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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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.

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
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 : - 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
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.
Genetic manipulation of structural color in bacterial colonies
Johansen, Villads Egede ; Catón, Laura ; Hamidjaja, Raditijo ; Oosterink, Els ; Wilts, Bodo D. ; Rasmussen, Torben Sølbeck ; Sherlock, Michael Mario ; Ingham, Colin J. ; Vignolini, Silvia - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)11. - ISSN 0027-8424 - p. 2652 - 2657.
Disorder - Flavobacteria - Genetics - Self-organization - Structural color
Naturally occurring photonic structures are responsible for the bright and vivid coloration in a large variety of living organisms. Despite efforts to understand their biological functions, development, and complex optical response, little is known of the underlying genes involved in the development of these nanostructures in any domain of life. Here, we used Flavobacterium colonies as a model system to demonstrate that genes responsible for gliding motility, cell shape, the stringent response, and tRNA modification contribute to the optical appearance of the colony. By structural and optical analysis, we obtained a detailed correlation of how genetic modifications alter structural color in bacterial colonies. Understanding of genotype and phenotype relations in this system opens the way to genetic engineering of on-demand living optical materials, for use as paints and living sensors.
Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777; use of NGS to analyse genomic and sub-genomic RNAs
Rasmussen, Thomas Bruun ; Boniotti, Maria Beatrice ; Papetti, Alice ; Grasland, Béatrice ; Frossard, Jean Pierre ; Dastjerdi, Akbar ; Hulst, Marcel ; Hanke, Dennis ; Pohlmann, Anne ; Blome, Sandra ; Poel, Wim H.M. Van Der; Steinbach, Falko ; Blanchard, Yannick ; Lavazza, Antonio ; Bøtner, Anette ; Belsham, Graham J. - \ 2018
PLoS ONE 13 (2018)3. - ISSN 1932-6203
Porcine epidemic diarrhoea virus, strain CV777, was initially characterized in 1978 as the causative agent of a disease first identified in the UK in 1971. This coronavirus has been widely distributed among laboratories and has been passaged both within pigs and in cell culture. To determine the variability between different stocks of the PEDV strain CV777, sequencing of the full-length genome (ca. 28kb) has been performed in 6 different laboratories, using different protocols. Not surprisingly, each of the different full genome sequences were distinct from each other and from the reference sequence (Accession number AF353511) but they are >99% identical. Unique and shared differences between sequences were identified. The coding region for the surface-exposed spike protein showed the highest proportion of variability including both point mutations and small deletions. The predicted expression of the ORF3 gene product was more dramatically affected in three different variants of this virus through either loss of the initiation codon or gain of a premature termination codon. The genome of one isolate had a substantially rearranged 5´-terminal sequence. This rearrangement was validated through the analysis of sub-genomic mRNAs from infected cells. It is clearly important to know the features of the specific sample of CV777 being used for experimental studies.
Oral bioaccessibility of toxic and essential elements in raw and cooked commercial seafood species available in European markets
Alves, Ricardo N. ; Maulvault, Ana L. ; Barbosa, Vera L. ; Fernandez-Tejedor, Margarita ; Tediosi, Alice ; Kotterman, Michiel ; Heuvel, Fredericus H.M. van den; Robbens, Johan ; Fernandes, José O. ; Romme Rasmussen, Rie ; Sloth, Jens J. ; Marques, António - \ 2018
Food Chemistry 267 (2018). - ISSN 0308-8146 - p. 15 - 27.
Bioaccessibility - Seafood - Steaming - Toxic/essential elements
The oral bioaccessibility of several essential and toxic elements was investigated in raw and cooked commercially available seafood species from European markets. Bioaccessibility varied between seafood species and elements. Methylmercury bioaccessibility varied between 10 (octopus) and 60% (monkfish). Arsenic (>64%) was the toxic element showing the highest bioaccessibility. Concerning essential elements bioaccessibility in raw seafood, selenium (73%) and iodine (71%) revealed the highest percentages. The bioaccessibility of elements in steamed products increased or decreased according to species. For example, methylmercury bioaccessibility decreased significantly after steaming in all species, while zinc bioaccessibility increased in fish (tuna and plaice) but decreased in molluscs (mussel and octopus).Together with human exposure assessment and risk characterization, this study could contribute to the establishment of new maximum permissible concentrations for toxic elements in seafood by the European food safety authorities, as well as recommended intakes for essential elements.
Assessing the effects of seawater temperature and pH on the bioaccumulation of emerging chemical contaminants in marine bivalves
Maulvault, Ana Luísa ; Camacho, Carolina ; Barbosa, Vera ; Alves, Ricardo ; Anacleto, Patrícia ; Fogaça, Fabiola ; Kwadijk, Christiaan ; Kotterman, Michiel ; Cunha, Sara C. ; Fernandes, José O. ; Rasmussen, Rie R. ; Sloth, Jens J. ; Aznar-Alemany, Òscar ; Eljarrat, Ethel ; Barceló, Damià ; Marques, António - \ 2018
Environmental Research 161 (2018). - ISSN 0013-9351 - p. 236 - 247.
Acidification - Bioaccumulation - Emerging chemical contaminants - Flame retardants - Perfluorinated compounds - Toxic elements - Warming
Emerging chemical contaminants [e.g. toxic metals speciation, flame retardants (FRs) and perfluorinated compounds (PFCs), among others], that have not been historically recognized as pollutants nor their toxicological hazards, are increasingly more present in the marine environment. Furthermore, the effects of environmental conditions (e.g. temperature and pH) on bioaccumulation and elimination mechanisms of these emerging contaminants in marine biota have been poorly studied until now. In this context, the aim of this study was to assess, for the first time, the effect of warmer seawater temperatures (Δ = + 4 °C) and lower pH levels (Δ = − 0.4 pH units), acting alone or combined, on the bioaccumulation and elimination of emerging FRs (dechloranes 602, 603 and 604, and TBBPA), inorganic arsenic (iAs), and PFCs (PFOA and PFOS) in two estuarine bivalve species (Mytilus galloprovincialis and Ruditapes philippinarum). Overall, results showed that warming alone or combined with acidification promoted the bioaccumulation of some compounds (i.e. dechloranes 602, 604, TBBPA), but also facilitated the elimination of others (i.e. iAs, TBBPA). Similarly, lower pH also resulted in higher levels of dechloranes, as well as enhanced iAs, PFOA and PFOS elimination. Data also suggests that, when both abiotic stressors are combined, bivalves' capacity to accumulate contaminants may be time-dependent, considering significantly drastic increase observed with Dec 602 and TBBPA, during the last 10 days of exposure, when compared to reference conditions. Such changes in contaminants' bioaccumulation/elimination patterns also suggest a potential increase of human health risks of some compounds, if the climate continues changing as forecasted. Therefore, this first study pointed out the urgent need for further research on the effects of abiotic conditions on emerging contaminants kinetics, to adequately estimate the potential toxicological hazards associated to these compounds and develop recommendations/regulations for their presence in seafood, considering the prevailing environmental conditions expected in tomorrow's ocean.
Non-Chemical Weed Management
Melander, Bo ; Liebman, Matt ; Davis, Adam S. ; Gallandt, Eric R. ; Bàrberi, Paolo ; Moonen, Anna Camilla ; Rasmussen, Jesper ; Weide, Rommie van der; Vidotto, Francesco - \ 2017
In: Weed Research / Hatcher, Paul E., Froud-Williams, Robert J., Wiley - ISBN 9781119969143 - p. 245 - 270.
Crop competition - Cultural methods - European weed research - Non-chemical weed management - North America - Organic crop production - Weed control methods - Weed germination

