Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Conceptual links between landscape diversity and diet diversity : A roadmap for transdisciplinary research
    Gergel, Sarah E. ; Powell, Bronwen ; Baudron, Frédéric ; Wood, Sylvia L.R. ; Rhemtulla, Jeanine M. ; Kennedy, Gina ; Rasmussen, Laura V. ; Ickowitz, Amy ; Fagan, Matthew E. ; Smithwick, Erica A.H. ; Ranieri, Jessica ; Wood, Stephen A. ; Groot, Jeroen C.J. ; Sunderland, Terry C.H. - \ 2020
    Bioscience 70 (2020)7. - ISSN 0006-3568 - p. 563 - 575.
    Food security and nutrition - Landscape approach - Remote sensing - Restoration - Sustainable development - Tropical forest conservation

    Malnutrition linked to poor quality diets affects at least 2 billion people. Forests, as well as agricultural systems linked to trees, are key sources of dietary diversity in rural settings. In the present article, we develop conceptual links between diet diversity and forested landscape mosaics within the rural tropics. First, we summarize the state of knowledge regarding diets obtained from forests, trees, and agroforests. We then hypothesize how disturbed secondary forests, edge habitats, forest access, and landscape diversity can function in bolstering dietary diversity. Taken together, these ideas help us build a framework illuminating four pathways (direct, agroecological, energy, and market pathways) connecting forested landscapes to diet diversity. Finally, we offer recommendations to fill remaining knowledge gaps related to diet and forest cover monitoring. We argue that better evaluation of the role of land cover complexity will help avoid overly simplistic views of food security and, instead, uncover nutritional synergies with forest conservation and restoration.

    Animal models for COVID-19
    Munoz-Fontela, César ; Dowling, William E. ; Funnell, Simon G.P. ; Gsell, Pierre S. ; Riveros Balta, Ximena ; Albrecht, Randy A. ; Andersen, Hanne ; Baric, Ralph S. ; Carroll, Miles W. ; Cavaleri, Marco ; Qin, Chuan ; Crozier, Ian ; Dallmeier, Kai ; Waal, Leon de; Wit, Emmie de; Delang, Leen ; Dohm, Erik ; Duprex, W.P. ; Falzarano, Darryl ; Finch, Courtney L. ; Frieman, Matthew B. ; Graham, Barney S. ; Gralinski, Lisa ; Guilfoyle, Kate ; Haagmans, Bart L. ; Hamilton, Geraldine A. ; Hartman, Amy L. ; Herfst, Sander ; Kaptein, Suzanne J.F. ; Klimstra, William ; Knezevic, Ivana ; Krause, Phillip R. ; Kuhn, Jens H. ; Grand, Roger Le; Lewis, Mark ; Liu, Wen-Chun ; Maisonnasse, Pauline ; McElroy, Anita K. ; Munster, Vincent ; Oreshkova, N.D. ; Rasmussen, Angela L. ; Rocha-Pereira, Joana ; Rockx, Barry ; Rodriguez, Estefania ; Rogers, Thomas ; Salguero, Francisco J. ; Schotsaert, Michael ; Stittelaar, Koert ; Thibaut, Hendrik Jan ; Tseng, Chien-Te ; Vergara-Alert, Júlia ; Beer, Martin ; Brasel, Trevor ; Chan, Jasper F.W. ; Garcia-Sastre, Adolfo ; Neyts, Johan ; Perlman, Stanley ; Reed, Douglas S. ; Richt, Jürgen A. ; Roy, Chad J. ; Segalés, Joaquim ; Vasan, Seshadri S. ; Henao-Restrepo, Ana Maria ; Barouch, Dan H. - \ 2020
    Nature 586 (2020)7830. - ISSN 0028-0836 - p. 509 - 515.
    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the aetiological agent of coronavirus disease 2019 (COVID-19), an emerging respiratory infection caused by the introduction of a novel coronavirus into humans late in 2019 (first detected in Hubei province, China). As of 18 September 2020, SARS-CoV-2 has spread to 215 countries, has infected more than 30 million people and has caused more than 950,000 deaths. As humans do not have pre-existing immunity to SARS-CoV-2, there is an urgent need to develop therapeutic agents and vaccines to mitigate the current pandemic and to prevent the re-emergence of COVID-19. In February 2020, the World Health Organization (WHO) assembled an international panel to develop animal models for COVID-19 to accelerate the testing of vaccines and therapeutic agents. Here we summarize the findings to date and provides relevant information for preclinical testing of vaccine candidates and therapeutic agents for COVID-19.
    Antenatal multiple micronutrient supplementation: call to action for change in recommendation
    Bourassa, Megan W. ; Osendarp, Saskia J.M. ; Adu‐Afarwuah, Seth ; Ahmed, Saima ; Ajello, Clayton ; Bergeron, Gilles ; Black, Robert ; Christian, Parul ; Cousens, Simon ; Pee, Saskia de; Dewey, Kathryn G. ; Arifeen, Shams El ; Engle‐Stone, Reina ; Fleet, Alison ; Gernand, Alison D. ; Hoddinott, John ; Klemm, Rolf ; Kraemer, Klaus ; Kupka, Roland ; McLean, Erin ; Moore, Sophie E. ; Neufeld, Lynnette M. ; Persson, L. ; Rasmussen, Kathleen M. ; Shankar, Anuraj H. ; Smith, Emily ; Sudfeld, Christopher R. ; Udomkesmalee, Emorn ; Vosti, Stephen A. - \ 2020
    Annals of the New York Academy Of Sciences 1465 (2020)1. - ISSN 0077-8923 - p. 5 - 7.
    Linking Morphology, Toxicokinetic, and Toxicodynamic Traits of Aquatic Invertebrates to Pyrethroid Sensitivity
    Dalhoff, Kristoffer ; Hansen, Anna M.B. ; Rasmussen, Jes J. ; Focks, Andreas ; Strobel, Bjarne W. ; Cedergreen, Nina - \ 2020
    Environmental Science and Technology 54 (2020)9. - ISSN 0013-936X - p. 5687 - 5699.

