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Showing papers by "Wageningen University and Research Centre published in 2011"


Journal ArticleDOI
12 May 2011-Nature
TL;DR: Three robust clusters (referred to as enterotypes hereafter) are identified that are not nation or continent specific and confirmed in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous.
Abstract: Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.

5,566 citations


Journal ArticleDOI
15 Jul 2011-Science
TL;DR: This empirical work supports long-standing theory about the role of top-down forcing in ecosystems but also highlights the unanticipated impacts of trophic cascades on processes as diverse as the dynamics of disease, wildfire, carbon sequestration, invasive species, and biogeochemical cycles.
Abstract: Until recently, large apex consumers were ubiquitous across the globe and had been for millions of years. The loss of these animals may be humankind's most pervasive influence on nature. Although such losses are widely viewed as an ethical and aesthetic problem, recent research reveals extensive cascading effects of their disappearance in marine, terrestrial, and freshwater ecosystems worldwide. This empirical work supports long-standing theory about the role of top-down forcing in ecosystems but also highlights the unanticipated impacts of trophic cascades on processes as diverse as the dynamics of disease, wildfire, carbon sequestration, invasive species, and biogeochemical cycles. These findings emphasize the urgent need for interdisciplinary research to forecast the effects of trophic downgrading on process, function, and resilience in global ecosystems.

3,130 citations


Journal ArticleDOI
Jens Kattge1, Sandra Díaz2, Sandra Lavorel3, Iain Colin Prentice4, Paul Leadley5, Gerhard Bönisch1, Eric Garnier3, Mark Westoby4, Peter B. Reich6, Peter B. Reich7, Ian J. Wright4, Johannes H. C. Cornelissen8, Cyrille Violle3, Sandy P. Harrison4, P.M. van Bodegom8, Markus Reichstein1, Brian J. Enquist9, Nadejda A. Soudzilovskaia8, David D. Ackerly10, Madhur Anand11, Owen K. Atkin12, Michael Bahn13, Timothy R. Baker14, Dennis D. Baldocchi10, Renée M. Bekker15, Carolina C. Blanco16, Benjamin Blonder9, William J. Bond17, Ross A. Bradstock18, Daniel E. Bunker19, Fernando Casanoves20, Jeannine Cavender-Bares7, Jeffrey Q. Chambers21, F. S. Chapin22, Jérôme Chave3, David A. Coomes23, William K. Cornwell8, Joseph M. Craine24, B. H. Dobrin9, Leandro da Silva Duarte16, Walter Durka25, James J. Elser26, Gerd Esser27, Marc Estiarte28, William F. Fagan29, Jingyun Fang, Fernando Fernández-Méndez30, Alessandra Fidelis31, Bryan Finegan20, Olivier Flores32, H. Ford33, Dorothea Frank1, Grégoire T. Freschet34, Nikolaos M. Fyllas14, Rachael V. Gallagher4, Walton A. Green35, Alvaro G. Gutiérrez25, Thomas Hickler, Steven I. Higgins36, John G. Hodgson37, Adel Jalili, Steven Jansen38, Carlos Alfredo Joly39, Andrew J. Kerkhoff40, Don Kirkup41, Kaoru Kitajima42, Michael Kleyer43, Stefan Klotz25, Johannes M. H. Knops44, Koen Kramer, Ingolf Kühn16, Hiroko Kurokawa45, Daniel C. Laughlin46, Tali D. Lee47, Michelle R. Leishman4, Frederic Lens48, Tanja Lenz4, Simon L. Lewis14, Jon Lloyd49, Jon Lloyd14, Joan Llusià28, Frédérique Louault50, Siyan Ma10, Miguel D. Mahecha1, Peter Manning51, Tara Joy Massad1, Belinda E. Medlyn4, Julie Messier9, Angela T. Moles52, Sandra Cristina Müller16, Karin Nadrowski53, Shahid Naeem54, Ülo Niinemets55, S. Nöllert1, A. Nüske1, Romà Ogaya28, Jacek Oleksyn56, Vladimir G. Onipchenko57, Yusuke Onoda58, Jenny C. Ordoñez59, Gerhard E. Overbeck16, Wim A. Ozinga59, Sandra Patiño14, Susana Paula60, Juli G. Pausas60, Josep Peñuelas28, Oliver L. Phillips14, Valério D. Pillar16, Hendrik Poorter, Lourens Poorter59, Peter Poschlod61, Andreas Prinzing62, Raphaël Proulx63, Anja Rammig64, Sabine Reinsch65, Björn Reu1, Lawren Sack66, Beatriz Salgado-Negret20, Jordi Sardans28, Satomi Shiodera67, Bill Shipley68, Andrew Siefert69, Enio E. Sosinski70, Jean-François Soussana50, Emily Swaine71, Nathan G. Swenson72, Ken Thompson37, Peter E. Thornton73, Matthew S. Waldram74, Evan Weiher47, Michael T. White75, S. White11, S. J. Wright76, Benjamin Yguel3, Sönke Zaehle1, Amy E. Zanne77, Christian Wirth58 
Max Planck Society1, National University of Cordoba2, Centre national de la recherche scientifique3, Macquarie University4, University of Paris-Sud5, University of Western Sydney6, University of Minnesota7, VU University Amsterdam8, University of Arizona9, University of California, Berkeley10, University of Guelph11, Australian National University12, University of Innsbruck13, University of Leeds14, University of Groningen15, Universidade Federal do Rio Grande do Sul16, University of Cape Town17, University of Wollongong18, New Jersey Institute of Technology19, Centro Agronómico Tropical de Investigación y Enseñanza20, Lawrence Berkeley National Laboratory21, University of Alaska Fairbanks22, University of Cambridge23, Kansas State University24, Helmholtz Centre for Environmental Research - UFZ25, Arizona State University26, University of Giessen27, Autonomous University of Barcelona28, University of Maryland, College Park29, Universidad del Tolima30, University of São Paulo31, University of La Réunion32, University of York33, University of Sydney34, Harvard University35, Goethe University Frankfurt36, University of Sheffield37, University of Ulm38, State University of Campinas39, Kenyon College40, Royal Botanic Gardens41, University of Florida42, University of Oldenburg43, University of Nebraska–Lincoln44, Tohoku University45, Northern Arizona University46, University of Wisconsin–Eau Claire47, Naturalis48, James Cook University49, Institut national de la recherche agronomique50, Newcastle University51, University of New South Wales52, Leipzig University53, Columbia University54, Estonian University of Life Sciences55, Polish Academy of Sciences56, Moscow State University57, Kyushu University58, Wageningen University and Research Centre59, Spanish National Research Council60, University of Regensburg61, University of Rennes62, Université du Québec à Trois-Rivières63, Potsdam Institute for Climate Impact Research64, Technical University of Denmark65, University of California, Los Angeles66, Hokkaido University67, Université de Sherbrooke68, Syracuse University69, Empresa Brasileira de Pesquisa Agropecuária70, University of Aberdeen71, Michigan State University72, Oak Ridge National Laboratory73, University of Leicester74, Utah State University75, Smithsonian Institution76, University of Missouri77
01 Sep 2011
TL;DR: TRY as discussed by the authors is a global database of plant traits, including morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs, which can be used for a wide range of research from evolutionary biology, community and functional ecology to biogeography.
Abstract: Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.

