Showing papers by "University of Marburg published in 2018"

Minimal information for studies of extracellular vesicles 2018 (MISEV2018) : a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

Abstract: The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.

Analysis of shared heritability in common disorders of the brain

Abstract: Disorders of the brain can exhibit considerable epidemiological comorbidity and often share symptoms, provoking debate about their etiologic overlap. We quantified the genetic sharing of 25 brain disorders from genome-wide association studies of 265,218 patients and 784,643 control participants and assessed their relationship to 17 phenotypes from 1,191,588 individuals. Psychiatric disorders share common variant risk, whereas neurological disorders appear more distinct from one another and from the psychiatric disorders. We also identified significant sharing between disorders and a number of brain phenotypes, including cognitive measures. Further, we conducted simulations to explore how statistical power, diagnostic misclassification, and phenotypic heterogeneity affect genetic correlations. These results highlight the importance of common genetic variation as a risk factor for brain disorders and the value of heritability-based methods in understanding their etiology.

Consensus Statement on the classification of tremors. from the task force on tremor of the International Parkinson and Movement Disorder Society

Abstract: Background Consensus criteria for classifying tremor disorders were published by the International Parkinson and Movement Disorder Society in 1998. Subsequent advances with regard to essential tremor, tremor associated with dystonia, and other monosymptomatic and indeterminate tremors make a significant revision necessary. Objectives Convene an international panel of experienced investigators to review the definition and classification of tremor. Methods Computerized MEDLINE searches in January 2013 and 2015 were conducted using a combination of text words and MeSH terms: “tremor”, “tremor disorders”, “essential tremor”, “dystonic tremor”, and “classification” limited to human studies. Agreement was obtained using consensus development methodology during four in-person meetings, two teleconferences, and numerous manuscript reviews. Results Tremor is defined as an involuntary, rhythmic, oscillatory movement of a body part and is classified along two axes: Axis 1—clinical characteristics, including historical features (age at onset, family history, and temporal evolution), tremor characteristics (body distribution, activation condition), associated signs (systemic, neurological), and laboratory tests (electrophysiology, imaging); and Axis 2—etiology (acquired, genetic, or idiopathic). Tremor syndromes, consisting of either isolated tremor or tremor combined with other clinical features, are defined within Axis 1. This classification scheme retains the currently accepted tremor syndromes, including essential tremor, and provides a framework for defining new syndromes. Conclusions This approach should be particularly useful in elucidating isolated tremor syndromes and syndromes consisting of tremor and other signs of uncertain significance. Consistently defined Axis 1 syndromes are needed to facilitate the elucidation of specific etiologies in Axis 2. © 2017 International Parkinson and Movement Disorder Society

The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder

Abstract: Background Increasing evidence connects the gut microbiota and the onset and/or phenotype of Parkinson's disease (PD). Differences in the abundances of specific bacterial taxa have been reported in PD patients. It is, however, unknown whether these differences can be observed in individuals at high risk, for example, with idiopathic rapid eye movement sleep behavior disorder, a prodromal condition of α-synuclein aggregation disorders including PD. Objectives To compare microbiota in carefully preserved nasal wash and stool samples of subjects with idiopathic rapid eye movement sleep behavior disorder, manifest PD, and healthy individuals. Methods Microbiota of flash-frozen stool and nasal wash samples from 76 PD patients, 21 idiopathic rapid eye movement sleep behavior disorder patients, and 78 healthy controls were assessed by 16S and 18S ribosomal RNA amplicon sequencing. Seventy variables, related to demographics, clinical parameters including nonmotor symptoms, and sample processing, were analyzed in relation to microbiome variability and controlled differential analyses were performed. Results Differentially abundant gut microbes, such as Akkermansia, were observed in PD, but no strong differences in nasal microbiota. Eighty percent of the differential gut microbes in PD versus healthy controls showed similar trends in idiopathic rapid eye movement sleep behavior disorder, for example, Anaerotruncus and several Bacteroides spp., and correlated with nonmotor symptoms. Metagenomic sequencing of select samples enabled the reconstruction of genomes of so far uncharacterized differentially abundant organisms. Conclusion Our study reveals differential abundances of gut microbial taxa in PD and its prodrome idiopathic rapid eye movement sleep behavior disorder in comparison to the healthy controls, and highlights the potential of metagenomics to identify and characterize microbial taxa, which are enriched or depleted in PD and/or idiopathic rapid eye movement sleep behavior disorder. © 2017 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.

Galectins at a glance.

Abstract: Galectins are carbohydrate-binding proteins that are involved in many physiological functions, such as inflammation, immune responses, cell migration, autophagy and signalling. They are also linked to diseases such as fibrosis, cancer and heart disease. How such a small family of only 15 members can have such widespread effects remains a conundrum. In this Cell Science at a Glance article, we summarise recent literature on the many cellular activities that have been ascribed to galectins. As shown on the accompanying poster, these include carbohydrate-independent interactions with cytosolic or nuclear targets and carbohydrate-dependent interactions with extracellular glycoconjugates. We discuss how these intra- and extracellular activities might be linked and point out the importance of unravelling molecular mechanisms of galectin function to gain a true understanding of their contributions to the physiology of the cell. We close with a short outlook on the organismal functions of galectins and a perspective on the major challenges in the field.

