Showing papers by "Leibniz Association published in 2017"
TL;DR: The number of adults with raised blood pressure increased from 594 million in 1975 to 1·13 billion in 2015, with the increase largely in low-income and middle-income countries, and the contributions of changes in prevalence versus population growth and ageing to the increase.
1,573 citations
University of Oldenburg1, University of Vienna2, University College London3, Zoological Society of London4, International Union for Conservation of Nature and Natural Resources5, Lincoln University (New Zealand)6, Free University of Berlin7, Leibniz Association8, University of Auckland9, Charles University in Prague10, Stellenbosch University11, Academy of Sciences of the Czech Republic12, National and Kapodistrian University of Athens13, University of Fribourg14, University of Sassari15, University of Porto16, Sapienza University of Rome17, Durham University18, University of Konstanz19, University of Concepción20, Charles Darwin Foundation21, CABI22, University of Göttingen23, Helmholtz Centre for Environmental Research - UFZ24, Martin Luther University of Halle-Wittenberg25, United States Forest Service26, Bielefeld University27, Botanical Society of Britain and Ireland28, Environment Agency29, National Museum of Natural History30, Institut national de la recherche agronomique31, University of Silesia in Katowice32
TL;DR: In this paper, the authors used a database of 45,813 first records of 16,926 established alien species and showed that the annual rate of first records worldwide has increased during the last 200 years, with 37% of all first records reported most recently (1970-2014).
Abstract: Although research on human-mediated exchanges of species has substantially intensified during the last centuries, we know surprisingly little about temporal dynamics of alien species accumulations across regions and taxa. Using a novel database of 45,813 first records of 16,926 established alien species, we show that the annual rate of first records worldwide has increased during the last 200 years, with 37% of all first records reported most recently (1970-2014). Inter-continental and inter-taxonomic variation can be largely attributed to the diaspora of European settlers in the nineteenth century and to the acceleration in trade in the twentieth century. For all taxonomic groups, the increase in numbers of alien species does not show any sign of saturation and most taxa even show increases in the rate of first records over time. This highlights that past efforts to mitigate invasions have not been effective enough to keep up with increasing globalization.
1,301 citations
Leibniz Association1, University of Zurich2, James Hutton Institute3, Murdoch University4, University of Minnesota5, National Institutes of Health6, University of California, Riverside7, European Bioinformatics Institute8, University of Udine9, University of Helsinki10, Norwich University11, Zhejiang University12, Kansas State University13, University of Adelaide14, University of East Anglia15, National Institute of Agricultural Botany16, Technische Universität München17, Lund University18, Government of Western Australia19, Yangtze University20, University of Dundee21, University of Western Australia22
TL;DR: The importance of the barley reference sequence for breeding is demonstrated by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
Abstract: Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
1,105 citations
TL;DR: The thoroughly updated antiSMASH version 4 is presented, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, and several usability features have been updated and improved.
Abstract: Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the â € antibiotics and secondary metabolite analysis shell - antiSMASH' has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules.
1,043 citations
TL;DR: This work extended MISA, a computational tool assisting the development of microsatellites, and reimplemented it as a web‐based application, and improved compound microsatellite detection and added the possibility to display and export MISA results in GFF3 format for downstream analysis.
Abstract: Motivation Microsatellites are a widely-used marker system in plant genetics and forensics. The development of reliable microsatellite markers from resequencing data is challenging. Results We extended MISA, a computational tool assisting the development of microsatellite markers, and reimplemented it as a web-based application. We improved compound microsatellite detection and added the possibility to display and export MISA results in GFF3 format for downstream analysis. Availability and Implementation MISA-web can be accessed under http://misaweb.ipk-gatersleben.de/. The website provides tutorials, usage note as well as download links to the source code. Contact scholz@ipk-gatersleben.de.
964 citations
Tel Aviv University1, University of New Hampshire2, Leibniz Association3, University of Saskatchewan4, Kansas State University5, Hebrew University of Jerusalem6, Agricultural Research Organization, Volcani Center7, Montana State University8, University of Haifa9, United States Department of Agriculture10, University of Illinois at Urbana–Champaign11, Weizmann Institute of Science12, University of Minnesota13, University of Bologna14, National Research Council15, Ben-Gurion University of the Negev16, University of Tsukuba17, Technische Universität München18
TL;DR: A 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat, as well as analyses of gene content, genome architecture, and genetic diversity reveal genomic regions bearing the signature of selection under domestication.