2,017 citations


Journal ArticleDOI
TL;DR: In this paper, the evolutionary relationship between CRISPR-Cas and Cas proteins is analyzed and a unified classification of these systems is proposed based on multiple criteria. But, the classification is based on the phylogenies of the most common cas genes, the sequence and organization of the CRISpr repeats and the architecture of the Cas loci.
Abstract: The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) modules are adaptive immunity systems that are present in many archaea and bacteria. These defence systems are encoded by operons that have an extraordinarily diverse architecture and a high rate of evolution for both the cas genes and the unique spacer content. Here, we provide an updated analysis of the evolutionary relationships between CRISPR-Cas systems and Cas proteins. Three major types of CRISPR-Cas system are delineated, with a further division into several subtypes and a few chimeric variants. Given the complexity of the genomic architectures and the extremely dynamic evolution of the CRISPR-Cas systems, a unified classification of these systems should be based on multiple criteria. Accordingly, we propose a 'polythetic' classification that integrates the phylogenies of the most common cas genes, the sequence and organization of the CRISPR repeats and the architecture of the CRISPR-cas loci.

2,011 citations


Journal ArticleDOI
27 May 2011-Science
TL;DR: It is indicated that upon attack by a fungal root pathogen, plants can exploit microbial consortia from soil for protection against infections.
Abstract: Disease-suppressive soils are exceptional ecosystems in which crop plants suffer less from specific soil-borne pathogens than expected owing to the activities of other soil microorganisms. For most disease-suppressive soils, the microbes and mechanisms involved in pathogen control are unknown. By coupling PhyloChip-based metagenomics of the rhizosphere microbiome with culture-dependent functional analyses, we identified key bacterial taxa and genes involved in suppression of a fungal root pathogen. More than 33,000 bacterial and archaeal species were detected, with Proteobacteria, Firmicutes, and Actinobacteria consistently associated with disease suppression. Members of the γ-Proteobacteria were shown to have disease-suppressive activity governed by nonribosomal peptide synthetases. Our data indicate that upon attack by a fungal root pathogen, plants can exploit microbial consortia from soil for protection against infections.

