Zur Vielfalt allgemein transduzierender Bakteriophagen in bakteriellen Gemeinschaften sowie innerhalb der Spezies Salmonella enterica serov. typhimurium

Die Rolle der Transduktion beim horizontalen Gentransfer ist bislang wenig untersucht. Die Bedeutung, die diesem Mechanismus beim Austausch von genetischem Material in der Natur zukommt, kann nur geklärt werden, wenn möglichst umfassende Informationen über das Vorkommen von transduzierenden Bakteriophagen verfügbar sind. Zur Erforschung des Ausmaßes des phagenvermittelten Gentransfers war es notwendig, Methoden zu entwickeln, die nicht auf die Verfügbarkeit kultivierbarer Indikatorbakterien zum Nachweis von Phagen sowie Spender- und Empfängerstämme zum Nachweis der Transduktion angewiesen sind. Im Rahmen dieser Arbeit wurde eine Methode zur indikatorunabhängigen Identifizierung transduzierender Bakteriophagen entwickelt. In Phagenpartikel verpackte DNA wurde als Template für die PCR-Amplifikation von bakterieller 16S rDNA eingesetzt. Dabei wurden PCR-Primer verwendet, die eine Amplifikation der 16S rRNA-Gene der meisten Eubakteria ermöglichen. Die Sequenzierung der klonierten Amplifikationsprodukte ermöglichte die retrospektive Identifizierung der Wirtsbakterien. Zur Etablierung dieser Methode wurde der generell transduzierende Salmonella-Phage P22 eingesetzt. Erste Anwendungen auf verschiedene Umweltproben zeigten, daß dieser Ansatz den Nachweis generell transduzierender Bakteriophagen ohne Isolierung und Kultivierung der Wirtszellen ermöglicht. Daher ist es auch möglich, Phagen, die am Gentransfer beteiligt sind, ohne Selektion durch die derzeit kultivierbaren Wirte zu detektieren. Schon in den ersten Testanwendungen konnten Phagen von 26 verschiedenen Gramnegativen Bakterienspezies nachgewiesen werden, bei denen bisher keine transduzierenden Viren bekannt waren. Die Untersuchung einer Moorquellwasserprobe brachte Informationen über Phagen mit bisher unbekannten Wirtszellen. Die hier vorgestellte Methode kann als Prototyp des indikatorunabhängigen Nachweises generell transduzierender Phagen für prinzipiell alle Bakterienarten gelten. Unter Einsatz verschiedener 16S rDNA-Primerpaare ist der Suche nach transduzierenden Partikeln in der Umwelt nahezu keine Grenze gesetzt. Dieser Ansatz erlaubt sowohl die Überprüfung einer Probe auf das Vorkommen transduzierender Phagen mit unterschiedlichen Wirtsspezifitäten als auch die gezielte Suche nach am DNA-Transfer beteiligten Phagen spezieller Vertreter der Prokaryonten. Ein weiteres Ziel der Arbeit war die Charakterisierung der bisher unbekannten Salmonella-Phagen 7D, PS79 und A12. Es konnte gezeigt werden, daß diese nicht mit P22 sowie anderen prominenten Bakterienviren verwandt sind und daher drei neue Phagenfamilien repräsentieren. Mikrobiologische Untersuchungen erbrachten, daß es sich dabei um zwei temperente und einen virulenten generell transduzierenden Phagen handelt. Bezüglich ihrer morphologischen und Nukleinsäure-Merkmale zählen sie zur Familie der Caudovirales. Die Phagen wurden in Hinsicht auf ihr Wirtsspektrum sowie auf phagenvermittelte Schutzmechanismen lysogener Zellen untersucht. Im Rahmen der molekulargenetischen Analyse konnte die Größe der Phagengenome ermittelt werden und für 7D und PS79 konnten Restriktionskarten für acht bzw. sieben Enzyme erstellt werden. Der Phage A12 entzog sich, wahrscheinlich aufgrund ausgeprägter DNASekundärstrukturen, einer ausführlichen Restriktionskartierung, so daß diese auf ein Enzym beschränkt werden mußte. Untersuchungen PS79-lysogener Zellen weisen darauf hin, daß der Prophage als extrachromosomale Replikationseinheit vorliegt. Für den Phagen 7D wurde die Integration durch ortsspezifische Rekombination sowie der Integrationsort auf dem Chromosom von Salmonella nachgewiesen. Die Charakterisierung der Phagen 7D, PS79 und A12 erbrachte neue Informationen über die Vielfalt generell transduzierender Bakteriophagen bei Salmonella. Insgesamt zeigen die erzielten Ergebnisse deutlich, daß der horizontale Transfer genetischen Materials durch Transduktion, insbesondere im Hinblick auf die Sicherheitsforschung im Zusammenhang mit der Freisetzung gentechnisch veränderter Organismen, nicht länger als vernachlässigbarer Faktor eingestuft werden kann