Abstract: Wheat (Triticum spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat's domestication requires knowledge about the genome of its allo-tetraploid progenitor, wild emmer (T. turgidum ssp. dicoccoides). We report a 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat, as well as analyses of gene content, genome architecture, and genetic diversity. With this fully assembled polyploid wheat genome, we identified the causal mutations in Brittle Rachis 1 (TtBtr1) genes controlling shattering, a key domestication trait. A study of genomic diversity among wild and domesticated accessions revealed genomic regions bearing the signature of selection under domestication. This reference assembly will serve as a resource for accelerating the genome-assisted improvement of modern wheat varieties.
622 citations
University of Coimbra1, University of Brasília2, University of the Basque Country3, University of California, Santa Barbara4, University of Vigo5, Technical University of Berlin6, Leibniz Association7, Swedish University of Agricultural Sciences8, National Scientific and Technical Research Council9, University of Tasmania10, Universidade Federal de Minas Gerais11, University of Toulouse12, Georgia Southern University13, University of Hong Kong14, Universidad San Francisco de Quito15, University of Concepción16, Cornell University17, Polish Academy of Sciences18, University of Tromsø19, Umeå University20, University of Toronto21, University of Yamanashi22, Egerton University23, University of Georgia24, University of Puerto Rico, Río Piedras25, University of Maryland, Baltimore County26, Monash University27, James Cook University28
TL;DR: It is hypothesized that litter quality would increase with latitude (despite variation within regions) and traits would be correlated to produce ‘syndromes’ resulting from phylogeny and environmental variation, and it is found lower litter quality and higher nitrogen:phosphorus ratios in the tropics.
Abstract: Plant litter represents a major basal resource in streams, where its decomposition is partly regulated by litter traits. Litter-trait variation may determine the latitudinal gradient in decomposition in streams, which is mainly microbial in the tropics and detritivore-mediated at high latitudes. However, this hypothesis remains untested, as we lack information on large-scale trait variation for riparian litter. Variation cannot easily be inferred from existing leaf-trait databases, since nutrient resorption can cause traits of litter and green leaves to diverge. Here we present the first global-scale assessment of riparian litter quality by determining latitudinal variation (spanning 107°) in litter traits (nutrient concentrations; physical and chemical defences) of 151 species from 24 regions and their relationships with environmental factors and phylogeny. We hypothesized that litter quality would increase with latitude (despite variation within regions) and traits would be correlated to produce ‘syndromes’ resulting from phylogeny and environmental variation. We found lower litter quality and higher nitrogen:phosphorus ratios in the tropics. Traits were linked but showed no phylogenetic signal, suggesting that syndromes were environmentally determined. Poorer litter quality and greater phosphorus limitation towards the equator may restrict detritivore-mediated decomposition, contributing to the predominance of microbial decomposers in tropical streams.
616 citations
Potsdam Institute for Climate Impact Research1, Joint Global Change Research Institute2, National Institute for Environmental Studies3, International Institute for Applied Systems Analysis4, Netherlands Environmental Assessment Agency5, Commonwealth Scientific and Industrial Research Organisation6, Lviv Polytechnic7, Wageningen University and Research Centre8, Leibniz Association9, Humboldt University of Berlin10, Graz University of Technology11, Utrecht University12
TL;DR: In this paper, a systematic interpretation of the Shared Socio-economic Pathways (SSPs) in terms of possible land-use changes and their consequences for the agricultural system, food provision and prices as well as greenhouse gas emissions is presented.