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Abstract: Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns—one at the base of ‘core leptosporangiates’ and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla–cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.

Interventions for increasing the use of shared decision making by healthcare professionals

Abstract: Background Shared decision making (SDM) is a process by which a healthcare choice is made by the patient, significant others, or both with one or more healthcare professionals. However, it has not yet been widely adopted in practice. This is the second update of this Cochrane review. Objectives To determine the effectiveness of interventions for increasing the use of SDM by healthcare professionals. We considered interventions targeting patients, interventions targeting healthcare professionals, and interventions targeting both. Search methods We searched CENTRAL, MEDLINE, Embase and five other databases on 15 June 2017. We also searched two clinical trials registries and proceedings of relevant conferences. We checked reference lists and contacted study authors to identify additional studies. Selection criteria Randomized and non-randomized trials, controlled before-after studies and interrupted time series studies evaluating interventions for increasing the use of SDM in which the primary outcomes were evaluated using observer-based or patient-reported measures. Data collection and analysis We used standard methodological procedures expected by Cochrane.We used GRADE to assess the certainty of the evidence. Main results We included 87 studies (45,641 patients and 3113 healthcare professionals) conducted mainly in the USA, Germany, Canada and the Netherlands. Risk of bias was high or unclear for protection against contamination, low for differences in the baseline characteristics of patients, and unclear for other domains.Forty-four studies evaluated interventions targeting patients. They included decision aids, patient activation, question prompt lists and training for patients among others and were administered alone (single intervention) or in combination (multifaceted intervention). The certainty of the evidence was very low. It is uncertain if interventions targeting patients when compared with usual care increase SDM whether measured by observation (standardized mean difference (SMD) 0.54, 95% confidence interval (CI) -0.13 to 1.22; 4 studies; N = 424) or reported by patients (SMD 0.32, 95% CI 0.16 to 0.48; 9 studies; N = 1386; risk difference (RD) -0.09, 95% CI -0.19 to 0.01; 6 studies; N = 754), reduce decision regret (SMD -0.10, 95% CI -0.39 to 0.19; 1 study; N = 212), improve physical (SMD 0.00, 95% CI -0.36 to 0.36; 1 study; N = 116) or mental health-related quality of life (QOL) (SMD 0.10, 95% CI -0.26 to 0.46; 1 study; N = 116), affect consultation length (SMD 0.10, 95% CI -0.39 to 0.58; 2 studies; N = 224) or cost (SMD 0.82, 95% CI 0.42 to 1.22; 1 study; N = 105).It is uncertain if interventions targeting patients when compared with interventions of the same type increase SDM whether measured by observation (SMD 0.88, 95% CI 0.39 to 1.37; 3 studies; N = 271) or reported by patients (SMD 0.03, 95% CI -0.18 to 0.24; 11 studies; N = 1906); (RD 0.03, 95% CI -0.02 to 0.08; 10 studies; N = 2272); affect consultation length (SMD -0.65, 95% CI -1.29 to -0.00; 1 study; N = 39) or costs. No data were reported for decision regret, physical or mental health-related QOL.Fifteen studies evaluated interventions targeting healthcare professionals. They included educational meetings, educational material, educational outreach visits and reminders among others. The certainty of evidence is very low. It is uncertain if these interventions when compared with usual care increase SDM whether measured by observation (SMD 0.70, 95% CI 0.21 to 1.19; 6 studies; N = 479) or reported by patients (SMD 0.03, 95% CI -0.15 to 0.20; 5 studies; N = 5772); (RD 0.01, 95%C: -0.03 to 0.06; 2 studies; N = 6303); reduce decision regret (SMD 0.29, 95% CI 0.07 to 0.51; 1 study; N = 326), affect consultation length (SMD 0.51, 95% CI 0.21 to 0.81; 1 study, N = 175), cost (no data available) or physical health-related QOL (SMD 0.16, 95% CI -0.05 to 0.36; 1 study; N = 359). Mental health-related QOL may slightly improve (SMD 0.28, 95% CI 0.07 to 0.49; 1 study, N = 359; low-certainty evidence).It is uncertain if interventions targeting healthcare professionals compared to interventions of the same type increase SDM whether measured by observation (SMD -0.30, 95% CI -1.19 to 0.59; 1 study; N = 20) or reported by patients (SMD 0.24, 95% CI -0.10 to 0.58; 2 studies; N = 1459) as the certainty of the evidence is very low. There was insufficient information to determine the effect on decision regret, physical or mental health-related QOL, consultation length or costs.Twenty-eight studies targeted both patients and healthcare professionals. The interventions used a combination of patient-mediated and healthcare professional directed interventions. Based on low certainty evidence, it is uncertain whether these interventions, when compared with usual care, increase SDM whether measured by observation (SMD 1.10, 95% CI 0.42 to 1.79; 6 studies; N = 1270) or reported by patients (SMD 0.13, 95% CI -0.02 to 0.28; 7 studies; N = 1479); (RD -0.01, 95% CI -0.20 to 0.19; 2 studies; N = 266); improve physical (SMD 0.08, -0.37 to 0.54; 1 study; N = 75) or mental health-related QOL (SMD 0.01, -0.44 to 0.46; 1 study; N = 75), affect consultation length (SMD 3.72, 95% CI 3.44 to 4.01; 1 study; N = 36) or costs (no data available) and may make little or no difference to decision regret (SMD 0.13, 95% CI -0.08 to 0.33; 1 study; low-certainty evidence).It is uncertain whether interventions targeting both patients and healthcare professionals compared to interventions of the same type increase SDM whether measured by observation (SMD -0.29, 95% CI -1.17 to 0.60; 1 study; N = 20); (RD -0.04, 95% CI -0.13 to 0.04; 1 study; N = 134) or reported by patients (SMD 0.00, 95% CI -0.32 to 0.32; 1 study; N = 150 ) as the certainty of the evidence was very low. There was insuffient information to determine the effects on decision regret, physical or mental health-related quality of life, or consultation length or costs. Authors' conclusions It is uncertain whether any interventions for increasing the use of SDM by healthcare professionals are effective because the certainty of the evidence is low or very low.