    Pyrethroid insecticides are known to be highly toxic to most aquatic nontarget organisms, but little is known about the mechanisms causing some species to be highly sensitive while others are hardly affected by the pyrethroids. The aim of the present study was to measure the sensitivity (EC50-values) of 10 aquatic invertebrates toward a 24 h pulse of the pyrethroid cypermethrin and subsequently test if the difference in sensitivity could be explained by measured morphological and physiological traits and modeled toxicokinetic (TK) and toxicodynamic (TD) parameters. Large differences were observed for the measured uptake and elimination kinetics, with bioconcentration factors (BCFs) ranging from 53 to 2337 at the end of the exposure. Similarly, large differences were observed for the TDs, and EC50-values after 168 h varied 120-fold. Modeling the whole organism cypermethrin concentrations indicated compartmentation into a sorbed fraction and two internal fractions: a bioavailable and non-bioavailable internal fraction. Strong correlations between surface/volume area and the TK parameters (sorption and uptake rate constants and the resulting BCF) were found, but none of the TK parameters correlated with sensitivity. The only parameter consistently correlating with sensitivity across all species was the killing rate constant of the GUTS-RED-SD model (the reduced general unified threshold models of survival assuming stochastic death), indicating that sensitivity toward cypermethrin is more related to the TD parameters than to TK parameters.

    Data from: Disease-free monoculture farming by fungus-growing termites
    Otani, Saria ; Challinor, Victoria L. ; Kreuzenbeck, Nina B. ; Kildgaard, Sara ; Christensen, Søren Krath ; Larsen, Louise Lee Munk ; Aanen, Duur ; Rasmussen, Silas Anselm ; Beemelmanns, Christine ; Poulsen, Michael - \ 2019
    Dryad
    Termitomyces - Macrotermes - Odontotermes - symbiosis - Amplicon Sequencing - LCMS
    Fungus-growing termites engage in an obligate mutualistic relationship with Termitomyces fungi, which they maintain in monocultures on specialised fungus comb structures, without apparent problems with infectious diseases. While other fungi have been reported in the symbiosis, detailed comb fungal community analyses have been lacking. Here we use culture-dependent and -independent methods to characterise fungus comb mycobiotas from three fungus-growing termite species (two genera). Internal Transcribed Spacer (ITS) gene analyses using 454 pyrosequencing and Illumina MiSeq showed that non-Termitomyces fungi were essentially absent in fungus combs, and that Termitomyces fungal crops are maintained in monocultures as heterokaryons with two or three abundant ITS variants in a single fungal strain. To explore whether the essential absence of other fungi within fungus combs is potentially due to the production of antifungal metabolites by Termitomyces or comb bacteria, we performed in vitro assays and found that both Termitomyces and chemical extracts of fungus comb material can inhibit potential fungal antagonists. Chemical analyses of fungus comb material point to a highly complex metabolome, including compounds with the potential to play roles in mediating these contaminant-free farming conditions in the termite symbiosis.
    Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
    Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, C.T. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo Da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
    Nature Biotechnology (2019). - ISSN 1087-0156