Systematic screening for novel, serologically reactive Hepatitis E Virus epitopes

<p>Abstract</p> <p>Background</p> <p>The National Institutes of Health classified Hepatitis E as an emerging disease since Hepatitis E Virus (HEV) is the major cause of acute hepatitis in developing countries. Interestingly, an increasing number of sporadic cases of HEV infections are described in industrialized countries as zoonosis from domestic livestock. Despite the increasing relevance of this pathogen in clinical virology, commercial antibody assays are mainly based on fragments of HEV open reading frame (ORF) 2 and ORF3. The largest ORF1 (poly-)protein, however, is not part of current testing formats.</p> <p>Methods</p> <p>From a synthesized full length HEV genotype 1 cDNA-bank we constructed a complete HEV gene library consisting of 15 respective HEV ORF domains. After bacterial expression and purification of nine recombinant HEV proteins under denaturating conditions serum profiling experiments using 55 sera from patients with known infection status were performed in microarray format. SPSS software assessed the antigenic potential of these nine ORF domains in comparison to seven commercial HEV antigens (genotype 1 and 3) by performing receiver operator characteristics, logistic regression and correlation analysis.</p> <p>Results</p> <p>HEV antigens produced with our method for serum profiling experiments exhibit the same quality and characteristics as commercial antigens. Serum profiling experiments detected Y, V and X domains as ORF1-antigens with potentially comparable diagnostic significance as the well established epitopes of ORF2 and ORF3. However no obvious additional increase in sensitivity or specificity was achieved in diagnostic testing as revealed by bioinformatic analysis. Additionally we found that the C-terminal domain of the potential transmembrane protein ORF3 is responsible for IgG and IgM seroreactivity. Data suggest that there might be a genotype specific seroreactivity of homologous ORF2-antigens.</p> <p>Conclusions</p> <p>The diagnostic value of identified ORF1 epitopes might not necessarily improve sensitivity and specificity, but broaden the overall quality of existing test systems. ORF2 and ORF3-antigens are still commonly used in diagnostic assays and possibly hold the potential to serologically differentiate between genotype 1 and 3 infections. Our systematic approach is a suitable method to investigate HEV domains for their serologic antigenicity. Epitope screening of native viral domains could be a preferable tool in developing new serologic test components.</p

Thin films with implemented molecular switches for the application in polymer-based optical waveguides

Complexes like iron (II)-triazoles exhibit spin crossover behavior at ambient temperature and are often considered for possible application. In previous studies, we implemented complexes of this type into polymer nanofibers and first polymer-based optical waveguide sensor systems. In our current study, we synthesized complexes of this type, implemented them into polymers and obtained composites through drop casting and doctor blading. We present that a certain combination of polymer and complex can lead to composites with high potential for optical devices. For this purpose, we used two different complexes [Fe(atrz)3](2ns)2 and [Fe(atrz)3]Cl1.5(BF4)0.5 with different polymers for each composite. We show through transmission measurements and UV/VIS spectroscopy that the optical properties of these composite materials can reversibly change due to the spin crossover effect

Puf6 primes 60S pre-ribosome nuclear export at low temperature

Productive ribosomal RNA (rRNA) compaction during ribosome assembly necessitates establishing correct tertiary contacts between distant secondary structure elements. Here, we quantify the response of the yeast proteome to low temperature (LT), a condition where aberrant mis-paired RNA folding intermediates accumulate. We show that, at LT, yeast cells globally boost production of their ribosome assembly machinery. We find that the LT-induced assembly factor, Puf6, binds to the nascent catalytic RNA-rich subunit interface within the 60S pre-ribosome, at a site that eventually loads the nuclear export apparatus. Ensemble Förster resonance energy transfer studies show that Puf6 mimics the role of Mg2+ to usher a unique long-range tertiary contact to compact rRNA. At LT, puf6 mutants accumulate 60S pre-ribosomes in the nucleus, thus unveiling Puf6-mediated rRNA compaction as a critical temperature-regulated rescue mechanism that counters rRNA misfolding to prime export competence.ISSN:2041-172

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Current Wildland Fire Patterns and Challenges in Europe : A Synthesis of National Perspectives