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.

Abstract: The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.

Structural brain abnormalities in the common epilepsies assessed in a worldwide ENIGMA study.

Abstract: Progressive functional decline in the epilepsies is largely unexplained. We formed the ENIGMA-Epilepsy consortium to understand factors that influence brain measures in epilepsy, pooling data from 24 research centres in 14 countries across Europe, North and South America, Asia, and Australia. Structural brain measures were extracted from MRI brain scans across 2149 individuals with epilepsy, divided into four epilepsy subgroups including idiopathic generalized epilepsies (n =367), mesial temporal lobe epilepsies with hippocampal sclerosis (MTLE; left, n = 415; right, n = 339), and all other epilepsies in aggregate (n = 1026), and compared to 1727 matched healthy controls. We ranked brain structures in order of greatest differences between patients and controls, by meta-analysing effect sizes across 16 subcortical and 68 cortical brain regions. We also tested effects of duration of disease, age at onset, and age-by-diagnosis interactions on structural measures. We observed widespread patterns of altered subcortical volume and reduced cortical grey matter thickness. Compared to controls, all epilepsy groups showed lower volume in the right thalamus (Cohen's d = -0.24 to -0.73; P < 1.49 × 10-4), and lower thickness in the precentral gyri bilaterally (d = -0.34 to -0.52; P < 4.31 × 10-6). Both MTLE subgroups showed profound volume reduction in the ipsilateral hippocampus (d = -1.73 to -1.91, P < 1.4 × 10-19), and lower thickness in extrahippocampal cortical regions, including the precentral and paracentral gyri, compared to controls (d = -0.36 to -0.52; P < 1.49 × 10-4). Thickness differences of the ipsilateral temporopolar, parahippocampal, entorhinal, and fusiform gyri, contralateral pars triangularis, and bilateral precuneus, superior frontal and caudal middle frontal gyri were observed in left, but not right, MTLE (d = -0.29 to -0.54; P < 1.49 × 10-4). Contrastingly, thickness differences of the ipsilateral pars opercularis, and contralateral transverse temporal gyrus, were observed in right, but not left, MTLE (d = -0.27 to -0.51; P < 1.49 × 10-4). Lower subcortical volume and cortical thickness associated with a longer duration of epilepsy in the all-epilepsies, all-other-epilepsies, and right MTLE groups (beta, b < -0.0018; P < 1.49 × 10-4). In the largest neuroimaging study of epilepsy to date, we provide information on the common epilepsies that could not be realistically acquired in any other way. Our study provides a robust ranking of brain measures that can be further targeted for study in genetic and neuropathological studies. This worldwide initiative identifies patterns of shared grey matter reduction across epilepsy syndromes, and distinctive abnormalities between epilepsy syndromes, which inform our understanding of epilepsy as a network disorder, and indicate that certain epilepsy syndromes involve more widespread structural compromise than previously assumed.

In Vitro Bactericidal and Virucidal Efficacy of Povidone-Iodine Gargle/Mouthwash Against Respiratory and Oral Tract Pathogens

