Showing papers by "Wageningen University and Research Centre published in 2015"
Stockholm Resilience Centre1, Australian National University2, University of Copenhagen3, McGill University4, Stellenbosch University5, University of Wisconsin-Madison6, Wageningen University and Research Centre7, Stockholm University8, Royal Swedish Academy of Sciences9, Potsdam Institute for Climate Impact Research10, Commonwealth Scientific and Industrial Research Organisation11, International Livestock Research Institute12, University College London13, Stockholm Environment Institute14, University of California, San Diego15, The Energy and Resources Institute16, Royal Institute of Technology17
TL;DR: An updated and extended analysis of the planetary boundary (PB) framework and identifies levels of anthropogenic perturbations below which the risk of destabilization of the Earth system (ES) is likely to remain low—a “safe operating space” for global societal development.
Abstract: The planetary boundaries framework defines a safe operating space for humanity based on the intrinsic biophysical processes that regulate the stability of the Earth system. Here, we revise and update the planetary boundary framework, with a focus on the underpinning biophysical science, based on targeted input from expert research communities and on more general scientific advances over the past 5 years. Several of the boundaries now have a two-tier approach, reflecting the importance of cross-scale interactions and the regional-level heterogeneity of the processes that underpin the boundaries. Two core boundaries—climate change and biosphere integrity—have been identified, each of which has the potential on its own to drive the Earth system into a new state should they be substantially and persistently transgressed.
7,169 citations
TL;DR: In the Global Burden of Disease Study 2013 (GBD 2013) as discussed by the authors, the authors used the GBD 2010 methods with some refinements to improve accuracy applied to an updated database of vital registration, survey, and census data.
5,792 citations
TL;DR: In the Global Burden of Disease Study 2013 (GBD 2013) as mentioned in this paper, the authors estimated the quantities for acute and chronic diseases and injuries for 188 countries between 1990 and 2013.
4,510 citations
TL;DR: In this paper, the authors characterized Cpf1, a putative class 2 CRISPR effector, which is a single RNA-guided endonuclease lacking tracrRNA and utilizes a T-rich protospacer-adjacent motif.
3,436 citations
University of Washington1, Institute for Health Metrics and Evaluation2, Iran University of Medical Sciences3, King's College London4, Arabian Gulf University5, University of North Texas6, Auckland University of Technology7, Alaska Native Tribal Health Consortium8, Columbia University9, Wuhan University10, Imperial College London11, University of Alabama at Birmingham12, University at Albany, SUNY13, City University of New York14, University of California, San Francisco15, Griffith University16, Environment Agency17, New York University18, Southern University College19, Emory University20, University of Ottawa21, Kosin University22, University of Toronto23, University of British Columbia24, United Arab Emirates University25, Albert Einstein College of Medicine26, University of São Paulo27, Nova Southeastern University28, University of Sydney29, Heidelberg University30, Case Western Reserve University31, Cancer Treatment Centers of America32, University of Oxford33, George Mason University34, James Cook University35, University of Trieste36, University of Calgary37, Wageningen University and Research Centre38, University of Gothenburg39, University of the Witwatersrand40, Harvard University41, Jackson State University42, University of Arizona43, University of Hong Kong44, Tehran University of Medical Sciences45, University of Western Australia46, Aintree University Hospitals NHS Foundation Trust47, University of Colorado Denver48, Veterans Health Administration49, University of Melbourne50, Royal Children's Hospital51, Australian National University52, University of Marburg53, Charité54, Health Canada55, College of Health Sciences, Bahrain56, Karolinska Institutet57, Northumbria University58, University of Edinburgh59, National Research University – Higher School of Economics60, Queen Mary University of London61, Addis Ababa University62, Northwestern University63, Northeastern University64, Mario Negri Institute for Pharmacological Research65, Arak University of Medical Sciences66, University of Nottingham67, University of Tokyo68, Public Health Foundation of India69, University of Groningen70, University of the Philippines Manila71, University of Bologna72, Kyung Hee University73, Brighton and Sussex Medical School74, Stavanger University Hospital75, University of Bergen76, University of Queensland77, National Centre for Disease Control78, University of Sheffield79, Universidad Autónoma Metropolitana80, University College London81, Genentech82, Universiti Tunku Abdul Rahman83, Norwegian Institute of Public Health84
TL;DR: To estimate mortality, incidence, years lived with disability, years of life lost, and disability-adjusted life-years for 28 cancers in 188 countries by sex from 1990 to 2013, the general methodology of the Global Burden of Disease 2013 study was used.