Abstract: In the future, the land system will be facing new intersecting challenges While food demand, especially for resource-intensive livestock based commodities, is expected to increase, the terrestrial system has large potentials for climate change mitigation through improved agricultural management, providing biomass for bioenergy, and conserving or even enhancing carbon stocks of ecosystems However, uncertainties in future socio-economic land use drivers may result in very different land-use dynamics and consequences for land-based ecosystem services This is the first study with a systematic interpretation of the Shared Socio-Economic Pathways (SSPs) in terms of possible land-use changes and their consequences for the agricultural system, food provision and prices as well as greenhouse gas emissions Therefore, five alternative Integrated Assessment Models with distinctive land-use modules have been used for the translation of the SSP narratives into quantitative projections The model results reflect the general storylines of the SSPs and indicate a broad range of potential land-use futures with global agricultural land of 4900 mio ha in 2005 decreasing by 743 mio ha until 2100 at the lower (SSP1) and increasing by 1080 mio ha (SSP3) at the upper end Greenhouse gas emissions from land use and land use change, as a direct outcome of these diverse land-use dynamics, and agricultural production systems differ strongly across SSPs (eg cumulative land use change emissions between 2005 and 2100 range from −54 to 402 Gt CO2) The inclusion of land-based mitigation efforts, particularly those in the most ambitious mitigation scenarios, further broadens the range of potential land futures and can strongly affect greenhouse gas dynamics and food prices In general, it can be concluded that low demand for agricultural commodities, rapid growth in agricultural productivity and globalized trade, all most pronounced in a SSP1 world, have the potential to enhance the extent of natural ecosystems, lead to lowest greenhouse gas emissions from the land system and decrease food prices over time The SSP-based land use pathways presented in this paper aim at supporting future climate research and provide the basis for further regional integrated assessments, biodiversity research and climate impact analysis
607 citations
Bielefeld University1, BRICS2, University of Düsseldorf3, Oregon State University4, University of California, San Diego5, Roskilde University6, University of Copenhagen7, Aarhus University8, Joint Genome Institute9, Pittsburgh Supercomputing Center10, Saint Petersburg State University11, Max Planck Society12, University of Vienna13, University of Technology, Sydney14, Centre national de la recherche scientifique15, Genome Institute of Singapore16, University of Warwick17, University of Tübingen18, Intel19, French Institute for Research in Computer Science and Automation20, Joint BioEnergy Institute21, Taipei Medical University22, Lawrence Berkeley National Laboratory23, Georgia Institute of Technology24, University of Calgary25, University of Göttingen26, National Health Research Institutes27, San Diego State University28, Boyce Thompson Institute for Plant Research29, Robert Koch Institute30, Coordenadoria de Aperfeiçoamento de Pessoal de Nível Superior31, University of Maryland, College Park32, Newcastle University33, Leibniz Association34, ETH Zurich35
TL;DR: The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups as discussed by the authors.
Abstract: Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.
593 citations
TL;DR: The first-ever calibrated satellite radiometer designed for night lights is used to show that from 2012 to 2016, Earth’s artificially lit outdoor area grew by 2.2% per year, with a total radiance growth of 1.8% peryear.
Abstract: A central aim of the "lighting revolution" (the transition to solid-state lighting technology) is decreased energy consumption. This could be undermined by a rebound effect of increased use in response to lowered cost of light. We use the first-ever calibrated satellite radiometer designed for night lights to show that from 2012 to 2016, Earth's artificially lit outdoor area grew by 2.2% per year, with a total radiance growth of 1.8% per year. Continuously lit areas brightened at a rate of 2.2% per year. Large differences in national growth rates were observed, with lighting remaining stable or decreasing in only a few countries. These data are not consistent with global scale energy reductions but rather indicate increased light pollution, with corresponding negative consequences for flora, fauna, and human well-being.
523 citations
TL;DR: Synthetic microgels allow combining features of chemical functionality, structural integrity, macromolecular architecture, adaptivity, permeability, and deformability in a unique way to include the "best of the colloidal, polymeric, and surfactant worlds.
Abstract: ConspectusMicrogels are macromolecular networks swollen by the solvent in which they are dissolved. They are unique systems that are distinctly different from common colloids, such as, e.g., rigid nanoparticles, flexible macromolecules, micelles, or vesicles. The size of the microgel networks is in the range of several micrometers down to nanometers (then sometimes called “nanogels”). In a collapsed state, they might resemble hard colloids but they can still contain significant amounts of solvent. When swollen, they are soft and have a fuzzy surface with dangling chains. The presence of cross-links provides structural integrity, in contrast to linear and (hyper)branched polymers. Obviously, the cross-linker content will allow control of whether microgels behave more “colloidal” or “macromolecular”.The combination of being soft and porous while still having a stable structure through the cross-linked network allows for designing microgels that have the same total chemical composition, but different propert...
TL;DR: A review of the existing literature on DBDs can be found in this article, where the main part is devoted to the progress on the investigation of different aspects of breakdown and plasma formation with the focus on single filaments or microdischarges.