Abstract: Recent virus epidemics and rising antibiotic resistance highlight the importance of hygiene measures to prevent and control outbreaks. We investigated the in vitro bactericidal and virucidal efficacy of povidone-iodine (PVP-I) 7% gargle/mouthwash at defined dilution against oral and respiratory tract pathogens. PVP-I was tested against Klebsiella pneumoniae and Streptococcus pneumoniae according to bactericidal quantitative suspension test EN13727 and against severe acute respiratory syndrome and Middle East respiratory syndrome coronaviruses (SARS-CoV and MERS-CoV), rotavirus strain Wa and influenza virus A subtype H1N1 according to virucidal quantitative suspension test EN14476. PVP-I 7% gargle/mouthwash was diluted 1:30 with water to a concentration of 0.23% (the recommended concentration for “real-life” use in Japan) and tested at room temperature under clean conditions [0.3 g/l bovine serum albumin (BSA), viruses only] and dirty conditions (3.0 g/l BSA + 3.0 ml/l erythrocytes) as an interfering substance for defined contact times (minimum 15 s). Rotavirus was tested without protein load. A ≥ 5 log10 (99.999%) decrease of bacteria and ≥ 4 log10 (99.99%) reduction in viral titre represented effective bactericidal and virucidal activity, respectively, per European standards. PVP-I gargle/mouthwash diluted 1:30 (equivalent to a concentration of 0.23% PVP-I) showed effective bactericidal activity against Klebsiella pneumoniae and Streptococcus pneumoniae and rapidly inactivated SARS-CoV, MERS-CoV, influenza virus A (H1N1) and rotavirus after 15 s of exposure. PVP-I 7% gargle/mouthwash showed rapid bactericidal activity and virucidal efficacy in vitro at a concentration of 0.23% PVP-I and may provide a protective oropharyngeal hygiene measure for individuals at high risk of exposure to oral and respiratory pathogens. Mundipharma Research GmbH & Co. KG (MRG).

Implications of Placebo and Nocebo Effects for Clinical Practice: Expert Consensus.

Abstract: Background: Placebo and nocebo effects occur in clinical or laboratory medical contexts after administration of an inert treatment or as part of active treatments and are due to psychobiological mechanisms such as expectancies of the patient. Placebo and nocebo studies have evolved from predominantly methodological research into a far-reaching interdisciplinary field that is unravelling the neurobiological, behavioural and clinical underpinnings of these phenomena in a broad variety of medical conditions. As a consequence, there is an increasing demand from health professionals to develop expert recommendations about evidence-based and ethical use of placebo and nocebo effects for clinical practice. Methods: A survey and interdisciplinary expert meeting by invitation was organized as part of the 1st Society for Interdisciplinary Placebo Studies (SIPS) conference in 2017. Twenty-nine internationally recognized placebo researchers participated. Results: There was consensus that maximizing placebo effects and minimizing nocebo effects should lead to better treatment outcomes with fewer side effects. Experts particularly agreed on the importance of informing patients about placebo and nocebo effects and training health professionals in patient-clinician communication to maximize placebo and minimize nocebo effects. Conclusions: The current paper forms a first step towards developing evidence-based and ethical recommendations about the implications of placebo and nocebo research for medical practice, based on the current state of evidence and the consensus of experts. Future research might focus on how to implement these recommendations, including how to optimize conditions for educating patients about placebo and nocebo effects and providing training for the implementation in clinical practice.

Impacts of salvage logging on biodiversity: A meta‐analysis

Abstract: Logging to "salvage" economic returns from forests affected by natural disturbances has become increasingly prevalent globally Despite potential negative effects on biodiversity, salvage logging is often conducted, even in areas otherwise excluded from logging and reserved for nature conservation, inter alia because strategic priorities for post-disturbance management are widely lackingA review of the existing literature revealed that most studies investigating the effects of salvage logging on biodiversity have been conducted less than 5 years following natural disturbances, and focused on non-saproxylic organismsA meta-analysis across 24 species groups revealed that salvage logging significantly decreases numbers of species of eight taxonomic groups Richness of dead wood dependent taxa (ie saproxylic organisms) decreased more strongly than richness of non-saproxylic taxa In contrast, taxonomic groups typically associated with open habitats increased in the number of species after salvage loggingBy analysing 134 original species abundance matrices, we demonstrate that salvage logging significantly alters community composition in 7 of 17 species groups, particularly affecting saproxylic assemblagesSynthesis and applications Our results suggest that salvage logging is not consistent with the management objectives of protected areas Substantial changes, such as the retention of dead wood in naturally disturbed forests, are needed to support biodiversity Future research should investigate the amount and spatio-temporal distribution of retained dead wood needed to maintain all components of biodiversity

Exacerbations of COPD

Abstract: Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide. While COPD is a mainly chronic disease, a substantial number of patients suffer from exacerbations. Severe exacerbations are related to a significantly worse survival outcome. This review summarises the current knowledge on the different aspects of COPD exacerbations. The impact of risk factors and triggers such as smoking, severe airflow limitation, bronchiectasis, bacterial and viral infections and comorbidities is discussed. More severe exacerbations should be treated with β-agonists and anticholinergics as well as systemic corticosteroids. Antibiotic therapy should only be given to patients with presumed bacterial infection. Noninvasive ventilation is indicated in patients with respiratory failure. Smoking cessation is key to prevent further COPD exacerbations. Other aspects include choice of pharmacotherapy, including bronchodilators, inhaled corticosteroids, phosphodiesterase-4 inhibitors, long-term antibiotics and mucolytics. Better education and self-management as well as increased physical activity are important. Influenza and pneumococcal vaccination is recommended. Treatment of hypoxaemia and hypercapnia reduce the rate of COPD exacerbations, while most interventional bronchoscopic therapies increase exacerbation risk within the first months after the procedure.