Abstract: Importance Cancer is among the leading causes of death worldwide. Current estimates of cancer burden in individual countries and regions are necessary to inform local cancer control strategies. Objective To estimate mortality, incidence, years lived with disability (YLDs), years of life lost (YLLs), and disability-adjusted life-years (DALYs) for 28 cancers in 188 countries by sex from 1990 to 2013. Evidence Review The general methodology of the Global Burden of Disease (GBD) 2013 study was used. Cancer registries were the source for cancer incidence data as well as mortality incidence (MI) ratios. Sources for cause of death data include vital registration system data, verbal autopsy studies, and other sources. The MI ratios were used to transform incidence data to mortality estimates and cause of death estimates to incidence estimates. Cancer prevalence was estimated using MI ratios as surrogates for survival data; YLDs were calculated by multiplying prevalence estimates with disability weights, which were derived from population-based surveys; YLLs were computed by multiplying the number of estimated cancer deaths at each age with a reference life expectancy; and DALYs were calculated as the sum of YLDs and YLLs. Findings In 2013 there were 14.9 million incident cancer cases, 8.2 million deaths, and 196.3 million DALYs. Prostate cancer was the leading cause for cancer incidence (1.4 million) for men and breast cancer for women (1.8 million). Tracheal, bronchus, and lung (TBL) cancer was the leading cause for cancer death in men and women, with 1.6 million deaths. For men, TBL cancer was the leading cause of DALYs (24.9 million). For women, breast cancer was the leading cause of DALYs (13.1 million). Age-standardized incidence rates (ASIRs) per 100 000 and age-standardized death rates (ASDRs) per 100 000 for both sexes in 2013 were higher in developing vs developed countries for stomach cancer (ASIR, 17 vs 14; ASDR, 15 vs 11), liver cancer (ASIR, 15 vs 7; ASDR, 16 vs 7), esophageal cancer (ASIR, 9 vs 4; ASDR, 9 vs 4), cervical cancer (ASIR, 8 vs 5; ASDR, 4 vs 2), lip and oral cavity cancer (ASIR, 7 vs 6; ASDR, 2 vs 2), and nasopharyngeal cancer (ASIR, 1.5 vs 0.4; ASDR, 1.2 vs 0.3). Between 1990 and 2013, ASIRs for all cancers combined (except nonmelanoma skin cancer and Kaposi sarcoma) increased by more than 10% in 113 countries and decreased by more than 10% in 12 of 188 countries. Conclusions and Relevance Cancer poses a major threat to public health worldwide, and incidence rates have increased in most countries since 1990. The trend is a particular threat to developing nations with health systems that are ill-equipped to deal with complex and expensive cancer treatments. The annual update on the Global Burden of Cancer will provide all stakeholders with timely estimates to guide policy efforts in cancer prevention, screening, treatment, and palliation.
2,375 citations
TL;DR: An approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR–cas loci into distinct classes, types and subtypes is presented.
Abstract: The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR-cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR-Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.
1,988 citations
TL;DR: AntiSMASH as mentioned in this paper is a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.org.
Abstract: Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software.
1,691 citations
TL;DR: This review addresses the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.
Abstract: All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.
1,677 citations
Mohammad H. Forouzanfar1, Lily Alexander1, H. Ross Anderson2, Victoria F Bachman1 +718 more•Institutions (295)
TL;DR: The Global Burden of Disease, Injuries, and Risk Factor study 2013 (GBD 2013) as mentioned in this paper provides a timely opportunity to update the comparative risk assessment with new data for exposure, relative risks, and evidence on the appropriate counterfactual risk distribution.
1,656 citations
University of Florida1, University of Bonn2, Institut national de la recherche agronomique3, Blaise Pascal University4, Stanford University5, Prince of Songkla University6, Agricultural Research Service7, University of Arizona8, International Maize and Wheat Improvement Center9, Kansas State University10, International Water Management Institute11, Washington State University12, Michigan State University13, University of Leeds14, CGIAR15, Counterintelligence Field Activity16, Spanish National Research Council17, University of Tübingen18, University of Guelph19, Texas A&M University20, University of Maryland, College Park21, Aarhus University22, Potsdam Institute for Climate Impact Research23, Indian Agricultural Research Institute24, Goddard Institute for Space Studies25, Rothamsted Research26, University of Hohenheim27, Wageningen University and Research Centre28, Chinese Academy of Sciences29, Commonwealth Scientific and Industrial Research Organisation30, China Agricultural University31, Nanjing Agricultural University32
TL;DR: The authors systematically tested 30 different wheat crop models of the Agricultural Model Intercomparison and Improvement Project against field experiments in which growing season mean temperatures ranged from 15 degrees C to 32 degrees C, including experiments with artificial heating.
Abstract: Crop models are essential tools for assessing the threat of climate change to local and global food production(1). Present models used to predict wheat grain yield are highly uncertain when simulating how crops respond to temperature(2). Here we systematically tested 30 different wheat crop models of the Agricultural Model Intercomparison and Improvement Project against field experiments in which growing season mean temperatures ranged from 15 degrees C to 32 degrees C, including experiments with artificial heating. Many models simulated yields well, but were less accurate at higher temperatures. The model ensemble median was consistently more accurate in simulating the crop temperature response than any single model, regardless of the input information used. Extrapolating the model ensemble temperature response indicates that warming is already slowing yield gains at a majority of wheat-growing locations. Global wheat production is estimated to fall by 6% for each degrees C of further temperature increase and become more variable over space and time.
1,461 citations
TL;DR: Capacitive deionization (CDI) is an emerging technology for the facile removal of charged ionic species from aqueous solutions, and is currently being widely explored for water desalination applications.