Changes in climate, land use, and land management impact the occurrence and severity of wildland fires in many parts of the world. This is particularly evident in Europe, where ongoing changes in land use have strongly modified fire patterns over the last decades. Although satellite data by the European Forest Fire Information System provide large-scale wildland fire statistics across European countries, there is still a crucial need to collect and summarize in-depth local analysis and understanding of the wildland fire condition and associated challenges across Europe. This article aims to provide a general overview of the current wildland fire patterns and challenges as perceived by national representatives, supplemented by national fire statistics (2009-2018) across Europe. For each of the 31 countries included, we present a perspective authored by scientists or practitioners from each respective country, representing a wide range of disciplines and cultural backgrounds. The authors were selected from members of the COST Action "Fire and the Earth System: Science & Society" funded by the European Commission with the aim to share knowledge and improve communication about wildland fire. Where relevant, a brief overview of key studies, particular wildland fire challenges a country is facing, and an overview of notable recent fire events are also presented. Key perceived challenges included (1) the lack of consistent and detailed records for wildland fire events, within and across countries, (2) an increase in wildland fires that pose a risk to properties and human life due to high population densities and sprawl into forested regions, and (3) the view that, irrespective of changes in management, climate change is likely to increase the frequency and impact of wildland fires in the coming decades. Addressing challenge (1) will not only be valuable in advancing national and pan-European wildland fire management strategies, but also in evaluating perceptions (2) and (3) against more robust quantitative evidence.Peer reviewe

The global methane budget 2000–2017

Understanding and quantifying the global methane (CH4) budget is important for assessing realistic pathways to mitigate climate change. Atmospheric emissions and concentrations of CH4 continue to increase, making CH4 the second most important human-influenced greenhouse gas in terms of climate forcing, after carbon dioxide (CO2). The relative importance of CH4 compared to CO2 depends on its shorter atmospheric lifetime, stronger warming potential, and variations in atmospheric growth rate over the past decade, the causes of which are still debated. Two major challenges in reducing uncertainties in the atmospheric growth rate arise from the variety of geographically overlapping CH4 sources and from the destruction of CH4 by short-lived hydroxyl radicals (OH). To address these challenges, we have established a consortium of multidisciplinary scientists under the umbrella of the Global Carbon Project to synthesize and stimulate new research aimed at improving and regularly updating the global methane budget. Following Saunois et al. (2016), we present here the second version of the living review paper dedicated to the decadal methane budget, integrating results of top-down studies (atmospheric observations within an atmospheric inverse-modelling framework) and bottom-up estimates (including process-based models for estimating land surface emissions and atmospheric chemistry, inventories of anthropogenic emissions, and data-driven extrapolations). For the 2008–2017 decade, global methane emissions are estimated by atmospheric inversions (a top-down approach) to be 576 Tg CH4 yr−1 (range 550–594, corresponding to the minimum and maximum estimates of the model ensemble). Of this total, 359 Tg CH4 yr−1 or ∼ 60 % is attributed to anthropogenic sources, that is emissions caused by direct human activity (i.e. anthropogenic emissions; range 336–376 Tg CH4 yr−1 or 50 %–65 %). The mean annual total emission for the new decade (2008–2017) is 29 Tg CH4 yr−1 larger than our estimate for the previous decade (2000–2009), and 24 Tg CH4 yr−1 larger than the one reported in the previous budget for 2003–2012 (Saunois et al., 2016). Since 2012, global CH4 emissions have been tracking the warmest scenarios assessed by the Intergovernmental Panel on Climate Change. Bottom-up methods suggest almost 30 % larger global emissions (737 Tg CH4 yr−1, range 594–881) than top-down inversion methods. Indeed, bottom-up estimates for natural sources such as natural wetlands, other inland water systems, and geological sources are higher than top-down estimates. The atmospheric constraints on the top-down budget suggest that at least some of these bottom-up emissions are overestimated. The latitudinal distribution of atmospheric observation-based emissions indicates a predominance of tropical emissions (∼ 65 % of the global budget, < 30∘ N) compared to mid-latitudes (∼ 30 %, 30–60∘ N) and high northern latitudes (∼ 4 %, 60–90∘ N). The most important source of uncertainty in the methane budget is attributable to natural emissions, especially those from wetlands and other inland waters. Some of our global source estimates are smaller than those in previously published budgets (Saunois et al., 2016; Kirschke et al., 2013). In particular wetland emissions are about 35 Tg CH4 yr−1 lower due to improved partition wetlands and other inland waters. Emissions from geological sources and wild animals are also found to be smaller by 7 Tg CH4 yr−1 by 8 Tg CH4 yr−1, respectively. However, the overall discrepancy between bottom-up and top-down estimates has been reduced by only 5 % compared to Saunois et al. (2016), due to a higher estimate of emissions from inland waters, highlighting the need for more detailed research on emissions factors. Priorities for improving the methane budget include (i) a global, high-resolution map of water-saturated soils and inundated areas emitting methane based on a robust classification of different types of emitting habitats; (ii) further development of process-based models for inland-water emissions; (iii) intensification of methane observations at local scales (e.g., FLUXNET-CH4 measurements) and urban-scale monitoring to constrain bottom-up land surface models, and at regional scales (surface networks and satellites) to constrain atmospheric inversions; (iv) improvements of transport models and the representation of photochemical sinks in top-down inversions; and (v) development of a 3D variational inversion system using isotopic and/or co-emitted species such as ethane to improve source partitioning