Continuous intravenous perioperative lidocaine infusion for postoperative pain and recovery in adults

Abstract: Background The management of postoperative pain and recovery is still unsatisfactory in a number of cases in clinical practice. Opioids used for postoperative analgesia are frequently associated with adverse effects, including nausea and constipation, preventing smooth postoperative recovery. Not all patients are suitable for, and benefit from, epidural analgesia that is used to improve postoperative recovery. The non‐opioid, lidocaine, was investigated in several studies for its use in multimodal management strategies to reduce postoperative pain and enhance recovery. This review was published in 2015 and updated in January 2017.

Tumor immunoevasion via acidosis-dependent induction of regulatory tumor-associated macrophages.

Abstract: Many tumors evolve sophisticated strategies to evade the immune system, and these represent major obstacles for efficient antitumor immune responses. Here we explored a molecular mechanism of metabolic communication deployed by highly glycolytic tumors for immunoevasion. In contrast to colon adenocarcinomas, melanomas showed comparatively high glycolytic activity, which resulted in high acidification of the tumor microenvironment. This tumor acidosis induced Gprotein-coupled receptor-dependent expression of the transcriptional repressor ICER in tumor-associated macrophages that led to their functional polarization toward a non-inflammatory phenotype and promoted tumor growth. Collectively, our findings identify a molecular mechanism of metabolic communication between non-lymphoid tissue and the immune system that was exploited by high-glycolytic-rate tumors for evasion of the immune system.

Flavin-Based Electron Bifurcation, Ferredoxin, Flavodoxin, and Anaerobic Respiration With Protons (Ech) or NAD+ (Rnf) as Electron Acceptors: A Historical Review.

Abstract: Flavin-based electron bifurcation is a newly discovered mechanism, by which a hydride electron pair from NAD(P)H, coenzyme F420H2, H2, or formate is split by flavoproteins into one-electron with a more negative reduction potential and one with a more positive reduction potential than that of the electron pair. Via this mechanism microorganisms generate low- potential electrons for the reduction of ferredoxins (Fd) and flavodoxins (Fld). The first example was described in 2008 when it was found that the butyryl-CoA dehydrogenase-electron-transferring flavoprotein complex (Bcd-EtfAB) of Clostridium kluyveri couples the endergonic reduction of ferredoxin (E0' = -420 mV) with NADH (-320 mV) to the exergonic reduction of crotonyl-CoA to butyryl-CoA (-10 mV) with NADH. The discovery was followed by the finding of an electron-bifurcating Fd- and NAD-dependent [FeFe]-hydrogenase (HydABC) in Thermotoga maritima (2009), Fd-dependent transhydrogenase (NfnAB) in various bacteria and archaea (2010), Fd- and H2-dependent heterodisulfide reductase (MvhADG-HdrABC) in methanogenic archaea (2011), Fd- and NADH-dependent caffeyl-CoA reductase (CarCDE) in Acetobacterium woodii (2013), Fd- and NAD-dependent formate dehydrogenase (HylABC-FdhF2) in Clostridium acidi-urici (2013), Fd- and NADP-dependent [FeFe]-hydrogenase (HytA-E) in Clostridium autoethanogrenum (2013), Fd(?)- and NADH-dependent methylene-tetrahydrofolate reductase (MetFV-HdrABC-MvhD) in Moorella thermoacetica (2014), Fd- and NAD-dependent lactate dehydrogenase (LctBCD) in A. woodii (2015), Fd- and F420H2-dependent heterodisulfide reductase (HdrA2B2C2) in Methanosarcina acetivorans (2017), and Fd- and NADH-dependent ubiquinol reductase (FixABCX) in Azotobacter vinelandii (2017). The electron-bifurcating flavoprotein complexes known to date fall into four groups that have evolved independently, namely those containing EtfAB (CarED, LctCB, FixBA) with bound FAD, a NuoF homolog (HydB, HytB, or HylB) harboring FMN, NfnB with bound FAD, or HdrA harboring FAD. All these flavoproteins are cytoplasmic except for the membrane-associated protein FixABCX. The organisms-in which they have been found-are strictly anaerobic microorganisms except for the aerobe A. vinelandii. The electron-bifurcating complexes are involved in a variety of processes such as butyric acid fermentation, methanogenesis, acetogenesis, anaerobic lactate oxidation, dissimilatory sulfate reduction, anaerobic- dearomatization, nitrogen fixation, and CO2 fixation. They contribute to energy conservation via the energy-converting ferredoxin: NAD+ reductase complex Rnf or the energy-converting ferredoxin-dependent hydrogenase complex Ech. This Review describes how this mechanism was discovered.