1,948 citations


Journal ArticleDOI
Xun Xu1, Shengkai Pan1, Shifeng Cheng1, Bo Zhang1, Mu D1, Peixiang Ni1, Gengyun Zhang1, Shuang Yang1, Ruiqiang Li1, Jun Wang1, Gisella Orjeda2, Frank Guzman2, Torres M2, Roberto Lozano2, Olga Ponce2, Diana Martinez2, De la Cruz G3, Chakrabarti Sk3, Patil Vu3, Konstantin G. Skryabin4, Boris B. Kuznetsov4, Nikolai V. Ravin4, Tatjana V. Kolganova4, Alexey V. Beletsky4, Andrey V. Mardanov4, Di Genova A5, Dan Bolser5, David M. A. Martin5, Li G, Yang Y, Hanhui Kuang6, Hu Q6, Xiong X7, Gerard J. Bishop8, Boris Sagredo, Nilo Mejía, Zagorski W9, Robert Gromadka9, Jan Gawor9, Pawel Szczesny9, Sanwen Huang, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Youjun Zhang, Xie B, Du Y, Qu D, Merideth Bonierbale10, Marc Ghislain10, Herrera Mdel R, Giovanni Giuliano, Marco Pietrella, Gaetano Perrotta, Paolo Facella, O'Brien K11, Sergio Enrique Feingold, Barreiro Le, Massa Ga, Luis Aníbal Diambra12, Brett R Whitty13, Brieanne Vaillancourt13, Lin H13, Alicia N. Massa13, Geoffroy M13, Lundback S13, Dean DellaPenna13, Buell Cr14, Sanjeev Kumar Sharma14, David Marshall14, Robbie Waugh14, Glenn J. Bryan14, Destefanis M15, Istvan Nagy15, Dan Milbourne15, Susan Thomson16, Mark Fiers16, Jeanne M. E. Jacobs16, Kåre Lehmann Nielsen17, Mads Sønderkær17, Marina Iovene18, Giovana Augusta Torres18, Jiming Jiang18, Richard E. Veilleux19, Christian W. B. Bachem20, de Boer J20, Theo Borm20, Bjorn Kloosterman20, van Eck H20, Erwin Datema20, Hekkert Bt20, Aska Goverse20, van Ham Rc20, Richard G. F. Visser20 
10 Jul 2011-Nature
TL;DR: The potato genome sequence provides a platform for genetic improvement of this vital crop and predicts 39,031 protein-coding genes and presents evidence for at least two genome duplication events indicative of a palaeopolyploid origin.
Abstract: Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

1,813 citations


Journal ArticleDOI
Xiaowu Wang1, Hanzhong Wang, Jun Wang2, Jun Wang3, Jun Wang4, Rifei Sun, Jian Wu, Shengyi Liu, Yinqi Bai2, Jeong-Hwan Mun5, Ian Bancroft6, Feng Cheng, Sanwen Huang, Xixiang Li, Wei Hua, Junyi Wang2, Xiyin Wang7, Xiyin Wang8, Michael Freeling9, J. Chris Pires10, Andrew H. Paterson8, Boulos Chalhoub, Bo Wang2, Alice Hayward11, Alice Hayward12, Andrew G. Sharpe13, Beom-Seok Park5, Bernd Weisshaar14, Binghang Liu2, Bo Li2, Bo Liu, Chaobo Tong, Chi Song2, Chris Duran12, Chris Duran15, Chunfang Peng2, Geng Chunyu2, Chushin Koh13, Chuyu Lin2, David Edwards12, David Edwards15, Desheng Mu2, Di Shen, Eleni Soumpourou6, Fei Li, Fiona Fraser6, Gavin C. Conant10, Gilles Lassalle16, Graham J.W. King3, Guusje Bonnema17, Haibao Tang9, Haiping Wang, Harry Belcram, Heling Zhou2, Hideki Hirakawa, Hiroshi Abe, Hui Guo8, Hui Wang, Huizhe Jin8, Isobel A. P. Parkin18, Jacqueline Batley11, Jacqueline Batley12, Jeong-Sun Kim5, Jérémy Just, Jianwen Li2, Jiaohui Xu2, Jie Deng, Jin A Kim5, Jingping Li8, Jingyin Yu, Jinling Meng19, Jinpeng Wang7, Jiumeng Min2, Julie Poulain20, Katsunori Hatakeyama, Kui Wu2, Li Wang7, Lu Fang, Martin Trick6, Matthew G. Links18, Meixia Zhao, Mina Jin5, Nirala Ramchiary21, Nizar Drou22, Paul J. Berkman12, Paul J. Berkman15, Qingle Cai2, Quanfei Huang2, Ruiqiang Li2, Satoshi Tabata, Shifeng Cheng2, Shu Zhang2, Shujiang Zhang, Shunmou Huang, Shusei Sato, Silong Sun, Soo-Jin Kwon5, Su-Ryun Choi21, Tae-Ho Lee8, Wei Fan2, Xiang Zhao2, Xu Tan8, Xun Xu2, Yan Wang, Yang Qiu, Ye Yin2, Yingrui Li2, Yongchen Du, Yongcui Liao, Yong Pyo Lim21, Yoshihiro Narusaka, Yupeng Wang7, Zhenyi Wang7, Zhenyu Li2, Zhiwen Wang2, Zhiyong Xiong10, Zhonghua Zhang 
TL;DR: The annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage, and used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution.
Abstract: We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.