    In the version of this article initially published, some reference citations were incorrect. The three references to Jupyter Notebooks should have cited Kluyver et al. instead of Gonzalez et al. The reference to Qiita should have cited Gonzalez et al. instead of Schloss et al. The reference to mothur should have cited Schloss et al. instead of McMurdie & Holmes. The reference to phyloseq should have cited McMurdie & Holmes instead of Huber et al. The reference to Bioconductor should have cited Huber et al. instead of Franzosa et al. And the reference to the biobakery suite should have cited Franzosa et al. instead of Kluyver et al. The errors have been corrected in the HTML and PDF versions of the article.

    Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
    Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, Titus C. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
    Nature Biotechnology 37 (2019)8. - ISSN 1087-0156 - p. 852 - 857.
    Disease-free monoculture farming by fungus-growing termites
    Otani, Saria ; Challinor, Victoria L. ; Kreuzenbeck, Nina B. ; Kildgaard, Sara ; Krath Christensen, Søren ; Larsen, Louise Lee Munk ; Aanen, Duur K. ; Rasmussen, Silas Anselm ; Beemelmanns, Christine ; Poulsen, Michael - \ 2019
    Scientific Reports 9 (2019)1. - ISSN 2045-2322

    Fungus-growing termites engage in an obligate mutualistic relationship with Termitomyces fungi, which they maintain in monocultures on specialised fungus comb structures, without apparent problems with infectious diseases. While other fungi have been reported in the symbiosis, detailed comb fungal community analyses have been lacking. Here we use culture-dependent and -independent methods to characterise fungus comb mycobiotas from three fungus-growing termite species (two genera). Internal Transcribed Spacer (ITS) gene analyses using 454 pyrosequencing and Illumina MiSeq showed that non-Termitomyces fungi were essentially absent in fungus combs, and that Termitomyces fungal crops are maintained in monocultures as heterokaryons with two or three abundant ITS variants in a single fungal strain. To explore whether the essential absence of other fungi within fungus combs is potentially due to the production of antifungal metabolites by Termitomyces or comb bacteria, we performed in vitro assays and found that both Termitomyces and chemical extracts of fungus comb material can inhibit potential fungal antagonists. Chemical analyses of fungus comb material point to a highly complex metabolome, including compounds with the potential to play roles in mediating these contaminant-free farming conditions in the termite symbiosis.

    Review of the evidence regarding the use of antenatal multiple micronutrient supplementation in low- and middle-income countries
    Bourassa, Megan W. ; Osendarp, Saskia J.M. ; Adu-Afarwuah, Seth ; Ahmed, Saima ; Ajello, Clayton ; Bergeron, Gilles ; Black, Robert ; Christian, Parul ; Cousens, Simon ; Pee, Saskia de; Dewey, Kathryn G. ; Arifeen, Shams El ; Engle-Stone, Reina ; Fleet, Alison ; Gernand, Alison D. ; Hoddinott, John ; Klemm, Rolf ; Kraemer, Klaus ; Kupka, Roland ; McLean, Erin ; Moore, Sophie E. ; Neufeld, Lynnette M. ; Persson, Lars Åke ; Rasmussen, Kathleen M. ; Shankar, Anuraj H. ; Smith, Emily ; Sudfeld, Christopher R. ; Udomkesmalee, Emorn ; Vosti, Stephen A. - \ 2019
    Annals of the New York Academy Of Sciences 1444 (2019)1. - ISSN 0077-8923 - p. 6 - 21.
    LMICs - micronutrient - pregnancy - supplements