Improving performance of spatio-temporal machine learning models using forward feature selection and target-oriented validation

Abstract: Importance of target-oriented validation strategies for spatio-temporal prediction models is illustrated using two case studies: (1) modelling of air temperature ( T a i r ) in Antarctica, and (2) modelling of volumetric water content (VW) for the R.J. Cook Agronomy Farm, USA. Performance of a random k-fold cross-validation (CV) was compared to three target-oriented strategies: Leave-Location-Out (LLO), Leave-Time-Out (LTO), and Leave-Location-and-Time-Out (LLTO) CV. Results indicate that considerable differences between random k-fold ( R 2 = 0.9 for T a i r and 0.92 for VW) and target-oriented CV (LLO R 2 = 0.24 for T a i r and 0.49 for VW) exist, highlighting the need for target-oriented validation to avoid an overoptimistic view on models. Differences between random k-fold and target-oriented CV indicate spatial over-fitting caused by misleading variables. To decrease over-fitting, a forward feature selection in conjunction with target-oriented CV is proposed. It decreased over-fitting and simultaneously improved target-oriented performances (LLO CV R 2 = 0.47 for T a i r and 0.55 for VW).

Lightwave valleytronics in a monolayer of tungsten diselenide

Abstract: As conventional electronics approaches its limits 1 , nanoscience has urgently sought methods of fast control of electrons at the fundamental quantum level 2 . Lightwave electronics 3 —the foundation of attosecond science 4 —uses the oscillating carrier wave of intense light pulses to control the translational motion of the electron’s charge faster than a single cycle of light5–15. Despite being particularly promising information carriers, the internal quantum attributes of spin 16 and valley pseudospin17–21 have not been switchable on the subcycle scale. Here we demonstrate lightwave-driven changes of the valley pseudospin and introduce distinct signatures in the optical readout. Photogenerated electron–hole pairs in a monolayer of tungsten diselenide are accelerated and collided by a strong lightwave. The emergence of high-odd-order sidebands and anomalous changes in their polarization direction directly attest to the ultrafast pseudospin dynamics. Quantitative computations combining density functional theory with a non-perturbative quantum many-body approach assign the polarization of the sidebands to a lightwave-induced change of the valley pseudospin and confirm that the process is coherent and adiabatic. Our work opens the door to systematic valleytronic logic at optical clock rates.

Dynamic biofilm architecture confers individual and collective mechanisms of viral protection.

Abstract: In nature, bacteria primarily live in surface-attached, multicellular communities, termed biofilms 1–6 . In medical settings, biofilms cause devastating damage during chronic and acute infections; indeed, bacteria are often viewed as agents of human disease 7 . However, bacteria themselves suffer from diseases, most notably in the form of viral pathogens termed bacteriophages 8–12 , which are the most abundant replicating entities on Earth. Phage–biofilm encounters are undoubtedly common in the environment, but the mechanisms that determine the outcome of these encounters are unknown. Using Escherichia coli biofilms and the lytic phage T7 as models, we discovered that an amyloid fibre network of CsgA (curli polymer) protects biofilms against phage attack via two separate mechanisms. First, collective cell protection results from inhibition of phage transport into the biofilm, which we demonstrate in vivo and in vitro. Second, CsgA fibres protect cells individually by coating their surface and binding phage particles, thereby preventing their attachment to the cell exterior. These insights into biofilm–phage interactions have broad-ranging implications for the design of phage applications in biotechnology, phage therapy and the evolutionary dynamics of phages with their bacterial hosts. At late stages of biofilm development, Escherichia coli cells express the curli polymer CsgA. CsgA assembles into a fibre network that protects biofilms from attack by lytic phages.

Flavin-Based Electron Bifurcation, A New Mechanism of Biological Energy Coupling.

Abstract: There are two types of electron bifurcation (EB), either quinone- or flavin-based (QBEB/FBEB), that involve reduction of a quinone or flavin by a two-electron transfer and two reoxidations by a high- and low-potential one-electron acceptor with a reactive semiquinone intermediate. In QBEB, the reduced low-potential acceptor (cytochrome b) is exclusively used to generate ΔμH+. In FBEB, the “energy-rich” low-potential reduced ferredoxin or flavodoxin has dual function. It can give rise to ΔμH+/Na+ via a ferredoxin:NAD reductase (Rnf) or ferredoxin:proton reductase (Ech) or conducts difficult reductions such as CO2 to CO. The QBEB membrane complexes are similar in structure and function and occur in all domains of life. In contrast, FBEB complexes are soluble and occur only in strictly anaerobic bacteria and archaea (FixABCX being an exception). The FBEB complexes constitute a group consisting of four unrelated families that contain (1) electron-transferring flavoproteins (EtfAB), (2) NAD(P)H dehydrogenase (...