1,811 citations


Journal ArticleDOI
TL;DR: This work presents the first comprehensive pipeline capable of identifying biosynthetic loci covering the whole range of known secondary metabolite compound classes, and integrates or cross-links all previously available secondary-metabolite specific gene analysis methods in one interactive view.
Abstract: Bacterial and fungal secondary metabolism is a rich source of novel bioactive compounds with potential pharmaceutical applications as antibiotics, anti-tumor drugs or cholesterol-lowering drugs To find new drug candidates, microbiologists are increasingly relying on sequencing genomes of a wide variety of microbes However, rapidly and reliably pinpointing all the potential gene clusters for secondary metabolites in dozens of newly sequenced genomes has been extremely challenging, due to their biochemical heterogeneity, the presence of unknown enzymes and the dispersed nature of the necessary specialized bioinformatics tools and resources Here, we present antiSMASH (antibiotics & Secondary Metabolite Analysis Shell), the first comprehensive pipeline capable of identifying biosynthetic loci covering the whole range of known secondary metabolite compound classes (polyketides, non-ribosomal peptides, terpenes, aminoglycosides, aminocoumarins, indolocarbazoles, lantibiotics, bacteriocins, nucleosides, beta-lactams, butyrolactones, siderophores, melanins and others) It aligns the identified regions at the gene cluster level to their nearest relatives from a database containing all other known gene clusters, and integrates or cross-links all previously available secondary-metabolite specific gene analysis methods in one interactive view antiSMASH is available at http://antismashsecondarymetabolitesorg

1,496 citations


Journal ArticleDOI
08 Sep 2011-Nature
TL;DR: It is shown that 84% of the 147 grassland plant species studied in 17 biodiversity experiments promoted ecosystem functioning at least once, and many species are needed to maintain multiple functions at multiple times and places in a changing world.
Abstract: Biodiversity is rapidly declining worldwide, and there is consensus that this can decrease ecosystem functioning and services. It remains unclear, though, whether few or many of the species in an ecosystem are needed to sustain the provisioning of ecosystem services. It has been hypothesized that most species would promote ecosystem services if many times, places, functions and environmental changes were considered; however, no previous study has considered all of these factors together. Here we show that 84% of the 147 grassland plant species studied in 17 biodiversity experiments promoted ecosystem functioning at least once. Different species promoted ecosystem functioning during different years, at different places, for different functions and under different environmental change scenarios. Furthermore, the species needed to provide one function during multiple years were not the same as those needed to provide multiple functions within one year. Our results indicate that even more species will be needed to maintain ecosystem functioning and services than previously suggested by studies that have either (1) considered only the number of species needed to promote one function under one set of environmental conditions, or (2) separately considered the importance of biodiversity for providing ecosystem functioning across multiple years, places, functions or environmental change scenarios. Therefore, although species may appear functionally redundant when one function is considered under one set of environmental conditions, many species are needed to maintain multiple functions at multiple times and places in a changing world.

1,268 citations


Journal ArticleDOI
25 Oct 2011
TL;DR: The Anthropocene is a reminder that the Holocene, during which complex human societies have developed, has been a stable, accommodating environment and is the only state of the Earth System that the authors know for sure can support contemporary society.
Abstract: Over the past century, the total material wealth of humanity has been enhanced. However, in the twenty-first century, we face scarcity in critical resources, the degradation of ecosystem services, and the erosion of the planet’s capability to absorb our wastes. Equity issues remain stubbornly difficult to solve. This situation is novel in its speed, its global scale and its threat to the resilience of the Earth System. The advent of the Anthropence, the time interval in which human activities now rival global geophysical processes, suggests that we need to fundamentally alter our relationship with the planet we inhabit. Many approaches could be adopted, ranging from geo-engineering solutions that purposefully manipulate parts of the Earth System to becoming active stewards of our own life support system. The Anthropocene is a reminder that the Holocene, during which complex human societies have developed, has been a stable, accommodating environment and is the only state of the Earth System that we know for sure can support contemporary society. The need to achieve effective planetary stewardship is urgent. As we go further into the Anthropocene, we risk driving the Earth System onto a trajectory toward more hostile states from which we cannot easily return.