Abstract: Capacitive deionization (CDI) is an emerging technology for the facile removal of charged ionic species from aqueous solutions, and is currently being widely explored for water desalination applications. The technology is based on ion electrosorption at the surface of a pair of electrically charged electrodes, commonly composed of highly porous carbon materials. The CDI community has grown exponentially over the past decade, driving tremendous advances via new cell architectures and system designs, the implementation of ion exchange membranes, and alternative concepts such as flowable carbon electrodes and hybrid systems employing a Faradaic (battery) electrode. Also, vast improvements have been made towards unraveling the complex processes inherent to interfacial electrochemistry, including the modelling of kinetic and equilibrium aspects of the desalination process. In our perspective, we critically review and evaluate the current state-of-the-art of CDI technology and provide definitions and performance metric nomenclature in an effort to unify the fast-growing CDI community. We also provide an outlook on the emerging trends in CDI and propose future research and development directions.
TL;DR: This paper used a rigorous statistical framework to standardize a global dataset of plastic marine debris measured using surface-trawling plankton nets and coupled this with three different ocean circulation models to spatially interpolate the observations.
Abstract: Microplastic debris floating at the ocean surface can harm marine life. Understanding the severity of this harm requires knowledge of plastic abundance and distributions. Dozens of expeditions measuring microplastics have been carried out since the 1970s, but they have primarily focused on the North Atlantic and North Pacific accumulation zones, with much sparser coverage elsewhere. Here, we use the largest dataset of microplastic measurements assembled to date to assess the confidence we can have in global estimates of microplastic abundance and mass. We use a rigorous statistical framework to standardize a global dataset of plastic marine debris measured using surface-trawling plankton nets and coupled this with three different ocean circulation models to spatially interpolate the observations. Our estimates show that the accumulated number of microplastic particles in 2014 ranges from 15 to 51 trillion particles, weighing between 93 and 236 thousand metric tons, which is only approximately 1% of global plastic waste estimated to enter the ocean in the year 2010. These estimates are larger than previous global estimates, but vary widely because the scarcity of data in most of the world ocean, differences in model formulations, and fundamental knowledge gaps in the sources, transformations and fates of microplastics in the ocean.
University of Minnesota1, Leipzig University2, University College Dublin3, Centre national de la recherche scientifique4, University of Zurich5, University of Bayreuth6, Iowa State University7, Martin Luther University of Halle-Wittenberg8, University of Jena9, Swansea University10, United States Department of Agriculture11, Utrecht University12, University of Oxford13, University of Greifswald14, Sewanee: The University of the South15, University of Bern16, Technische Universität München17, Yokohama National University18, Columbia University19, University of Western Sydney20, Colorado State University21, University of California, Santa Barbara22, Virginia Tech23, Wageningen University and Research Centre24
TL;DR: Biodiversity mainly stabilizes ecosystem productivity, and productivity-dependent ecosystem services, by increasing resistance to climate events, and restoration of biodiversity to increase it, mainly by changing the resistance of ecosystem productivity toClimate events.
Abstract: It remains unclear whether biodiversity buffers ecosystems against climate extremes, which are becoming increasingly frequent worldwide1. Early results suggested that the ecosystem productivity of diverse grassland plant communities was more resistant, changing less during drought, and more resilient, recovering more quickly after drought, than that of depauperate communities2. However, subsequent experimental tests produced mixed results3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13. Here we use data from 46 experiments that manipulated grassland plant diversity to test whether biodiversity provides resistance during and resilience after climate events. We show that biodiversity increased ecosystem resistance for a broad range of climate events, including wet or dry, moderate or extreme, and brief or prolonged events. Across all studies and climate events, the productivity of low-diversity communities with one or two species changed by approximately 50% during climate events, whereas that of high-diversity communities with 16–32 species was more resistant, changing by only approximately 25%. By a year after each climate event, ecosystem productivity had often fully recovered, or overshot, normal levels of productivity in both high- and low-diversity communities, leading to no detectable dependence of ecosystem resilience on biodiversity. Our results suggest that biodiversity mainly stabilizes ecosystem productivity, and productivity-dependent ecosystem services, by increasing resistance to climate events. Anthropogenic environmental changes that drive biodiversity loss thus seem likely to decrease ecosystem stability14, and restoration of biodiversity to increase it, mainly by changing the resistance of ecosystem productivity to climate events.
University of Leeds1, University of Exeter2, Imperial College London3, James Cook University4, Environmental Change Institute5, University College London6, University of Kent7, Duke University8, National Institute of Amazonian Research9, National Institute for Space Research10, Universidad Autónoma Gabriel René Moreno11, Wageningen University and Research Centre12, University of Amsterdam13, Florida International University14, Institut national de la recherche agronomique15, Universidade Federal do Acre16, Tropenbos International17, Empresa Brasileira de Pesquisa Agropecuária18, National Chung Hsing University19, Paul Sabatier University20, National Park Service21, Amazon.com22, Federal University of Pará23, Universidade do Estado de Mato Grosso24, University of Texas at Austin25, Smithsonian Institution26, World Wide Fund for Nature27, Universidad Mayor28, Field Museum of Natural History29, Universidad Nacional de la Amazonía Peruana30, University of Los Andes31, National University of Colombia32, Museu Paraense Emílio Goeldi33, Utrecht University34, Naturalis35, University of Wisconsin–Milwaukee36, Smithsonian Tropical Research Institute37, Northumbria University38, State University of Campinas39
TL;DR: It is confirmed that Amazon forests have acted as a long-term net biomass sink, but the observed decline of the Amazon sink diverges markedly from the recent increase in terrestrial carbon uptake at the global scale, and is contrary to expectations based on models
Abstract: Atmospheric carbon dioxide records indicate that the land surface has acted as a strong global carbon sink over recent decades, with a substantial fraction of this sink probably located in the tropics, particularly in the Amazon. Nevertheless, it is unclear how the terrestrial carbon sink will evolve as climate and atmospheric composition continue to change. Here we analyse the historical evolution of the biomass dynamics of the Amazon rainforest over three decades using a distributed network of 321 plots. While this analysis confirms that Amazon forests have acted as a long-term net biomass sink, we find a long-term decreasing trend of carbon accumulation. Rates of net increase in above-ground biomass declined by one-third during the past decade compared to the 1990s. This is a consequence of growth rate increases levelling off recently, while biomass mortality persistently increased throughout, leading to a shortening of carbon residence times. Potential drivers for the mortality increase include greater climate variability, and feedbacks of faster growth on mortality, resulting in shortened tree longevity. The observed decline of the Amazon sink diverges markedly from the recent increase in terrestrial carbon uptake at the global scale, and is contrary to expectations based on models.