Non-chemical weed management covers all management practices that influence weeds except herbicides. This chapter summarises the major achievements in European research, as well as work undertaken in North America. Research groups from both continents have interacted strongly on the topic over the years and shared common interests on the development of non-chemical tactics. The chapter encompasses preventive, cultural and direct weed control methods, explaining the basic principles and the integration of these tactics in weed management strategies for agricultural and horticultural crops and in some cases amenity areas as well. Preventive methods reduce weed germination, cultural methods improve crop competition and direct physical weed control reduces weed survival. Non-chemical weed management is mainly adopted in organic crop production, as conventional growers still perceive it as more costly and less reliable than herbicide-based weed control programmes.

Plant Cytokinesis : Terminology for Structures and Processes
Smertenko, Andrei ; Assaad, Farhah ; Baluška, František ; Bezanilla, Magdalena ; Buschmann, Henrik ; Drakakaki, Georgia ; Hauser, Marie Theres ; Janson, Marcel ; Mineyuki, Yoshinobu ; Moore, Ian ; Müller, Sabine ; Murata, Takashi ; Otegui, Marisa S. ; Panteris, Emmanuel ; Rasmussen, Carolyn ; Schmit, Anne Catherine ; Šamaj, Jozef ; Samuels, Lacey ; Staehelin, L.A. ; Damme, Daniel Van; Wasteneys, Geoffrey ; Žárský, Viktor - \ 2017
Trends in Cell Biology 27 (2017)12. - ISSN 0962-8924 - p. 885 - 894.
Cell plate - Cytokinesis - Division plane - Phragmoplast - Preprophase band

Plant cytokinesis is orchestrated by a specialized structure, the phragmoplast. The phragmoplast first occurred in representatives of Charophyte algae and then became the main division apparatus in land plants. Major cellular activities, including cytoskeletal dynamics, vesicle trafficking, membrane assembly, and cell wall biosynthesis, cooperate in the phragmoplast under the guidance of a complex signaling network. Furthermore, the phragmoplast combines plant-specific features with the conserved cytokinetic processes of animals, fungi, and protists. As such, the phragmoplast represents a useful system for understanding both plant cell dynamics and the evolution of cytokinesis. We recognize that future research and knowledge transfer into other fields would benefit from standardized terminology. Here, we propose such a lexicon of terminology for specific structures and processes associated with plant cytokinesis. A large number of phragmoplast proteins have been identified.Electron microscopy/tomography studies have produced nanoscale information about the architecture of phragmoplast and cell plate assembly stages in cryofixed cells.Novel components of the cortical division zone and cell plate fusion site have been discovered. This information lays a foundation for understanding how plant cells memorize the division plane throughout mitosis and how the cell plate is guided to its predetermined attachment site.MAP65 and plus end-directed kinesins contribute to the maintenance of the antiparallel overlap of phragmoplast microtubules. In addition, the MAP65-TRAPPII interaction plays a key role in cell plate assembly.Actin filaments align parallel to microtubules in the phragmoplast, while some microfilaments extend from cell plate margin to guide its expansion towards the fusion site.

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