1,222 citations


Journal ArticleDOI
TL;DR: This article used repeat photography, long-term ecological monitoring and dendrochronology to document shrub expansion in arctic, high-latitude and alpine tundra.
Abstract: Recent research using repeat photography, long-term ecological monitoring and dendrochronology has documented shrub expansion in arctic, high-latitude and alpine tundra


Journal ArticleDOI
TL;DR: Attention is paid to mobile genetic elements such as plasmids, transposons, and integrons, which are associated with AR genes, and involved in the dispersal of antimicrobial determinants between different bacteria.
Abstract: In this review an overview is given on antibiotic resistance (AR) mechanisms with special attentions to the AR genes described so far preceded by a short introduction on the discovery and mode of action of the different classes of antibiotics. As this review is only dealing with acquired resistance, attention is also paid to mobile genetic elements such as plasmids, transposons, and integrons, which are associated with AR genes, and involved in the dispersal of antimicrobial determinants between different bacteria.

Journal ArticleDOI
14 Oct 2011-Science
TL;DR: Empirical reconstruction of the basins of attraction indicates that the resilience of the states varies in a universal way with precipitation, and this results allow the identification of regions where forest or savanna may most easily tip into an alternative state.
Abstract: It has been suggested that tropical forest and savanna could represent alternative stable states, implying critical transitions at tipping points in response to altered climate or other drivers. So far, evidence for this idea has remained elusive, and integrated climate models assume smooth vegetation responses. We analyzed data on the distribution of tree cover in Africa, Australia, and South America to reveal strong evidence for the existence of three distinct attractors: forest, savanna, and a treeless state. Empirical reconstruction of the basins of attraction indicates that the resilience of the states varies in a universal way with precipitation. These results allow the identification of regions where forest or savanna may most easily tip into an alternative state, and they pave the way to a new generation of coupled climate models.

Journal ArticleDOI
TL;DR: In this paper, the authors upscaled FLUXNET observations of carbon dioxide, water, and energy fluxes to the global scale using the machine learning technique, model tree ensembles (MTE), to predict site-level gross primary productivity (GPP), terrestrial ecosystem respiration (TER), net ecosystem exchange (NEE), latent energy (LE), and sensible heat (H) based on remote sensing indices, climate and meteorological data, and information on land use.
Abstract: We upscaled FLUXNET observations of carbon dioxide, water, and energy fluxes to the global scale using the machine learning technique, model tree ensembles (MTE). We trained MTE to predict site-level gross primary productivity (GPP), terrestrial ecosystem respiration (TER), net ecosystem exchange (NEE), latent energy (LE), and sensible heat (H) based on remote sensing indices, climate and meteorological data, and information on land use. We applied the trained MTEs to generate global flux fields at a 0.5 degrees x 0.5 degrees spatial resolution and a monthly temporal resolution from 1982 to 2008. Cross-validation analyses revealed good performance of MTE in predicting among-site flux variability with modeling efficiencies (MEf) between 0.64 and 0.84, except for NEE (MEf = 0.32). Performance was also good for predicting seasonal patterns (MEf between 0.84 and 0.89, except for NEE (0.64)). By comparison, predictions of monthly anomalies were not as strong (MEf between 0.29 and 0.52). Improved accounting of disturbance and lagged environmental effects, along with improved characterization of errors in the training data set, would contribute most to further reducing uncertainties. Our global estimates of LE (158 +/- 7 J x 10(18) yr(-1)), H (164 +/- 15 J x 10(18) yr(-1)), and GPP (119 +/- 6 Pg C yr(-1)) were similar to independent estimates. Our global TER estimate (96 +/- 6 Pg C yr(-1)) was likely underestimated by 5-10%. Hot spot regions of interannual variability in carbon fluxes occurred in semiarid to semihumid regions and were controlled by moisture supply. Overall, GPP was more important to interannual variability in NEE than TER. Our empirically derived fluxes may be used for calibration and evaluation of land surface process models and for exploratory and diagnostic assessments of the biosphere.

Journal ArticleDOI
TL;DR: The human intestinal epithelium is formed by a single layer of epithelial cells that separates the intestinal lumen from the underlying lamina propria, which is sealed by tight junctions (TJ), which regulate the permeability of the intestinal barrier.
Abstract: The human intestinal epithelium is formed by a single layer of epithelial cells that separates the intestinal lumen from the underlying lamina propria. The space between these cells is sealed by tight junctions (TJ), which regulate the permeability of the intestinal barrier. TJ are complex protein structures comprised of transmembrane proteins, which interact with the actin cytoskeleton via plaque proteins. Signaling pathways involved in the assembly, disassembly, and maintenance of TJ are controlled by a number of signaling molecules, such as protein kinase C, mitogen-activated protein kinases, myosin light chain kinase, and Rho GTPases. The intestinal barrier is a complex environment exposed to many dietary components and many commensal bacteria. Studies have shown that the intestinal bacteria target various intracellular pathways, change the expression and distribution of TJ proteins, and thereby regulate intestinal barrier function. The presence of some commensal and probiotic strains leads to an increase in TJ proteins at the cell boundaries and in some cases prevents or reverses the adverse effects of pathogens. Various dietary components are also known to regulate epithelial permeability by modifying expression and localization of TJ proteins.