TL;DR: In this phase 2 trial, there was no statistically significant difference in clinical and endoscopic remission between patients with UC who received fecal transplants from healthy donors and those who received their own fecal microbiota, which may be due to limited numbers.
TL;DR: A new analysis shows that global warming could be limited to 1.5 °C by 2100, but that the window for achieving this is small and rapidly closing as mentioned in this paper, but this analysis does not consider the effects of human activities.
Abstract: A new analysis shows that global warming could be limited to 1.5 °C by 2100, but that the window for achieving this is small and rapidly closing.
TL;DR: This review assesses the current literature on the occurrence of environmentally released micro- and nanoplastics in the human food production chain and their potential health impact and discusses the potential use of the very sensitive analytical techniques developed for the detection and quantification of engineered nanoparticles.
Abstract: High concentrations of plastic debris have been observed in the oceans. Much of the recent concern has focused on microplastics in the marine environment. Recent studies of the size distribution of the plastic debris suggested that continued fragmenting of microplastics into nanosized particles may occur. In this review we assess the current literature on the occurrence of environmentally released micro- and nanoplastics in the human food production chain and their potential health impact. The currently used analytical techniques introduce a great bias in the knowledge, since they are only able to detect plastic particles well above the nanorange. We discuss the potential use of the very sensitive analytical techniques that have been developed for the detection and quantification of engineered nanoparticles. We recognize three possible toxic effects of plastic particles: first due to the plastic particles themselves, second to the release of persistent organic pollutant adsorbed to the plastics, and third to the leaching of additives of the plastics. The limited data on microplastics in foods do not predict adverse effect of these pollutants or additives. Potential toxic effects of microplastic particles will be confined to the gut. The potential human toxicity of nanoplastics is poorly studied. Based on our experiences in nanotoxicology we prioritized future research questions.
TL;DR: The food changes performed in subjects from the same populations resulted in remarkable reciprocal changes in mucosal biomarkers of cancer risk and in aspects of the microbiota and metabolome known to affect cancer risk, best illustrated by increased saccharolytic fermentation and butyrogenesis and suppressed secondary bile acid synthesis in the African Americans.
Abstract: Rates of colon cancer are much higher in African Americans (65:100,000) than in rural South Africans (<5:100,000). The higher rates are associated with higher animal protein and fat, and lower fibre consumption, higher colonic secondary bile acids, lower colonic short-chain fatty acid quantities and higher mucosal proliferative biomarkers of cancer risk in otherwise healthy middle-aged volunteers. Here we investigate further the role of fat and fibre in this association. We performed 2-week food exchanges in subjects from the same populations, where African Americans were fed a high-fibre, low-fat African-style diet and rural Africans a high-fat, low-fibre western-style diet, under close supervision. In comparison with their usual diets, the food changes resulted in remarkable reciprocal changes in mucosal biomarkers of cancer risk and in aspects of the microbiota and metabolome known to affect cancer risk, best illustrated by increased saccharolytic fermentation and butyrogenesis, and suppressed secondary bile acid synthesis in the African Americans.
University of Konstanz1, University of Vienna2, Academy of Sciences of the Czech Republic3, University of Potsdam4, University of Göttingen5, Russian Academy of Sciences6, University of Canterbury7, Spanish National Research Council8, Alexander von Humboldt Biological Resources Research Institute9, Monash University10, University of Costa Rica11, Tomsk State University12, University of Coimbra13, Nelson Mandela Metropolitan University14, University of Concepción15, Botanic Garden Meise16, University of Delhi17, University of the Republic18, Southern Illinois University Carbondale19, Department of National Parks, Wildlife and Plant Conservation20, Martin Luther University of Halle-Wittenberg21, University of Oldenburg22, Sun Yat-sen University23, King Saud University24, Naturalis25, Wageningen University and Research Centre26, Charles University in Prague27, Stellenbosch University28
TL;DR: The results quantify for the first time the extent of plant naturalizations worldwide, and illustrate the urgent need for globally integrated efforts to control, manage and understand the spread of alien species.