    Inadequate micronutrient intakes are relatively common in low- and middle-income countries (LMICs), especially among pregnant women, who have increased micronutrient requirements. This can lead to an increase in adverse pregnancy and birth outcomes. This review presents the conclusions of a task force that set out to assess the prevalence of inadequate micronutrient intakes and adverse birth outcomes in LMICs; the data from trials comparing multiple micronutrient supplements (MMS) that contain iron and folic acid (IFA) with IFA supplements alone; the risks of reaching the upper intake levels with MMS; and the cost-effectiveness of MMS compared with IFA. Recent meta-analyses demonstrate that MMS can reduce the risks of preterm birth, low birth weight, and small for gestational age in comparison with IFA alone. An individual-participant data meta-analysis also revealed even greater benefits for anemic and underweight women and female infants. Importantly, there was no increased risk of harm for the pregnant women or their infants with MMS. These data suggest that countries with inadequate micronutrient intakes should consider supplementing pregnant women with MMS as a cost-effective method to reduce the risk of adverse birth outcomes.

    Assessing the State of Demersal Fish to Address Formal Ecosystem Based Management Needs: Making Fisheries Independent Trawl Survey Data ‘Fit for Purpose’
    Moriarty, Meadhbh ; Greenstreet, Simon P.R. ; Rasmussen, Jens ; Boois, Ingeborg De - \ 2019
    Frontiers in Marine Science 6 (2019). - ISSN 2296-7745 - 10 p.
    Data quality - data quality audit - marine strategy framework directive - Common fisheries policy - data management - ecoystem-based management
    In Europe, introduction of the Marine Strategy Framework Directive (MSFD) represents formal, legally-binding, adoption of ecosystem-based management (EBM) across most European waters. Member States of the European Union have invariably nominated their groundfish surveys as part of the marine monitoring programmes required under the MSFD. Groundfish surveys were originally intended to provide fisheries independent abundance indices for commercially valuable species to support fisheries stock assessments and fisheries management. However, early studies, primarily intended to make the case for the need for EBM, exposed these data to a broader range of uses and highlighted various data quality issues. Individual scientists, pursuing personal research agendas, addressed these as each thought best. This informal approach to assuring data quality is not sufficient to support formal assessments of fish species status and fish community status required under legally-mandated EBM, such as the MSFD, because quality audit, formal logging of issues identified, and remedial measures taken, is often lacking. Groundfish survey data, needed to implement legally-mandated EBM, should be subjected to a formal Quality Assurance–Quality Audit (QAQA) process to ensure that they are properly fit for purpose. This paper describes a QAQA process applied European groundfish survey data to ensure their adequacy to support MSFD needs and considers how this process might be taken forward in the future
    Fungicides: An Overlooked Pesticide Class?
    Zubrod, Jochen P. ; Bundschuh, Mirco ; Arts, Gertie ; Brühl, Carsten A. ; Imfeld, Gwenaël ; Knäbel, Anja ; Payraudeau, Sylvain ; Rasmussen, Jes J. ; Rohr, Jason ; Scharmüller, Andreas ; Smalling, Kelly ; Stehle, Sebastian ; Schulz, Ralf ; Schäfer, Ralf B. - \ 2019
    Environmental Science and Technology 53 (2019)7. - ISSN 0013-936X - p. 3347 - 3365.

    Fungicides are indispensable to global food security and their use is forecasted to intensify. Fungicides can reach aquatic ecosystems and occur in surface water bodies in agricultural catchments throughout the entire growing season due to their frequent, prophylactic application. However, in comparison to herbicides and insecticides, the exposure to and effects of fungicides have received less attention. We provide an overview of the risk of fungicides to aquatic ecosystems covering fungicide exposure (i.e., environmental fate, exposure modeling, and mitigation measures) as well as direct and indirect effects of fungicides on microorganisms, macrophytes, invertebrates, and vertebrates. We show that fungicides occur widely in aquatic systems, that the accuracy of predicted environmental concentrations is debatable, and that fungicide exposure can be effectively mitigated. We additionally demonstrate that fungicides can be highly toxic to a broad range of organisms and can pose a risk to aquatic biota. Finally, we outline central research gaps that currently challenge our ability to predict fungicide exposure and effects, promising research avenues, and shortcomings of the current environmental risk assessment for fungicides.

    Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage
    Hendriksen, Rene S. ; Munk, Patrick ; Njage, Patrick ; Bunnik, Bram Van; Mcnally, Luke ; Lukjancenko, Oksana ; Röder, Timo ; Nieuwenhuijse, David ; Pedersen, Susanne Karlsmose ; Kjeldgaard, Jette ; Kaas, Rolf S. ; Clausen, Philip Thomas Lanken Conradsen ; Vogt, Josef Korbinian ; Leekitcharoenphon, Pimlapas ; De Schans, Milou G.M. Van; Zuidema, Tina ; Roda Husman, Ana Maria De; Rasmussen, Simon ; Petersen, Bent ; Amid, Clara ; Cochrane, Guy ; Sicheritz-ponten, Thomas ; Schmitt, Heike ; Alvarez, Jorge Raul Matheu ; Aidara-kane, Awa ; Pamp, Sünje J. ; Lund, Ole ; Hald, Tine ; Woolhouse, Mark ; Koopmans, Marion P. ; Vigre, Håkan ; Petersen, Thomas Nordahl ; Aarestrup, Frank M. - \ 2019
    Nature Communications 10 (2019)1. - ISSN 2041-1723 - 12 p.
    Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use meta-genomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.
    The impact of dispersal, plant genotype and nematodes on arbuscular mycorrhizal fungal colonization
    Rasmussen, Pil U. ; Chareesri, Anupol ; Neilson, Roy ; Bennett, Alison E. ; Tack, Ayco J.M. - \ 2019
    Soil Biology and Biochemistry 132 (2019). - ISSN 0038-0717 - p. 28 - 35.
    Arbuscular mycorrhizal fungi - Colonization ability - Dispersal - Genotype - Nematodes - Plantago lanceolata

    While the majority of parasitic and mutualistic microbes have the potential for long-range dispersal, the high turnover in community composition among nearby hosts has often been interpreted to reflect dispersal constraints. To resolve this apparent contradiction, we need further insights into the relative importance of dispersal limitation, host genotype and the biotic environment on the colonization process. We focused on the important root symbionts, the arbuscular mycorrhizal (AM) fungi. We studied AM fungal colonization ability in a controlled mesocosm setting, where we placed Plantago lanceolata plants belonging to four different genotypes in sterile soil at 10, 30 and 70 cm from a central AM fungal inoculated P. lanceolata plant. In part of the mesocosms, we also inoculated the source plants with nematodes. AM fungi colonized receiver plants <1 m away over the course of ten weeks, with a strong effect of distance from source plant on AM fungal colonization. Plant genotype influenced AM fungal colonization during the early stages of colonization, while nematode inoculation had no effect on AM fungal colonization. Overall, the effect of both dispersal limitation and plant genetic variation may underlie the small-scale heterogeneity found in natural AM fungal communities.

    Regulatory Status of Nanotechnologies in Food in the EU
    Rasmussen, Kirsten ; Rauscher, Hubert ; Gottardo, Stefania ; Hoekstra, Eddo ; Schoonjans, Reinhilde ; Peters, Ruud ; Aschberger, Karin - \ 2018
    In: Nanomaterials for Food Applications Elsevier - ISBN 9780128141304 - p. 381 - 410.
    Food - Legislation - Nanomaterials - Nanotechnology - Risk assessment - Safety

    This chapter provides a state-of-the-art description, as of November 2017, of legislation covering food-related applications of nanotechnology and nanomaterials in the European Union (EU). These applications include novel foods, food contact materials, feed and food additives, food supplements, and plant protection products. In general, the EU legislation requires a market authorization of nanomaterial applications in foods on the basis of a safety assessment by the European Food Safety Authority (EFSA) of the potential health risks, which may be associated with nanomaterials in foods. EFSA is an integral part of the EU's food safety system to ensure the safety of foods and to protect the health of consumers, animals, and the environment from food-related risks. Among others, EFSA evaluates and assesses the risk of nanomaterials and develops scientific methodologies and guidance needed for identifying emerging risks to food safety. In addition to EFSA, the Joint Research Centre of the European Commission provides technical and scientific support to the policies on nanomaterials in foods.