Abstract: Dielectric Barrier Discharges (DBDs) are plasmas generated in configurations with an insulating (dielectric) material between the electrodes which is responsible for a self-pulsing operation. DBDs are a typical example of nonthermal atmospheric or normal pressure gas discharges. Initially used for the generation of ozone, they have opened up many other fields of application. Therefore DBDs are a relevant tool in current plasma technology as well as an object for fundamental studies. Another motivation for further research is the fact, that so-called partial discharges in insulated high voltage systems are special types of DBDs. The breakdown processes, the formation of structures, and the role of surface processes are currently under investigation. This review is intended to give an update to the already existing literature on DBDs considering the research and development within the last two decades. The main principles and different modes of discharge generation are summarized. A collection of known as well as special electrode configurations and reactor designs will be presented. This shall demonstrate the different and broad possibilities, but also the similarities and common aspects of devices for different fields of applications explored within the last years. The main part is devoted to the progress on the investigation of different aspects of breakdown and plasma formation with the focus on single filaments or microdischarges. This includes a summary of the current knowledge on the electrical characterization of filamentary DBDs. In particular, the recent new insights on the elementary volume and surface memory mechanisms in these discharges will be discussed. An outlook for the forthcoming challenges on research and development will be given. Page 1 of 47 AUTHOR SUBMITTED MANUSCRIPT PSST-101368.R1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 A cc ep e M nu sc rip t Progress on DBD Sources and Filaments 2
Hannover Medical School1, University of Cologne2, University Hospital Heidelberg3, University of Düsseldorf4, Sapienza University of Rome5, VU University Medical Center6, University of Zurich7, National Institutes of Health8, Katholieke Universiteit Leuven9, Leibniz Association10, Dresden University of Technology11
TL;DR: An abbreviated version of the risk assessment strategy proposed by the current European PH guidelines provides accurate mortality estimates in patients with PAH and proved valid at follow-up and in major PAH subgroups.
Abstract: The 2015 European pulmonary hypertension (PH) guidelines propose a risk stratification strategy for patients with pulmonary arterial hypertension (PAH). Low-, intermediate- and high-risk strata are defined by estimated 1-year mortality risks of 10%, respectively. This risk assessment strategy awaits validation. We analysed data from patients with newly diagnosed PAH enrolled into COMPERA (Comparative, Prospective Registry of Newly Initiated Therapies for Pulmonary Hypertension), a European-based PH registry. An abbreviated version of the risk assessment strategy proposed by the European PH guidelines was applied, using the following variables: World Health Organization functional class, 6-min walking distance, brain natriuretic peptide or its N-terminal fragment, right atrial pressure, cardiac index and mixed venous oxygen saturation. Data from 1588 patients were analysed. Mortality rates were significantly different between the three risk strata (p An abbreviated version of the risk assessment strategy proposed by the current European PH guidelines provides accurate mortality estimates in patients with PAH.
TL;DR: In this paper, new developments in identifying the heterogeneous freezing mechanisms, atmospheric relevance, uncertainties, and unknowns about ice nucleating particles (INPs) have been described, and the change in conventional wisdom regarding the requirements of INPs as new studies discover physical and chemical properties of these particles is explained.
Abstract: Ice particle formation in tropospheric clouds significantly changes cloud radiative and microphysical properties. Ice nucleation in the troposphere via homogeneous freezing occurs at temperatures lower than −38°C and relative humidity with respect to ice above 140%. In the absence of these conditions, ice formation can proceed via heterogeneous nucleation aided by aerosol particles known as ice nucleating particles (INPs). In this chapter, new developments in identifying the heterogeneous freezing mechanisms, atmospheric relevance, uncertainties, and unknowns about INPs are described. The change in conventional wisdom regarding the requirements of INPs as new studies discover physical and chemical properties of these particles is explained. INP sources and known reasons for their ice nucleating properties are presented. The need for more studies to systematically identify particle properties that facilitate ice nucleation is highlighted. The atmospheric relevance of long-range transport, aerosol a...
TL;DR: Type and reference strains of members of the onygenalean family Arthrodermataceae have been sequenced for rDNA ITS and partial LSU, and fragments of β-tubulin and translation elongation factor 3 showed Trichophyton to be polyphyletic.