Abstract: All around the globe, humans have greatly altered the abiotic and biotic environment with ever-increasing speed. One defining feature of the Anthropocene epoch is the erosion of biogeographical barriers by human-mediated dispersal of species into new regions, where they can naturalize and cause ecological, economic and social damage. So far, no comprehensive analysis of the global accumulation and exchange of alien plant species between continents has been performed, primarily because of a lack of data. Here we bridge this knowledge gap by using a unique global database on the occurrences of naturalized alien plant species in 481 mainland and 362 island regions. In total, 13,168 plant species, corresponding to 3.9% of the extant global vascular flora, or approximately the size of the native European flora, have become naturalized somewhere on the globe as a result of human activity. North America has accumulated the largest number of naturalized species, whereas the Pacific Islands show the fastest increase in species numbers with respect to their land area. Continents in the Northern Hemisphere have been the major donors of naturalized alien species to all other continents. Our results quantify for the first time the extent of plant naturalizations worldwide, and illustrate the urgent need for globally integrated efforts to control, manage and understand the spread of alien species.
Wageningen University and Research Centre1, Rutgers University2, Spanish National Research Council3, Naturalis4, University of Leeds5, Institut national de la recherche agronomique6, Michigan State University7, University of Freiburg8, University of California, Berkeley9, University of New England (United States)10, University of Vermont11, University of California, Davis12, National University of Singapore13, Hungarian Academy of Sciences14, University of Göttingen15, Cornell University16, Swedish University of Agricultural Sciences17, Stellenbosch University18, Centre national de la recherche scientifique19, Simon Fraser University20, University of Reading21, University of Würzburg22, Plant & Food Research23, University of Giessen24, University of Texas at Austin25, University of Bern26, Hebrew University of Jerusalem27, Lund University28, Federal University of Bahia29
TL;DR: It is shown that, while the contribution of wild bees to crop production is significant, service delivery is restricted to a limited subset of all known bee species, suggesting that cost-effective management strategies to promote crop pollination should target a different set of species than management Strategies to promote threatened bees.
Abstract: There is compelling evidence that more diverse ecosystems deliver greater benefits to people, and these ecosystem services have become a key argument for biodiversity conservation. However, it is unclear how much biodiversity is needed to deliver ecosystem services in a cost-effective way. Here we show that, while the contribution of wild bees to crop production is significant, service delivery is restricted to a limited subset of all known bee species. Across crops, years and biogeographical regions, crop-visiting wild bee communities are dominated by a small number of common species, and threatened species are rarely observed on crops. Dominant crop pollinators persist under agricultural expansion and many are easily enhanced by simple conservation measures, suggesting that cost-effective management strategies to promote crop pollination should target a different set of species than management strategies to promote threatened bees. Conserving the biological diversity of bees therefore requires more than just ecosystem-service-based arguments.
TL;DR: In this article, the authors present a concept that shows the current state of art and challenges for monitoring programs, fate and risk assessment tools and requirements for policies with respect to emerging pollutants as a base for sustainable water resource management.
TL;DR: It is found that schemes implemented after revision of the EU's agri-environmental programs in 2007 were not more effective than schemes implemented before revision and schemes aimed at areas out of production are more effective at enhancing species richness than those aimed at productive areas.
Abstract: Over half of the European landscape is under agricultural management and has been for millennia. Many species and ecosystems of conservation concern in Europe depend on agricultural management and are showing ongoing declines. Agri-environment schemes (AES) are designed partly to address this. They are a major source of nature conservation funding within the European Union (EU) and the highest conservation expenditure in Europe. We reviewed the structure of current AES across Europe. Since a 2003 review questioned the overall effectiveness of AES for biodiversity, there has been a plethora of case studies and meta-analyses examining their effectiveness. Most syntheses demonstrate general increases in farmland biodiversity in response to AES, with the size of the effect depending on the structure and management of the surrounding landscape. This is important in the light of successive EU enlargement and ongoing reforms of AES. We examined the change in effect size over time by merging the data sets of 3 recent meta-analyses and found that schemes implemented after revision of the EU's agri-environmental programs in 2007 were not more effective than schemes implemented before revision. Furthermore, schemes aimed at areas out of production (such as field margins and hedgerows) are more effective at enhancing species richness than those aimed at productive areas (such as arable crops or grasslands). Outstanding research questions include whether AES enhance ecosystem services, whether they are more effective in agriculturally marginal areas than in intensively farmed areas, whether they are more or less cost-effective for farmland biodiversity than protected areas, and how much their effectiveness is influenced by farmer training and advice? The general lesson from the European experience is that AES can be effective for conserving wildlife on farmland, but they are expensive and need to be carefully designed and targeted.