    Detection and characterization of distinct alphacoronaviruses in five different bat species in Denmark
    Lazov, Christina M. ; Chriél, Mariann ; Baagøe, Hans J. ; Fjederholt, Esben ; Deng, Yu ; Kooi, Engbert A. ; Belsham, Graham J. ; Bøtner, Anette ; Rasmussen, Thomas Bruun - \ 2018
    Viruses 10 (2018)9. - ISSN 1999-4915
    Coronavirus - Europe - Host restriction - Nucleotide sequencing - Phylogenetic analysis - Vespertilionidae

    Bat populations harbour a multitude of viruses; some of these are pathogenic or potentially pathogenic in other animals or humans. Therefore, it is important to monitor the populations and characterize these viruses. In this study, the presence of coronaviruses (CoVs) in different species of Danish bats was investigated using active surveillance at different geographical locations in Denmark. Faecal samples were screened for the presence of CoVs using pan-CoV real-time RT-PCR assays. The amplicons, obtained from five different species of bats, were sequenced. Phylogenetic analysis revealed a species-specific clustering with the samples from Myotis daubentonii, showing a close resemblance to coronavirus sequences obtained from the same species of bat in Germany and the United Kingdom. Our results show, for the first time, that multiple, distinct alphacoronaviruses are present in the Danish bat populations.

