grant from the Netherlands Genomics Initiative (NGI)/Netherlands Organization for Scientific Research (NWO) within the framework of the Forensic Genomics Consortium Netherlands (FGCN). D.J.S. is a Royal Society Wolfson Research Merit Award holder.Determining the time a biological trace was left at a scene of crime reflects a crucial aspect of forensic investigations as - if possible - it would permit testing the sample donor's alibi directly from the trace evidence, helping to link (or not) the DNA-identified sample donor with the crime event. However, reliable and robust methodology is lacking thus far. In this study, we assessed the suitability of mRNA for the purpose of estimating blood deposition time, and its added value relative to melatonin and cortisol, two circadian hormones we previously introduced for this purpose. By analysing 21 candidate mRNA markers in blood samples from 12 individuals collected around the clock at 2 h intervals for 36 h under real-life, controlled conditions, we identified 11 mRNAs with statistically significant expression rhythms. We then used these 11 significantly rhythmic mRNA markers, with and without melatonin and cortisol also analysed in these samples, to establish statistical models for predicting day/night time categories. We found that although in general mRNA-based estimation of time categories was less accurate than hormone-based estimation, the use of three mRNA markers HSPA1B, MKNK2 and PER3 together with melatonin and cortisol generally enhanced the time prediction accuracy relative to the use of the two hormones alone. Our data best support a model that by using these five molecular biomarkers estimates three time categories, i.e., night/early morning, morning/noon, and afternoon/evening with prediction accuracies expressed as AUC values of 0.88, 0.88, and 0.95, respectively. For the first time, we demonstrate the value of mRNA for blood deposition timing and introduce a statistical model for estimating day/night time categories based on molecular biomarkers, which shall be further validated with additional samples in the future. Moreover, our work provides new leads for molecular approaches on time of death estimation using the significantly rhythmic mRNA markers established here.PostprintPeer reviewe

Genetic influences on social attention in free-ranging rhesus macaques

An ethological approach to attention predicts that organisms orient preferentially to valuable sources of information in the environment. For many gregarious species, orienting to other individuals provides valuable social information but competes with food acquisition, water consumption and predator avoidance. Individual variation in vigilance behaviour in humans spans a continuum from inattentive to pathological levels of interest in others. To assess the comparative biology of this behavioural variation, we probed vigilance rates in free-ranging macaques during water drinking, a behaviour incompatible with the gaze and postural demands of vigilance. Males were significantly more vigilant than females. Moreover, vigilance showed a clear genetic component, with an estimated heritability of 12%. Monkeys carrying a relatively infrequent ‘long’ allele of TPH2, a regulatory gene that influences serotonin production in the brain, were significantly less vigilant compared to monkeys that did not carry the allele. These findings resonate with the hypothesis that the serotonin pathway regulates vigilance in primates and by extension provoke the idea that individual variation in vigilance and its underlying biology may be adaptive rather than pathological

Functional and Crystal Structure Analysis of Active Site Adaptations of a Potent Anti-Angiogenic Human tRNA Synthetase

SummaryHigher eukaryote tRNA synthetases have expanded functions that come from enlarged, more differentiated structures that were adapted to fit aminoacylation function. How those adaptations affect catalytic mechanisms is not known. Presented here is the structure of a catalytically active natural splice variant of human tryptophanyl-tRNA synthetase (TrpRS) that is a potent angiostatic factor. This and related structures suggest that a eukaryote-specific N-terminal extension of the core enzyme changed substrate recognition by forming an active site cap. At the junction of the extension and core catalytic unit, an arginine is recruited to replace a missing landmark lysine almost 200 residues away. Mutagenesis, rapid kinetic, and substrate binding studies support the functional significance of the cap and arginine recruitment. Thus, the enzyme function of human TrpRS has switched more to the N terminus of the sequence. This switch has the effect of creating selective pressure to retain the N-terminal extension for functional expansion

Acute dietary zinc deficiency in rats exacerbates myocardial ischaemia-reperfusion injury through depletion of glutathione.