Diagnosis and management of pemphigus: Recommendations of an international panel of experts

Abstract: Background Several European countries recently developed international diagnostic and management guidelines for pemphigus, which have been instrumental in the standardization of pemphigus management. Objective We now present results from a subsequent Delphi consensus to broaden the generalizability of the recommendations. Methods A preliminary survey, based on the European Dermatology Forum and the European Academy of Dermatology and Venereology guidelines, was sent to a panel of international experts to determine the level of consensus. The results were discussed at the International Bullous Diseases Consensus Group in March 2016 during the annual American Academy of Dermatology conference. Following the meeting, a second survey was sent to more experts to achieve greater international consensus. Results The 39 experts participated in the first round of the Delphi survey, and 54 experts from 21 countries completed the second round. The number of statements in the survey was reduced from 175 topics in Delphi I to 24 topics in Delphi II on the basis of Delphi results and meeting discussion. Limitations Each recommendation represents the majority opinion and therefore may not reflect all possible treatment options available. Conclusions We present here the recommendations resulting from this Delphi process. This international consensus includes intravenous CD20 inhibitors as a first-line therapy option for moderate-to-severe pemphigus.

Acceleration of electrons in the plasma wakefield of a proton bunch

Abstract: High-energy particle accelerators have been crucial in providing a deeper understanding of fundamental particles and the forces that govern their interactions. To increase the energy or to reduce the size of the accelerator, new acceleration schemes need to be developed. Plasma wakefield acceleration1–5, in which the electrons in a plasma are excited, leading to strong electric fields, is one such promising novel acceleration technique. Pioneering experiments have shown that an intense laser pulse6–9 or electron bunch10,11 traversing a plasma drives electric fields of tens of gigavolts per metre and above. These values are well beyond those achieved in conventional radio-frequency accelerators, which are limited to about 0.1 gigavolt per metre. A limitation of laser pulses and electron bunches is their low stored energy, which motivates the use of multiple stages to reach very high energies5,12. The use of proton bunches is compelling, as they have the potential to drive wakefields and accelerate electrons to high energy in a single accelerating stage13. The long proton bunches currently available can be used, as they undergo a process called self-modulation14–16, a particle–plasma interaction which longitudinally splits the bunch into a series of high-density microbunches, which then act resonantly to create large wakefields. The Advanced Wakefield (AWAKE) experiment at CERN17–19 uses intense bunches of protons, each of energy 400 gigaelectronvolts (GeV), with a total bunch energy of 19 kilojoules, to drive a wakefield in a 10-metre-long plasma. Bunches of electrons are injected into the wakefield formed by the proton microbunches. Here we present measurements of electrons accelerated up to 2 GeV at the AWAKE experiment. This constitutes the first demonstration of proton-driven plasma wakefield acceleration. The potential for this scheme to produce very high-energy electron bunches in a single accelerating stage20 means that the results shown here are a significant step towards the development of future high-energy particle accelerators21,22.

Sorafenib promotes graft-versus-leukemia activity in mice and humans through IL-15 production in FLT3-ITD-mutant leukemia cells.

Abstract: Individuals with acute myeloid leukemia (AML) harboring an internal tandem duplication (ITD) in the gene encoding Fms-related tyrosine kinase 3 (FLT3) who relapse after allogeneic hematopoietic cell transplantation (allo-HCT) have a 1-year survival rate below 20%. We observed that sorafenib, a multitargeted tyrosine kinase inhibitor, increased IL-15 production by FLT3-ITD+ leukemia cells. This synergized with the allogeneic CD8+ T cell response, leading to long-term survival in six mouse models of FLT3-ITD+ AML. Sorafenib-related IL-15 production caused an increase in CD8+CD107a+IFN-γ+ T cells with features of longevity (high levels of Bcl-2 and reduced PD-1 levels), which eradicated leukemia in secondary recipients. Mechanistically, sorafenib reduced expression of the transcription factor ATF4, thereby blocking negative regulation of interferon regulatory factor 7 (IRF7) activation, which enhanced IL-15 transcription. Both IRF7 knockdown and ATF4 overexpression in leukemia cells antagonized sorafenib-induced IL-15 production in vitro. Human FLT3-ITD+ AML cells obtained from sorafenib responders following sorafenib therapy showed increased levels of IL-15, phosphorylated IRF7, and a transcriptionally active IRF7 chromatin state. The mitochondrial spare respiratory capacity and glycolytic capacity of CD8+ T cells increased upon sorafenib treatment in sorafenib responders but not in nonresponders. Our findings indicate that the synergism of T cells and sorafenib is mediated via reduced ATF4 expression, causing activation of the IRF7-IL-15 axis in leukemia cells and thereby leading to metabolic reprogramming of leukemia-reactive T cells in humans. Therefore, sorafenib treatment has the potential to contribute to an immune-mediated cure of FLT3-ITD-mutant AML relapse, an otherwise fatal complication after allo-HCT.

Comparing species interaction networks along environmental gradients.