    Research data supporting "Genetic manipulation of structural colour in bacterial colonies"
    Johansen, Villads Egede ; Catón, Laura ; Hamidjaja, Raditijo ; Oosterink, E. ; Wilts, Bodo D. ; Rasmussen, Torben Sølbeck ; Sherlock, Michael Mario ; Ingham, Colin J. ; Vignolini, Silvia - \ 2018
    University of Cambridge
    photonics - microbiology - structural colour
    This data supports the publication "Living colours: Genetic manipulation of structural colour in bacterial colonies" and consists of electron microscopy images, a microscope video and goniometer data.
    Effects of steaming on contaminants of emerging concern levels in seafood
    Barbosa, Vera ; Maulvault, Ana Luísa ; Alves, Ricardo N. ; Kwadijk, Christian ; Kotterman, Michiel ; Tediosi, Alice ; Fernández-Tejedor, Margarita ; Sloth, Jens J. ; Granby, Kit ; Rasmussen, Rie R. ; Robbens, Johan ; Witte, Bavo De; Trabalón, Laura ; Fernandes, José O. ; Cunha, Sara C. ; Marques, António - \ 2018
    Food and Chemical Toxicology 118 (2018). - ISSN 0278-6915 - p. 490 - 504.
    Musk fragrances and UV-Filters - PAHs - PFCs - Seafood - Steaming - Toxic elements
    Seafood consumption is a major route for human exposure to environmental contaminants of emerging concern (CeCs). However, toxicological information about the presence of CeCs in seafood is still insufficient, especially considering the effect of cooking procedures on contaminant levels. This study is one among a few who evaluated the effect of steaming on the levels of different CeCs (toxic elements, PFCs, PAHs, musk fragrances and UV-filters) in commercially relevant seafood in Europe, and estimate the potential risks associated with its consumption for consumers. In most cases, an increase in contaminant levels was observed after steaming, though varying according to contaminant and seafood species (e.g. iAs, perfluorobutanoate, dibenzo(ah)anthracene in Mytilus edulis, HHCB-Lactone in Solea sp., 2-Ethylhexyl salicylate in Lophius piscatorius). Furthermore, the increase in some CeCs, like Pb, MeHg, iAs, Cd and carcinogenic PAHs, in seafood after steaming reveals that adverse health effects can never be excluded, regardless contaminants concentration. However, the risk of adverse effects can vary. The drastic changes induced by steaming suggest that the effect of cooking should be integrated in food risk assessment, as well as accounted in CeCs regulations and recommendations issued by food safety authorities, in order to avoid over/underestimation of risks for consumer health.
    Enhancing the Saliency of climate services for marine mobility sectors in European Arctic seas (SALIENSEAS) : Stakeholder Advisory Group workshop report
    Lamers, M.A.J. ; Knol, Maaike ; Müller, Malte ; Blair, Berill ; Jeuring, J.H.G. ; Rasmussen, Till ; Sivle, Anders - \ 2018
    Wageningen : SALIENSEAS (Enhancing the Saliency of climate services for marine mobility Sectors in European Arctic Seas) - 28 p.
    SALIENSEAS brings together a team of social and natural scientists, metocean service personnel, and end-users, with the aim to 1). Better understand the mobility patterns, constraints, challenges, decision-making contexts and information needs of end-users in different European Arctic marine sectors; 2). Develop and apply participatory tools for co-producing salient weather and sea ice services with Arctic marine end-users, and 3). Co-develop user-relevant and sector specific weather and sea ice services and dissemination systems dedicated to Arctic marine end-users tailored to key social, environmental and economic needs. This report provides an overview of the activities and discussions that took place during the first SALIENSEAS Stakeholder Advisory Group (SAG) workshop, held on 25 January 2018 at UiT The Arctic University of Norway in Tromsø, Norway. Participants of the SAG represented a wide variety of perspectives and needs related to maritime activities in the European Arctic, including expedition cruising, ice pilotage, ice breaking, fishing and hunting, and shipping. During this participatory workshop participants reflected on important information needs pertinent to planning and operations in their sectors. The core purpose of the workshop was twofold: 1) to identify the most pressing issues around metocean information availability and access, in terms of sector-specific needs to increase safety and efficiency of operations; and 2) to formulate a plan for efficient and relevant data collection from end users.
    Sequence diversity of CV777 PEDV strains
    Rasmussen, Thomas Bruun ; Boniotti, Maria Beatrice ; Papetti, Alice ; Grasland, Béatrice ; Frossard, Jean Pierre ; Dastjerdi, Akbar ; Hulst, M.M. ; Hanke, Dennis ; Pohlmann, Anne ; Blome, Sandra ; Poel, W.H.M. van der; Steinbach, Falko ; Blanchard, Yannick ; Lavazza, Antonio ; Bøtner, Anette ; Belsham, Graham J. - \ 2018
    Friedrich-Loeffler-Institut
    PRJEB20818 - ERP023004
    The influence of microplastics and halogenated contaminants in feed on toxicokinetics and gene expression in European seabass (Dicentrarchus labrax)
    Granby, Kit ; Rainieri, Sandra ; Rasmussen, Rie Romme ; Kotterman, Michiel J.J. ; Sloth, Jens Jørgen ; Cederberg, Tommy Licht ; Barranco, Alex ; Marques, António ; Larsen, Bodil Katrine - \ 2018
    Environmental Research 164 (2018). - ISSN 0013-9351 - p. 430 - 443.
    Elimination - Gene expression - Microplastics - PBDE - PCB
    When microplastics pollute fish habitats, it may be ingested by fish, thereby contaminating fish with sorbed contaminants. The present study investigates how combinations of halogenated contaminants and microplastics associated with feed are able to alter toxicokinetics in European seabass and affect the fish. Microplastic particles (2%) were added to the feed either with sorbed contaminants or as a mixture of clean microplastics and chemical contaminants, and compared to feed containing contaminants without microplastics. For the contaminated microplastic diet, the accumulation of polychlorinated biphenyls (PCBs) and brominated flame retardants (BFRs) in fish was significantly higher, increasing up to 40 days of accumulation and then reversing to values comparable to the other diets at the end of accumulation. The significant gene expression results of liver (cyp1a, il1β gstα) after 40 days of exposure indicate that microplastics might indeed exacerbate the toxic effects (liver metabolism, immune system, oxidative stress) of some chemical contaminants sorbed to microplastics. Seabass quickly metabolised BDE99 to BDE47 by debromination, probably mediated by deiodinase enzymes, and unlike other contaminants, this metabolism was unaffected by the presence of microplastics. For the other PCBs and BFRs, the elimination coefficients were significantly lower in fish fed the diet with contaminants sorbed to microplastic compared to the other diets. The results indicate that microplastics affects liver detoxification and lipid distribution, both of which affect the concentration of contaminants.
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