Abstract: Type and reference strains of members of the onygenalean family Arthrodermataceae have been sequenced for rDNA ITS and partial LSU, the ribosomal 60S protein, and fragments of β-tubulin and translation elongation factor 3. The resulting phylogenetic trees showed a large degree of correspondence, and topologies matched those of earlier published phylogenies demonstrating that the phylogenetic representation of dermatophytes and dermatophyte-like fungi has reached an acceptable level of stability. All trees showed Trichophyton to be polyphyletic. In the present paper, Trichophyton is restricted to mainly the derived clade, resulting in classification of nearly all anthropophilic dermatophytes in Trichophyton and Epidermophyton, along with some zoophilic species that regularly infect humans. Microsporum is restricted to some species around M. canis, while the geophilic species and zoophilic species that are more remote from the human sphere are divided over Arthroderma, Lophophyton and Nannizzia. A new genus Guarromyces is proposed for Keratinomyces ceretanicus. Thirteen new combinations are proposed; in an overview of all described species it is noted that the largest number of novelties was introduced during the decades 1920-1940, when morphological characters were used in addition to clinical features. Species are neo- or epi-typified where necessary, which was the case in Arthroderma curreyi, Epidermophyton floccosum, Lophophyton gallinae, Trichophyton equinum, T. mentagrophytes, T. quinckeanum, T. schoenleinii, T. soudanense, and T. verrucosum. In the newly proposed taxonomy, Trichophyton contains 16 species, Epidermophyton one species, Nannizzia 9 species, Microsporum 3 species, Lophophyton 1 species, Arthroderma 21 species and Ctenomyces 1 species, but more detailed studies remain needed to establish species borderlines. Each species now has a single valid name. Two new genera are introduced: Guarromyces and Paraphyton. The number of genera has increased, but species that are relevant to routine diagnostics now belong to smaller groups, which enhances their identification.
TL;DR: An exhaustive examination of current research trends with a focus on nanomaterials (NMs) to considerably improve the performance of classical wastewater treatment technologies, e.g. adsorption, catalysis, separation, and disinfection is undertaken.
Abstract: The efficient handling of wastewater pollutants is a must, since they are continuously defiling limited fresh water resources, seriously affecting the terrestrial, aquatic, and aerial flora and fauna. Our vision is to undertake an exhaustive examination of current research trends with a focus on nanomaterials (NMs) to considerably improve the performance of classical wastewater treatment technologies, e.g. adsorption, catalysis, separation, and disinfection. Additionally, NM-based sensor technologies are considered, since they have been significantly used for monitoring water contaminants. We also suggest future directions to inform investigators of potentially disruptive NM technologies that have to be investigated in more detail. The fate and environmental transformations of NMs, which need to be addressed before large-scale implementation of NMs for water purification, are also highlighted.
TL;DR: The authors examined the rate of change in the production and variety of pesticides, pharmaceuticals, and other synthetic chemicals over the past four decades and compared these rates to those for well-recognized drivers of global change such as rising atmospheric CO2 concentrations, nutrient pollution, habitat destruction, and biodiversity loss.
Abstract: Though concerns about the proliferation of synthetic chemicals – including pesticides – gave rise to the modern environmental movement in the early 1960s, synthetic chemical pollution has not been included in most analyses of global change. We examined the rate of change in the production and variety of pesticides, pharmaceuticals, and other synthetic chemicals over the past four decades. We compared these rates to those for well-recognized drivers of global change such as rising atmospheric CO2 concentrations, nutrient pollution, habitat destruction, and biodiversity loss. Our analysis showed that increases in synthetic chemical production and diversification, particularly within the developing world, outpaced these other agents of global change. Despite these trends, mainstream ecological journals, ecological meetings, and ecological funding through the US National Science Foundation devote less than 2% of their journal pages, meeting talks, and science funding, respectively, to the study of synthetic chemicals.
Utrecht University1, United States Department of Energy2, National Autonomous University of Mexico3, National and Kapodistrian University of Athens4, University of Debrecen5, Leiden University6, Commonwealth Scientific and Industrial Research Organisation7, University of Göttingen8, Maynooth University9, University of Natural Resources and Life Sciences, Vienna10, University of Seville11, Broad Institute12, Huazhong Agricultural University13, State University of Campinas14, International Sleep Products Association15, Université libre de Bruxelles16, University of Nottingham17, Aix-Marseille University18, Pasteur Institute19, King Abdulaziz University20, Institut national de la recherche agronomique21, University of Helsinki22, University of Amsterdam23, University of Ioannina24, University of St Andrews25, Saint Petersburg State University26, Spanish National Research Council27, Federal University of São Carlos28, Swedish University of Agricultural Sciences29, Technical University of Berlin30, National Scientific and Technical Research Council31, Concordia University32, Kyungpook National University33, University of the Republic34, Karlsruhe Institute of Technology35, University of Sulaymaniyah36, University of Ljubljana37, Leibniz Association38, Stanford University39, Kansas State University40, Technical University of Denmark41, University of Wisconsin-Madison42, Pacific Northwest National Laboratory43, University of Jena44, University of São Paulo45, University of Kansas46, Imperial College London47, Université Paris-Saclay48, Vienna University of Technology49
TL;DR: In this article, a comparative genomics and experimental study of the aspergilli genus is presented, which allows for the first time a genus-wide view of the biological diversity of the Aspergillus and in many, but not all, cases linked genome differences to phenotype.