University of East Anglia1, University of Oslo2, Commonwealth Scientific and Industrial Research Organisation3, University of Exeter4, Oak Ridge National Laboratory5, Woods Hole Research Center6, University of Bristol7, Scripps Institution of Oceanography8, National Oceanic and Atmospheric Administration9, Karlsruhe Institute of Technology10, University of Miami11, Centre national de la recherche scientifique12, University of Maryland, College Park13, Aix-Marseille University14, Flanders Marine Institute15, Alfred Wegener Institute for Polar and Marine Research16, Max Planck Society17, University of Illinois at Urbana–Champaign18, Plymouth Marine Laboratory19, Netherlands Environmental Assessment Agency20, Lawrence Berkeley National Laboratory21, ETH Zurich22, Bjerknes Centre for Climate Research23, University of Paris24, Woods Hole Oceanographic Institution25, Institute of Arctic and Alpine Research26, Japan Agency for Marine-Earth Science and Technology27, National Institute for Environmental Studies28, University of Washington29, University of Bergen30, Spanish National Research Council31, Montana State University32, Leibniz Institute for Baltic Sea Research33, Japan Meteorological Agency34, Leibniz Institute of Marine Sciences35, Imperial College London36, University of Bern37, Joint Institute for the Study of the Atmosphere and Ocean38, Lamont–Doherty Earth Observatory39, Hobart Corporation40, Wageningen University and Research Centre41, VU University Amsterdam42, University of New Hampshire43, Met Office44
TL;DR: In this article, the authors presented a methodology to quantify all major components of the global carbon budget, including their uncertainties, based on the combination of a range of data, algorithms, statistics, and model estimates and their interpretation by a broad scientific community.
Abstract: Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and a methodology to quantify all major components of the global carbon budget, including their uncertainties, based on the combination of a range of data, algorithms, statistics, and model estimates and their interpretation by a broad scientific community. We discuss changes compared to previous estimates as well as consistency within and among components, alongside methodology and data limitations. CO2 emissions from fossil fuels and industry (EFF) are based on energy statistics and cement production data, while emissions from land-use change (ELUC), mainly deforestation, are based on combined evidence from land-cover-change data, fire activity associated with deforestation, and models. The global atmospheric CO2 concentration is measured directly and its rate of growth (GATM) is computed from the annual changes in concentration. The mean ocean CO2 sink (SOCEAN) is based on observations from the 1990s, while the annual anomalies and trends are estimated with ocean models. The variability in SOCEAN is evaluated with data products based on surveys of ocean CO2 measurements. The global residual terrestrial CO2 sink (SLAND) is estimated by the difference of the other terms of the global carbon budget and compared to results of independent dynamic global vegetation models forced by observed climate, CO2, and land-cover change (some including nitrogen–carbon interactions). We compare the mean land and ocean fluxes and their variability to estimates from three atmospheric inverse methods for three broad latitude bands. All uncertainties are reported as ±1σ, reflecting the current capacity to characterise the annual estimates of each component of the global carbon budget. For the last decade available (2005–2014), EFF was 9.0 ± 0.5 GtC yr−1, ELUC was 0.9 ± 0.5 GtC yr−1, GATM was 4.4 ± 0.1 GtC yr−1, SOCEAN was 2.6 ± 0.5 GtC yr−1, and SLAND was 3.0 ± 0.8 GtC yr−1. For the year 2014 alone, EFF grew to 9.8 ± 0.5 GtC yr−1, 0.6 % above 2013, continuing the growth trend in these emissions, albeit at a slower rate compared to the average growth of 2.2 % yr−1 that took place during 2005–2014. Also, for 2014, ELUC was 1.1 ± 0.5 GtC yr−1, GATM was 3.9 ± 0.2 GtC yr−1, SOCEAN was 2.9 ± 0.5 GtC yr−1, and SLAND was 4.1 ± 0.9 GtC yr−1. GATM was lower in 2014 compared to the past decade (2005–2014), reflecting a larger SLAND for that year. The global atmospheric CO2 concentration reached 397.15 ± 0.10 ppm averaged over 2014. For 2015, preliminary data indicate that the growth in EFF will be near or slightly below zero, with a projection of −0.6 [range of −1.6 to +0.5] %, based on national emissions projections for China and the USA, and projections of gross domestic product corrected for recent changes in the carbon intensity of the global economy for the rest of the world. From this projection of EFF and assumed constant ELUC for 2015, cumulative emissions of CO2 will reach about 555 ± 55 GtC (2035 ± 205 GtCO2) for 1870–2015, about 75 % from EFF and 25 % from ELUC. This living data update documents changes in the methods and data sets used in this new carbon budget compared with previous publications of this data set (Le Quere et al., 2015, 2014, 2013). All observations presented here can be downloaded from the Carbon Dioxide Information Analysis Center (doi:10.3334/CDIAC/GCP_2015).
University of East Anglia1, University of Oslo2, Centre national de la recherche scientifique3, University of Exeter4, National Oceanic and Atmospheric Administration5, Karlsruhe Institute of Technology6, Oak Ridge National Laboratory7, University of Paris8, Commonwealth Scientific and Industrial Research Organisation9, University of Maryland, College Park10, Alfred Wegener Institute for Polar and Marine Research11, Woods Hole Research Center12, University of Bristol13, University of Illinois at Urbana–Champaign14, Geophysical Institute, University of Bergen15, Bjerknes Centre for Climate Research16, National Institute for Environmental Studies17, University of California, San Diego18, Plymouth Marine Laboratory19, Netherlands Environmental Assessment Agency20, Lawrence Berkeley National Laboratory21, ETH Zurich22, Hobart Corporation23, Woods Hole Oceanographic Institution24, Appalachian State University25, Wageningen University and Research Centre26, Montana State University27, Australian National University28, Université libre de Bruxelles29, Max Planck Society30, Japan Meteorological Agency31, University of New Hampshire32, Leibniz Institute of Marine Sciences33, Oeschger Centre for Climate Change Research34, Imperial College London35, Joint Institute for the Study of the Atmosphere and Ocean36, Lamont–Doherty Earth Observatory37, VU University Amsterdam38, Atlantic Oceanographic and Meteorological Laboratory39, Met Office40
TL;DR: In this paper, the authors present a methodology to quantify all major components of the global carbon budget, including their uncertainties, based on the combination of a range of data, algorithms, statistics, and model estimates and their interpretation by a broad scientific community.