Zinc (Zn) plays an important role in maintaining the anti-oxidant status within the heart, and helps to counter the acute redox stress that occurs during myocardial ischaemia and reperfusion. Individuals with low zinc (Zn) levels are at greater risk of developing an acute myocardial infarction; however, the impact of this on the extent of myocardial injury is unknown. The present study aimed to compare the effects of dietary zinc depletion with in vitro removal of Zn (TPEN) on the outcome of acute myocardial infarction and vascular function. Male Sprague-Dawley rats were fed either a zinc adequate (ZA; 35mg Zn/kg diet) or zinc deficient (ZD; < 1mg Zn/kg diet) diet for two weeks prior to heart isolation. Perfused hearts were subjected to a thirty-minute ischaemia/two-hour reperfusion (I/R) protocol, during which time ventricular arrhythmias were recorded and after which infarct size was measured, along with markers of anti-oxidant status. In separate experiments hearts were challenged with the Zn chelator TPEN (10μM) prior to ischaemia onset. Both dietary and TPEN-induced Zn depletion significantly extended infarct size; dietary Zn depletion was associated with reduced total cardiac glutathione (GSH) levels, while TPEN decreased cardiac SOD-1 levels. TPEN, but not dietary Zn depletion also suppressed ventricular arrhythmias and depressed vascular responses to nitric oxide (NO). These findings demonstrate that both modes of zinc depletion worsen the outcome from I/R but through different mechanisms. Dietary Zn deficiency, resulting in reduced cardiac GSH, is the most appropriate model for determining the role of endogenous Zn in I/R injury

Selective in-plane Fabry-Pérot gas sensor functionalized with polymer

Smell is one of the last senses still not completely replicated. Artificial gas sensors do manage to reach enough sensitivity but selectivity is still an issue. However, it is essential to several industries and smart cities. In this work, the selectivity of a previously reported optical gas sensor is demonstrated using three polymers for functionalization. Different sensitivities are obtained for toluene, 1-butanol, limonene and valeric acid

Total ankle replacement versus arthrodesis (TARVA): protocol for a multicentre randomised controlled trial.

INTRODUCTION: Total ankle replacement (TAR) or ankle arthrodesis (fusion) is the main surgical treatments for end-stage ankle osteoarthritis (OA). The popularity of ankle replacement is increasing while ankle fusion rates remain static. Both treatments have efficacy but to date all studies comparing the 2 have been observational without randomisation, and there are no published guidelines as to the most appropriate management. The TAR versus arthrodesis (TARVA) trial aims to compare the clinical and cost-effectiveness of TAR against ankle arthrodesis in the treatment of end-stage ankle OA in patients aged 50-85 years. METHODS AND ANALYSIS: TARVA is a multicentre randomised controlled trial that will randomise 328 patients aged 50-85 years with end-stage ankle arthritis. The 2 arms of the study will be TAR or ankle arthrodesis with 164 patients in each group. Up to 16 UK centres will participate. Patients will have clinical assessments and complete questionnaires before their operation and at 6, 12, 26 and 52 weeks after surgery. The primary clinical outcome of the study is a validated patient-reported outcome measure, the Manchester Oxford foot questionnaire, captured preoperatively and 12 months after surgery. Secondary outcomes include quality-of-life scores, complications, revision, reoperation and a health economic analysis. ETHICS AND DISSEMINATION: The protocol has been approved by the National Research Ethics Service Committee (London, Bloomsbury 14/LO/0807). This manuscript is based on V.5.0 of the protocol. The trial findings will be disseminated through peer-reviewed publications and conference presentations. TRIAL REGISTRATION NUMBER: NCT02128555

Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans

Single-nucleus RNA sequencing (snRNA-seq) is used as an alternative to single-cell RNA-seq, as it allows transcriptomic profiling of frozen tissue. However, it is unclear whether snRNA-seq is able to detect cellular state in human tissue. Indeed, snRNA-seq analyses of human brain samples have failed to detect a consistent microglial activation signature in Alzheimer's disease. Our comparison of microglia from single cells and single nuclei of four human subjects reveals that, although most genes show similar relative abundances in cells and nuclei, a small population of genes (∼1%) is depleted in nuclei compared to whole cells. This population is enriched for genes previously implicated in microglial activation, including APOE, CST3, SPP1, and CD74, comprising 18% of previously identified microglial-disease-associated genes. Given the low sensitivity of snRNA-seq to detect many activation genes, we conclude that snRNA-seq is not suited for detecting cellular activation in microglia in human disease