Abstract: Background: The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. Results: We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. Conclusions: Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.
TL;DR: All NSAIDs, including naproxen, were found to be associated with an increased risk of acute myocardial infarction.
Abstract: Objective To characterise the determinants, time course, and risks of acute myocardial infarction associated with use of oral non-steroidal anti-inflammatory drugs (NSAIDs). Design Systematic review followed by a one stage bayesian individual patient data meta-analysis. Data sources Studies from Canadian and European healthcare databases. Review methods Eligible studies were sourced from computerised drug prescription or medical databases, conducted in the general or an elderly population, documented acute myocardial infarction as specific outcome, studied selective cyclo-oxygenase-2 inhibitors (including rofecoxib) and traditional NSAIDs, compared risk of acute myocardial infarction in NSAID users with non-users, allowed for time dependent analyses, and minimised effects of confounding and misclassification bias. Exposure and outcomes Drug exposure was modelled as an indicator variable incorporating the specific NSAID, its recency, duration of use, and dose. The outcome measures were the summary adjusted odds ratios of first acute myocardial infarction after study entry for each category of NSAID use at index date (date of acute myocardial infarction for cases, matched date for controls) versus non-use in the preceding year and the posterior probability of acute myocardial infarction. Results A cohort of 446 763 individuals including 61 460 with acute myocardial infarction was acquired. Taking any dose of NSAIDs for one week, one month, or more than a month was associated with an increased risk of myocardial infarction. With use for one to seven days the probability of increased myocardial infarction risk (posterior probability of odds ratio >1.0) was 92% for celecoxib, 97% for ibuprofen, and 99% for diclofenac, naproxen, and rofecoxib. The corresponding odds ratios (95% credible intervals) were 1.24 (0.91 to 1.82) for celecoxib, 1.48 (1.00 to 2.26) for ibuprofen, 1.50 (1.06 to 2.04) for diclofenac, 1.53 (1.07 to 2.33) for naproxen, and 1.58 (1.07 to 2.17) for rofecoxib. Greater risk of myocardial infarction was documented for higher dose of NSAIDs. With use for longer than one month, risks did not appear to exceed those associated with shorter durations. Conclusions All NSAIDs, including naproxen, were found to be associated with an increased risk of acute myocardial infarction. Risk of myocardial infarction with celecoxib was comparable to that of traditional NSAIDS and was lower than for rofecoxib. Risk was greatest during the first month of NSAID use and with higher doses.
TL;DR: This Review will give the first systematic overview on enzymes catalyzing the formation of organosulfur natural products by investigating a broad range of enzymes, sulfur shuttles, and chemical mechanisms for generating carbon-sulfur bonds.
Abstract: Sulfur plays a critical role for the development and maintenance of life on earth, which is reflected by the wealth of primary metabolites, macromolecules, and cofactors bearing this element. Whereas a large body of knowledge has existed for sulfur trafficking in primary metabolism, the secondary metabolism involving sulfur has long been neglected. Yet, diverse sulfur functionalities have a major impact on the biological activities of natural products. Recent research at the genetic, biochemical, and chemical levels has unearthed a broad range of enzymes, sulfur shuttles, and chemical mechanisms for generating carbon–sulfur bonds. This Review will give the first systematic overview on enzymes catalyzing the formation of organosulfur natural products.
TL;DR: A novel in silico framework for phylogeny and classification of prokaryotic viruses is presented, in line with the principles of phylogenetic systematics, and using a large reference dataset of officially classified viruses.