Abstract: Accurate assessment of anthropogenic carbon dioxide (CO 2 ) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and a methodology to quantify all major components of the global carbon budget, including their uncertainties, based on the combination of a range of data, algorithms, statistics, and model estimates and their interpretation by a broad scientific community. We discuss changes compared to previous estimates, consistency within and among components, alongside methodology and data limitations. CO 2 emissions from fossil fuel combustion and cement production (E FF ) are based on energy statistics and cement production data, respectively, while emissions from land-use change (E LUC ), mainly deforestation, are based on combined evidence from land-cover-change data, fire activity associated with deforestation, and models. The global atmospheric CO 2 concentration is measured directly and its rate of growth (G ATM ) is computed from the annual changes in concentration. The mean ocean CO 2 sink (S OCEAN ) is based on observations from the 1990s, while the annual anomalies and trends are estimated with ocean models. The variability in S OCEAN is evaluated with data products based on surveys of ocean CO 2 measurements. The global residual terrestrial CO 2 sink (S LAND ) is estimated by the difference of the other terms of the global carbon budget and compared to results of independent dynamic global vegetation models forced by observed climate, CO 2 , and land-cover-change (some including nitrogen–carbon interactions). We compare the mean land and ocean fluxes and their variability to estimates from three atmospheric inverse methods for three broad latitude bands. All uncertainties are reported as ±1σ, reflecting the current capacity to characterise the annual estimates of each component of the global carbon budget. For the last decade available (2004–2013), E FF was 8.9 ± 0.4 GtC yr −1 , E LUC 0.9 ± 0.5 GtC yr −1 , G ATM 4.3 ± 0.1 GtC yr −1 , S OCEAN 2.6 ± 0.5 GtC yr −1 , and S LAND 2.9 ± 0.8 GtC yr −1 . For year 2013 alone, E FF grew to 9.9 ± 0.5 GtC yr −1 , 2.3% above 2012, continuing the growth trend in these emissions, E LUC was 0.9 ± 0.5 GtC yr −1 , G ATM was 5.4 ± 0.2 GtC yr −1 , S OCEAN was 2.9 ± 0.5 GtC yr −1 and S LAND was 2.5 ± 0.9 GtC yr −1 . G ATM was high in 2013, reflecting a steady increase in E FF and smaller and opposite changes between S OCEAN and S LAND compared to the past decade (2004–2013). The global atmospheric CO 2 concentration reached 395.31 ± 0.10 ppm averaged over 2013. We estimate that E FF will increase by 2.5% (1.3–3.5%) to 10.1 ± 0.6 GtC in 2014 (37.0 ± 2.2 GtCO 2 yr −1 ), 65% above emissions in 1990, based on projections of world gross domestic product and recent changes in the carbon intensity of the global economy. From this projection of E FF and assumed constant E LUC for 2014, cumulative emissions of CO 2 will reach about 545 ± 55 GtC (2000 ± 200 GtCO 2 ) for 1870–2014, about 75% from EF FF and 25% from E LUC . This paper documents changes in the methods and data sets used in this new carbon budget compared with previous publications of this living data set (Le Quere et al., 2013, 2014). All observations presented here can be downloaded from the Carbon Dioxide Information Analysis Center (doi:10.3334/CDIAC/GCP_2014).
01 Sep 2015
TL;DR: It is demonstrated that Cpf1 mediates robust DNA interference with features distinct from Cas9, and this mechanism of interference broadens the understanding of CRISPR-Cas systems and advances their genome editing applications.
Abstract: The microbial adaptive immune system CRISPR mediates defense against foreign genetic elements through two classes of RNA-guided nuclease effectors. Class 1 effectors utilize multi-protein complexes, whereas class 2 effectors rely on single-component effector proteins such as the well-characterized Cas9. Here, we report characterization of Cpf1, a putative class 2 CRISPR effector. We demonstrate that Cpf1 mediates robust DNA interference with features distinct from Cas9. Cpf1 is a single RNA-guided endonuclease lacking tracrRNA, and it utilizes a T-rich protospacer-adjacent motif. Moreover, Cpf1 cleaves DNA via a staggered DNA double-stranded break. Out of 16 Cpf1-family proteins, we identified two candidate enzymes from Acidaminococcus and Lachnospiraceae, with efficient genome-editing activity in human cells. Identifying this mechanism of interference broadens our understanding of CRISPR-Cas systems and advances their genome editing applications.
TL;DR: This work proposes the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard, to facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters.
Abstract: A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.