Journal ArticleDOI
TL;DR: It is argued that plant resistance is determined by immune receptors that recognize appropriate ligands to activate defense, the amplitude of which is likely determined by the level required for effective immunity.
Abstract: Typically, pathogen-associated molecular patterns (PAMPs) are considered to be conserved throughout classes of microbes and to contribute to general microbial fitness, whereas effectors are species, race, or strain specific and contribute to pathogen virulence. Both types of molecule can trigger plant immunity, designated PAMP-triggered and effector-triggered immunity (PTI and ETI, respectively). However, not all microbial defense activators conform to the common distinction between PAMPs and effectors. For example, some effectors display wide distribution, while some PAMPs are rather narrowly conserved or contribute to pathogen virulence. As effectors may elicit defense responses and PAMPs may be required for virulence, single components cannot exclusively be referred to by one of the two terms. Therefore, we put forward that the distinction between PAMPs and effectors, between PAMP receptors and resistance proteins, and, therefore, also between PTI and ETI, cannot strictly be maintained. Rather, as illustrated by examples provided here, there is a continuum between PTI and ETI. We argue that plant resistance is determined by immune receptors that recognize appropriate ligands to activate defense, the amplitude of which is likely determined by the level required for effective immunity.

Journal ArticleDOI
TL;DR: Global and deep molecular analysis of fecal samples indicates that patients with IBS have a different composition of microbiota, and correlation analysis of the microbial groups indicated the involvement of several groups of Firmicutes and Proteobacteria in the pathogenesis of IBS.

Journal ArticleDOI
TL;DR: Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea, and shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating.
Abstract: Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to ,1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.

Journal ArticleDOI
TL;DR: In this article, the results of a broad intercomparison of a total of 15 global aerosol models within the AeroCom project are compared to observations related to desert dust aerosols, their direct radiative effect, and their impact on the biogeochemical cycle, i.e., aerosol optical depth and dust deposition.
Abstract: . This study presents the results of a broad intercomparison of a total of 15 global aerosol models within the AeroCom project. Each model is compared to observations related to desert dust aerosols, their direct radiative effect, and their impact on the biogeochemical cycle, i.e., aerosol optical depth (AOD) and dust deposition. Additional comparisons to Angstrom exponent (AE), coarse mode AOD and dust surface concentrations are included to extend the assessment of model performance and to identify common biases present in models. These data comprise a benchmark dataset that is proposed for model inspection and future dust model development. There are large differences among the global models that simulate the dust cycle and its impact on climate. In general, models simulate the climatology of vertically integrated parameters (AOD and AE) within a factor of two whereas the total deposition and surface concentration are reproduced within a factor of 10. In addition, smaller mean normalized bias and root mean square errors are obtained for the climatology of AOD and AE than for total deposition and surface concentration. Characteristics of the datasets used and their uncertainties may influence these differences. Large uncertainties still exist with respect to the deposition fluxes in the southern oceans. Further measurements and model studies are necessary to assess the general model performance to reproduce dust deposition in ocean regions sensible to iron contributions. Models overestimate the wet deposition in regions dominated by dry deposition. They generally simulate more realistic surface concentration at stations downwind of the main sources than at remote ones. Most models simulate the gradient in AOD and AE between the different dusty regions. However the seasonality and magnitude of both variables is better simulated at African stations than Middle East ones. The models simulate the offshore transport of West Africa throughout the year but they overestimate the AOD and they transport too fine particles. The models also reproduce the dust transport across the Atlantic in the summer in terms of both AOD and AE but not so well in winter-spring nor the southward displacement of the dust cloud that is responsible of the dust transport into South America. Based on the dependency of AOD on aerosol burden and size distribution we use model bias with respect to AOD and AE to infer the bias of the dust emissions in Africa and the Middle East. According to this analysis we suggest that a range of possible emissions for North Africa is 400 to 2200 Tg yr−1 and in the Middle East 26 to 526 Tg yr−1.

Journal ArticleDOI
12 Aug 2011-Science
TL;DR: The isolation and characterization of a human monoclonal antibody CR8020 with broad neutralizing activity against most group 2 viruses, including H3N2 and H7N7, which cause severe human infection are reported.
Abstract: Current flu vaccines provide only limited coverage against seasonal strains of influenza viruses. The identification of VH1-69 antibodies that broadly neutralize almost all influenza A group 1 viruses constituted a breakthrough in the influenza field. Here, we report the isolation and characterization of a human monoclonal antibody CR8020 with broad neutralizing activity against most group 2 viruses, including H3N2 and H7N7, which cause severe human infection. The crystal structure of Fab CR8020 with the 1968 pandemic H3 hemagglutinin (HA) reveals a highly conserved epitope in the HA stalk distinct from the epitope recognized by the VH1-69 group 1 antibodies. Thus, a cocktail of two antibodies may be sufficient to neutralize most influenza A subtypes and, hence, enable development of a universal flu vaccine and broad-spectrum antibody therapies.