Abstract: Motivation Bacterial and archaeal viruses are crucial for global biogeochemical cycles and might well be game-changing therapeutic agents in the fight against multi-resistant pathogens. Nevertheless, it is still unclear how to best use genome sequence data for a fast, universal and accurate taxonomic classification of such viruses. Results We here present a novel in silico framework for phylogeny and classification of prokaryotic viruses, in line with the principles of phylogenetic systematics, and using a large reference dataset of officially classified viruses. The resulting trees revealed a high agreement with the classification. Except for low resolution at the family level, the majority of taxa was well supported as monophyletic. Clusters obtained with distance thresholds chosen for maximizing taxonomic agreement appeared phylogenetically reasonable, too. Analysis of an expanded dataset, containing >4000 genomes from public databases, revealed a large number of novel species, genera, subfamilies and families. Availability and implementation The selected methods are available as the easy-to-use web service 'VICTOR' at https://victor.dsmz.de. Contact jan.meier-kolthoff@dsmz.de. Supplementary information Supplementary data are available at Bioinformatics online.
TL;DR: In this paper, a 3D-printable, flexible, and conductive thermoplastic-based material was successfully developed for strain sensing applications, and the results demonstrate TPU/MWCNT as an excellent piezoresistive feedstock for 3D printing with potential applications in wearable electronics, soft robotics, and prosthetics.
Washington State University1, University of Oregon2, University of Minnesota3, Rutgers University4, Illinois State University5, York University6, University of Wisconsin-Madison7, University of Saskatchewan8, University of Vermont9, Leibniz Association10, Uppsala University11, University of Helsinki12, University of Michigan13, Yale University14, Virginia Tech15, University of St. Thomas (Minnesota)16, University of Barcelona17, University of Potsdam18, Estonian University of Life Sciences19, University of New Brunswick20, International Institute for Sustainable Development21, United States Fish and Wildlife Service22, Tallinn University of Technology23, University of California, Santa Barbara24, University College London25, Bowling Green State University26, Brandenburg University of Technology27, Ontario Ministry of the Environment28, Université du Québec à Chicoutimi29, United States Geological Survey30, University of Nottingham31, University of California, Davis32, Irkutsk State University33, Colorado School of Public Health34, Clarkson University35, Trent University36, Environment Canada37, Loughborough University38
TL;DR: This is the first global quantitative synthesis on under-ice lake ecology, including 36 abiotic and biotic variables from 42 research groups and 101 lakes, examining seasonal differences and connections as well as how seasonal differences vary with geophysical factors.
Abstract: Winter conditions are rapidly changing in temperate ecosystems, particularly for those that experience periods of snow and ice cover. Relatively little is known of winter ecology in these systems, due to a historical research focus on summer ‘growing seasons’. We executed the first global quantitative synthesis on under-ice lake ecology, including 36 abiotic and biotic variables from 42 research groups and 101 lakes, examining seasonal differences and connections as well as how seasonal differences vary with geophysical factors. Plankton were more abundant under ice than expected; mean winter values were 43.2% of summer values for chlorophyll a, 15.8% of summer phytoplankton biovolume and 25.3% of summer zooplankton density. Dissolved nitrogen concentrations were typically higher during winter, and these differences were exaggerated in smaller lakes. Lake size also influenced winter-summer patterns for dissolved organic carbon (DOC), with higher winter DOC in smaller lakes. At coarse levels of taxonomic aggregation, phytoplankton and zooplankton community composition showed few systematic differences between seasons, although literature suggests that seasonal differences are frequently lake-specific, species-specific, or occur at the level of functional group. Within the subset of lakes that had longer time series, winter influenced the subsequent summer for some nutrient variables and zooplankton biomass.
TL;DR: A positive magneto-thermoelectric conductance in the Weyl semimetal niobium phosphide (NbP) for collinear temperature gradients and magnetic fields that vanishes in the ultra-quantum limit, when only a single Landau level is occupied is consistent with the presence of a mixed axial–gravitational anomaly.