Aristotle University of Thessaloniki1, Centre national de la recherche scientifique2, Wageningen University and Research Centre3, Lund University4, University of Manchester5, Swedish University of Agricultural Sciences6, University of Copenhagen7, University of Giessen8, University of Marburg9, Academy of Sciences of the Czech Republic10, University of Helsinki11, University of Reading12, University of Kent13, University of Vienna14
TL;DR: Intensive agriculture reduces soil biodiversity, making soil food webs less diverse and composed of smaller bodied organisms, and how changes in soil biodiversity due to land-use intensification may threaten the functioning of soil in agricultural production systems is discussed.
Abstract: Soil biodiversity plays a key role in regulating the processes that underpin the delivery of ecosystem goods and services in terrestrial ecosystems. Agricultural intensification is known to change the diversity of individual groups of soil biota, but less is known about how intensification affects biodiversity of the soil food web as a whole, and whether or not these effects may be generalized across regions. We examined biodiversity in soil food webs from grasslands, extensive, and intensive rotations in four agricultural regions across Europe: in Sweden, the UK, the Czech Republic and Greece. Effects of land-use intensity were quantified based on structure and diversity among functional groups in the soil food web, as well as on community-weighted mean body mass of soil fauna. We also elucidate land-use intensity effects on diversity of taxonomic units within taxonomic groups of soil fauna. We found that between regions soil food web diversity measures were variable, but that increasing land-use intensity caused highly consistent responses. In particular, land-use intensification reduced the complexity in the soil food webs, as well as the community-weighted mean body mass of soil fauna. In all regions across Europe, species richness of earthworms, Collembolans, and oribatid mites was negatively affected by increased land-use intensity. The taxonomic distinctness, which is a measure of taxonomic relatedness of species in a community that is independent of species richness, was also reduced by land-use intensification. We conclude that intensive agriculture reduces soil biodiversity, making soil food webs less diverse and composed of smaller bodied organisms. Land-use intensification results in fewer functional groups of soil biota with fewer and taxonomically more closely related species. We discuss how these changes in soil biodiversity due to land-use intensification may threaten the functioning of soil in agricultural production systems.
01 Jan 2015
TL;DR: In future records of interactions between marine debris and wildlife, it is recommended to focus on standardized data on frequency of occurrence and quantities of debris ingested, to allow more detailed assessments of the deleterious effects of marine debris on individuals and populations.
Abstract: In this review we report new findings concerning interaction between marine debris and wildlife. Deleterious effects and consequences of entanglement, consumption and smothering are highlighted and discussed. The number of species known to have been affected by either entanglement or ingestion of plastic debris has doubled since 1997, from 267 to 557 species among all groups of wildlife. For marine turtles the number of affected species increased from 86 to 100 % (now 7 of 7 species), for marine mammals from 43 to 66 % (now 81 of 123 species) and for seabirds from 44 to 50 % of species (now 203 of 406 species). Strong increases in records were also listed for fish and invertebrates, groups that were previously not considered in detail. In future records of interactions between marine debris and wildlife we recommend to focus on standardized data on frequency of occurrence and quantities of debris ingested. In combination with dedicated impact studies in the wild or experiments, this will allow more detailed assessments of the deleterious effects of marine debris on individuals and populations.
Thomas W. Winkler1, Anne E. Justice2, Mariaelisa Graff2, Llilda Barata3 +435 more•Institutions (106)
TL;DR: In this paper, the authors performed meta-analyses of 114 studies with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT) Consortium.
Abstract: Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age- and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of European descent) with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT) Consortium. Each study tested the association of up to ~2.8M SNPs with BMI and WHRadjBMI in four strata (men ≤50y, men >50y, women ≤50y, women >50y) and summary statistics were combined in stratum-specific meta-analyses. We then screened for variants that showed age-specific effects (G x AGE), sex-specific effects (G x SEX) or age-specific effects that differed between men and women (G x AGE x SEX). For BMI, we identified 15 loci (11 previously established for main effects, four novel) that showed significant (FDR<5%) age-specific effects, of which 11 had larger effects in younger (<50y) than in older adults (≥50y). No sex-dependent effects were identified for BMI. For WHRadjBMI, we identified 44 loci (27 previously established for main effects, 17 novel) with sex-specific effects, of which 28 showed larger effects in women than in men, five showed larger effects in men than in women, and 11 showed opposite effects between sexes. No age-dependent effects were identified for WHRadjBMI. This is the first genome-wide interaction meta-analysis to report convincing evidence of age-dependent genetic effects on BMI. In addition, we confirm the sex-specificity of genetic effects on WHRadjBMI. These results may provide further insights into the biology that underlies weight change with age or the sexually dimorphism of body shape.
Norwich Research Park1, University of California, Riverside2, University of Florida3, West Bengal State University4, Mediterranea University of Reggio Calabria5, Agro ParisTech6, University of Nice Sophia Antipolis7, Deakin University8, National Research Council9, College of Horticulture10, University of Massachusetts Amherst11, James Hutton Institute12, University of Tennessee13, Agriculture and Agri-Food Canada14, Oregon State University15, Agricultural Research Service16, University of Alabama at Birmingham17, University of Warwick18, University of Worcester19, Utrecht University20, Virginia Tech21, University of Manitoba22, Cornell University23, International Potato Center24, Wageningen University and Research Centre25, Institut national de la recherche agronomique26, North Carolina State University27
TL;DR: A survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance received 263 votes from 62 scientists in 15 countries for a total of 33 species and the Top 10 species are provided.
Abstract: Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.