Journal ArticleDOI
TL;DR: This paper examines the full spectrum of sustainable phosphorus recovery and reuse options (from small-scale low-cost to large-scale high-tech), facilitates integrated decision-making and identifies future opportunities and challenges for achieving global phosphorus security.

Journal ArticleDOI
TL;DR: It is proposed that the crRNA seed sequence plays a role in the initial scanning of invader DNA for a match, before base pairing of the full-length spacer occurs, which may enhance the protospacer locating efficiency of the E. coli Cascade complex.
Abstract: Prokaryotic clustered regularly interspaced short palindromic repeat (CRISPR)/Cas (CRISPR-associated sequences) systems provide adaptive immunity against viruses when a spacer sequence of small CRISPR RNA (crRNA) matches a protospacer sequence in the viral genome. Viruses that escape CRISPR/Cas resistance carry point mutations in protospacers, though not all protospacer mutations lead to escape. Here, we show that in the case of Escherichia coli subtype CRISPR/Cas system, the requirements for crRNA matching are strict only for a seven-nucleotide seed region of a protospacer immediately following the essential protospacer-adjacent motif. Mutations in the seed region abolish CRISPR/Cas mediated immunity by reducing the binding affinity of the crRNA-guided Cascade complex to protospacer DNA. We propose that the crRNA seed sequence plays a role in the initial scanning of invader DNA for a match, before base pairing of the full-length spacer occurs, which may enhance the protospacer locating efficiency of the E. coli Cascade complex. In agreement with this proposal, single or multiple mutations within the protospacer but outside the seed region do not lead to escape. The relaxed specificity of the CRISPR/Cas system limits escape possibilities and allows a single crRNA to effectively target numerous related viruses.

Journal ArticleDOI
06 Jun 2011-PLOS ONE
TL;DR: High intake of red and processed meat is associated with significant increased risk of colorectal, colon and rectal cancers, and the overall evidence of prospective studies supports limiting red and processing meat consumption as one of the dietary recommendations for the prevention of colOREctal cancer.
Abstract: Background The evidence that red and processed meat influences colorectal carcinogenesis was judged convincing in the 2007 World Cancer Research Fund/American Institute of Cancer Research report. Since then, ten prospective studies have published new results. Here we update the evidence from prospective studies and explore whether there is a non-linear association of red and processed meats with colorectal cancer risk. Methods and Findings Relevant prospective studies were identified in PubMed until March 2011. For each study, relative risks and 95% confidence intervals (CI) were extracted and pooled with a random-effects model, weighting for the inverse of the variance, in highest versus lowest intake comparison, and dose-response meta-analyses. Red and processed meats intake was associated with increased colorectal cancer risk. The summary relative risk (RR) of colorectal cancer for the highest versus the lowest intake was 1.22 (95% CI = 1.11−1.34) and the RR for every 100 g/day increase was 1.14 (95% CI = 1.04−1.24). Non-linear dose-response meta-analyses revealed that colorectal cancer risk increases approximately linearly with increasing intake of red and processed meats up to approximately 140 g/day, where the curve approaches its plateau. The associations were similar for colon and rectal cancer risk. When analyzed separately, colorectal cancer risk was related to intake of fresh red meat (RR for 100 g/day increase = 1.17, 95% CI = 1.05−1.31) and processed meat (RR for 50 g/day increase = 1.18, 95% CI = 1.10−1.28). Similar results were observed for colon cancer, but for rectal cancer, no significant associations were observed. Conclusions High intake of red and processed meat is associated with significant increased risk of colorectal, colon and rectal cancers. The overall evidence of prospective studies supports limiting red and processed meat consumption as one of the dietary recommendations for the prevention of colorectal cancer.

Journal ArticleDOI
TL;DR: Photobioreactors may become attractive for microalgal biofuel production and become a promising feedstock for biodiesel and bulk chemicals at a cost level below € 0.68 per kg.

Journal ArticleDOI
TL;DR: In this article, the authors introduce a measure of Social Value Orientation (SVO), which measures the magnitude of the concern people have for others, sometimes referred to as social value orientation, and provide evidence of its solid psychometric properties.
Abstract: Narrow self-interest is often used as a simplifying assumption when studying people making decisions in social contexts. Nonetheless, people exhibit a wide range of different motivations when choosing unilaterally among interdependent outcomes. Measuring the magnitude of the concern people have for others, sometimes called Social Value Orientation (SVO), has been an interest of many social scientists for decades and several different measurement methods have been developed so far. Here we introduce a new measure of SVO that has several advantages over existent methods. A detailed description of the new measurement method is presented, along with norming data that provide evidence of its solid psychometric properties. We conclude with a brief discussion of the research streams that would benefit from a more sensitive and higher resolution measure of SVO, and extend an invitation to others to use this new measure which is freely available