Abstract: The conservation laws, such as those of charge, energy and momentum, have a central role in physics. In some special cases, classical conservation laws are broken at the quantum level by quantum fluctuations, in which case the theory is said to have quantum anomalies. One of the most prominent examples is the chiral anomaly, which involves massless chiral fermions. These particles have their spin, or internal angular momentum, aligned either parallel or antiparallel with their linear momentum, labelled as left and right chirality, respectively. In three spatial dimensions, the chiral anomaly is the breakdown (as a result of externally applied parallel electric and magnetic fields) of the classical conservation law that dictates that the number of massless fermions of each chirality are separately conserved. The current that measures the difference between left- and right-handed particles is called the axial current and is not conserved at the quantum level. In addition, an underlying curved space-time provides a distinct contribution to a chiral imbalance, an effect known as the mixed axial-gravitational anomaly, but this anomaly has yet to be confirmed experimentally. However, the presence of a mixed gauge-gravitational anomaly has recently been tied to thermoelectrical transport in a magnetic field, even in flat space-time, suggesting that such types of mixed anomaly could be experimentally probed in condensed matter systems known as Weyl semimetals. Here, using a temperature gradient, we observe experimentally a positive magneto-thermoelectric conductance in the Weyl semimetal niobium phosphide (NbP) for collinear temperature gradients and magnetic fields that vanishes in the ultra-quantum limit, when only a single Landau level is occupied. This observation is consistent with the presence of a mixed axial-gravitational anomaly, providing clear evidence for a theoretical concept that has so far eluded experimental detection.
McGill University1, Zoological Society of London2, University College London3, Williams College4, Queen's University Belfast5, Canterbury of New Zealand6, University of Victoria7, Free University of Berlin8, Leibniz Association9, United States Forest Service10, Rutgers University11, University of Windsor12, Academy of Sciences of the Czech Republic13, Charles University in Prague14, Stellenbosch University15, Smithsonian Environmental Research Center16, University of Tennessee17, University of Cambridge18, Swedish University of Agricultural Sciences19, Nanyang Technological University20
TL;DR: Diverse issues suggest an expanding interdisciplinary role for invasion science in biosecurity and ecosystem management, burgeoning applications of biotechnology in alien species detection and control, and new frontiers in the microbial ecology of invasions.
Abstract: We identified emerging scientific, technological, and sociopolitical issues likely to affect how biological invasions are studied and managed over the next two decades. Issues were ranked according to their probability of emergence, pervasiveness, potential impact, and novelty. Top-ranked issues include the application of genomic modification tools to control invasions, effects of Arctic globalization on invasion risk in the Northern Hemisphere, commercial use of microbes to facilitate crop production, the emergence of invasive microbial pathogens, and the fate of intercontinental trade agreements. These diverse issues suggest an expanding interdisciplinary role for invasion science in biosecurity and ecosystem management, burgeoning applications of biotechnology in alien species detection and control, and new frontiers in the microbial ecology of invasions.
Humboldt University of Berlin1, Helmholtz Centre for Environmental Research - UFZ2, Stockholm Resilience Centre3, Autonomous University of Barcelona4, Technical University of Berlin5, Erasmus University Rotterdam6, University of Pennsylvania7, University of Łódź8, Leibniz Association9, Technische Universität München10, Dresden University of Technology11
TL;DR: In this article, the authors reflect on the current debate of the social effects of greening using selected examples and discuss what trade-offs between social and ecological developments in cities mean for the future debate on greening cities and a socially balanced and inclusive way of developing our cities for various groups of urban dwellers.
University of East Anglia1, Joint Genome Institute2, Norwich Research Park3, Stazione Zoologica Anton Dohrn4, J. Craig Venter Institute5, Scripps Institution of Oceanography6, Alfred Wegener Institute for Polar and Marine Research7, Université Paris-Saclay8, École Normale Supérieure9, University of Paris10, Leibniz Association11, University of Cologne12, University of Konstanz13, Medical University of South Carolina14, University of Duisburg-Essen15, Leibniz Institute for Neurobiology16, University of Washington17, University of Nevada, Las Vegas18, Monterey Bay Aquarium Research Institute19, University of British Columbia20, University of California, Berkeley21
TL;DR: In this article, the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms was studied.
Abstract: The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.
TL;DR: The analysis of plant microbiome data has brought about a paradigm shift in understanding of its role in health and disease and has substantial consequences for biocontrol and health issues.
International Crops Research Institute for the Semi-Arid Tropics1, Institut de recherche pour le développement2, University of Georgia3, Leibniz Association4, Fort Valley State University5, Cornell University6, University of Florida7, Junagadh Agricultural University8, United States Department of Agriculture9, University of Vienna10, Amity University11, University of Arizona12, Indian Council of Agricultural Research13, University of Montpellier14, University of Lyon15, Oklahoma State University–Stillwater16, DuPont Pioneer17, Aberystwyth University18, Visva-Bharati University19, Agricultural Research Service20
TL;DR: This work resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication, and establishes marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance.
Abstract: Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ~1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.