Abstract: Knowledge of species composition and their interactions, in the form of interaction networks, is required to understand processes shaping their distribution over time and space. As such, comparing ecological networks along environmental gradients represents a promising new research avenue to understand the organization of life. Variation in the position and intensity of links within networks along environmental gradients may be driven by turnover in species composition, by variation in species abundances and by abiotic influences on species interactions. While investigating changes in species composition has a long tradition, so far only a limited number of studies have examined changes in species interactions between networks, often with differing approaches. Here, we review studies investigating variation in network structures along environmental gradients, highlighting how methodological decisions about standardization can influence their conclusions. Due to their complexity, variation among ecological networks is frequently studied using properties that summarize the distribution or topology of interactions such as number of links, connectance, or modularity. These properties can either be compared directly or using a procedure of standardization. While measures of network structure can be directly related to changes along environmental gradients, standardization is frequently used to facilitate interpretation of variation in network properties by controlling for some co-variables, or via null models. Null models allow comparing the deviation of empirical networks from random expectations and are expected to provide a more mechanistic understanding of the factors shaping ecological networks when they are coupled with functional traits. As an illustration, we compare approaches to quantify the role of trait matching in driving the structure of plant-hummingbird mutualistic networks, i.e. a direct comparison, standardized by null models and hypothesis-based metaweb. Overall, our analysis warns against a comparison of studies that rely on distinct forms of standardization, as they are likely to highlight different signals. Fostering a better understanding of the analytical tools available and the signal they detect will help produce deeper insights into how and why ecological networks vary along environmental gradients.

Observation of alkaline earth complexes M(CO)8 (M = Ca, Sr, or Ba) that mimic transition metals

Abstract: The alkaline earth metals calcium (Ca), strontium (Sr), and barium (Ba) typically engage in chemical bonding as classical main-group elements through their n s and n p valence orbitals, where n is the principal quantum number. Here we report the isolation and spectroscopic characterization of eight-coordinate carbonyl complexes M(CO) 8 (where M = Ca, Sr, or Ba) in a low-temperature neon matrix. Analysis of the electronic structure of these cubic O h -symmetric complexes reveals that the metal–carbon monoxide (CO) bonds arise mainly from [M(d π )] → (CO) 8 π backdonation, which explains the strong observed red shift of the C-O stretching frequencies. The corresponding radical cation complexes were also prepared in gas phase and characterized by mass-selected infrared photodissociation spectroscopy, confirming adherence to the 18-electron rule more conventionally associated with transition metal chemistry.

Subcycle observation of lightwave-driven Dirac currents in a topological surface band

Abstract: Harnessing the carrier wave of light as an alternating-current bias may enable electronics at optical clock rates1. Lightwave-driven currents have been assumed to be essential for high-harmonic generation in solids2-6, charge transport in nanostructures7,8, attosecond-streaking experiments9-16 and atomic-resolution ultrafast microscopy17,18. However, in conventional semiconductors and dielectrics, the finite effective mass and ultrafast scattering of electrons limit their ballistic excursion and velocity. The Dirac-like, quasi-relativistic band structure of topological insulators19-29 may allow these constraints to be lifted and may thus open a new era of lightwave electronics. To understand the associated, complex motion of electrons, comprehensive experimental access to carrier-wave-driven currents is crucial. Here we report angle-resolved photoemission spectroscopy with subcycle time resolution that enables us to observe directly how the carrier wave of a terahertz light pulse accelerates Dirac fermions in the band structure of the topological surface state of Bi2Te3. While terahertz streaking of photoemitted electrons traces the electromagnetic field at the surface, the acceleration of Dirac states leads to a strong redistribution of electrons in momentum space. The inertia-free surface currents are protected by spin-momentum locking and reach peak densities as large as two amps per centimetre, with ballistic mean free paths of several hundreds of nanometres, opening up a realistic parameter space for all-coherent lightwave-driven electronic devices. Furthermore, our subcycle-resolution analysis of the band structure may greatly improve our understanding of electron dynamics and strong-field interaction in solids.

Blood-brain barrier breakdown, neuroinflammation, and cognitive decline in older adults

Abstract: Introduction Blood-brain barrier (BBB) breakdown is observed in older versus younger adults and in late-onset Alzheimer's disease versus age-matched controls, but its causes and consequences in aging are unclear. We tested the hypothesis that BBB breakdown is associated with cognitive decline and inflammation in nondemented elders. Methods Cerebrospinal fluid and serum inflammatory markers were measured using sandwich immunoassays in 120 subjects. Least Absolute Shrinkage and Selection Operator-logistic regression selected cerebrospinal fluid and serum signatures that best classified BBB impairment defined by the cerebrospinal fluid albumin index ≥9. Linear regression examined changes in Clinical Dementia Rating sum of boxes as a function of BBB integrity at baseline. Results Mean age was 70 years, mean Mini–Mental State Examination was 27, and BBB impairment was recorded in 13.5%. BBB breakdown was associated with cognitive decline ( P = .015). Cerebrospinal fluid intercellular adhesion molecule-1, vascular endothelial growth factor, interleukin-8, serum amyloid A, macrophage derived chemokine, and gender generated an area under the curve of 0.95 for BBB impairment, and serum IL-16, VEGF-D, IL-15, and other variables generated an AUC of 0.92 for BBB impairment. Discussion BBB breakdown is associated with more rapid cognitive decline. Inflammatory mechanisms, including cell adhesion, neutrophil migration, lipid metabolism, and angiogenesis may be implicated.