Journal ArticleDOI
Olle Terenius1, Alexie Papanicolaou2, Alexie Papanicolaou3, Jennie S. Garbutt4, Ioannis Eleftherianos5, Hanneke Huvenne6, Sriramana Kanginakudru7, Merete Albrechtsen8, Chunju An9, Jean Luc Aymeric10, Andrea Barthel11, Piotr Bebas12, Kavita Bitra13, Alejandra Bravo14, François Chevalier10, Derek Collinge15, Derek Collinge3, Cristina M. Crava16, Ruud A. de Maagd17, Bernard Duvic10, Martin A. Erlandson18, Martin A. Erlandson19, Ingrid Faye20, G Felfoldi21, Haruhiko Fujiwara22, Ryo Futahashi22, Ryo Futahashi23, Archana S. Gandhe7, H.S. Gatehouse24, L. N. Gatehouse24, Jadwiga M. Giebultowicz25, Isabel Gómez14, Cornelis J. P. Grimmelikhuijzen8, Astrid T. Groot11, Frank Hauser8, David G. Heckel11, Dwayne D. Hegedus19, Dwayne D. Hegedus18, Steven Hrycaj2, Lihua Huang3, J. Joe Hull26, Kostas Iatrou6, Masatoshi Iga6, Michael R. Kanost9, Joanna Kotwica12, Changyou Li3, Jianghong Li3, Jisheng Liu6, Magnus Lundmark8, Shogo Matsumoto4, Martina Meyering-Vos7, Peter J. Millichap4, Antónia Monteiro8, Nirotpal Mrinal7, Teruyuki Niimi9, Daniela Nowara8, Atsushi Ohnishi4, Vicencio Oostra27, Katsuhisa Ozaki, Maria P. Papakonstantinou6, Aleksandar Popadic2, Manchikatla Venkat Rajam12, Suzanne V. Saenko27, Robert M. Simpson24, Mario Soberón14, Michael R. Strand13, Shuichiro Tomita13, Umut Toprak18, Ping Wang3, Choon Wei Wee15, Steven Whyard28, Wenqing Zhang17, Javaregowda Nagaraju7, Richard H. ffrench-Constant2, Salvador Herrero16, Salvador Herrero17, Karl H.J. Gordon3, Luc Swevers6, Guy Smagghe6 
TL;DR: Despite a large variation in the data, trends that are found are that RNAi is particularly successful in the family Saturniidae and in genes involved in immunity and that gene expression in epidermal tissues seems to be most difficult to silence.

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TL;DR: In this article, the distribution of ESBL genes, plasmids and strain genotypes in Escherichia coli obtained from poultry and retail chicken meat in the Netherlands was determined and defined as ‘poultry-associated’ (PA).

Journal ArticleDOI
15 Apr 2011-Geoderma
TL;DR: In this article, the use of optical and microwave remote sensing data for soil and terrain mapping with emphasis on applications at regional and coarser scales is reviewed. But, most studies so far have been performed on a local scale and only few on regional or smaller map scale.

Journal ArticleDOI
TL;DR: The Health Council of the Netherlands (HCN) discusses the need for this, considering consistency, applicability, quantification, causality, comprehensibility and acceptability, and concludes that it seems unlikely that a change of dosimetric quantity will help us forward in the discussion on the scientific controversies regarding the existence or non-thermal effects in humans following long duration, low intensity exposure to electromagnetic fields as discussed by the authors.
Abstract: The Health Council of the Netherlands (HCN) and other organisations hold the basic assumption that induced electric current and the generation and absorption of heat in biological material caused by radiofrequency electromagnetic fields are the only causal effects with possible adverse consequences for human health that have been scientifically established to date. Hence, the exposure guidelines for the 10 MHz-10 GHz frequency range are based on avoiding adverse effects of increased temperatures that may occur of the entire human body at a specific absorption rate (SAR) level above 4 W/kg. During the workshop on Thermal Aspects of Radio Frequency Exposure on 11-12 January 2010 in Gaithersburg, Maryland, USA, the question was raised whether there would be a practical advantage in shifting from expressing the exposure limits in SAR to expressing them in terms of a maximum allowable temperature increase. This would mean defining adverse time-temperature thresholds. In this paper, the HCN discusses the need for this, considering six points: consistency, applicability, quantification, causality, comprehensibility and acceptability. The HCN concludes that it seems unlikely that a change of dosimetric quantity will help us forward in the discussion on the scientific controversies regarding the existence or non-existence of non-thermal effects in humans following long duration, low intensity exposure to electromagnetic fields. Therefore, the HCN favours maintaining the current approach of basic restrictions and reference levels being expressed as SAR and in V/m or µT, respectively. © 2011 Informa UK Ltd All rights reserved.