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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    Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers
    Ploetz, Evelyn ; Lerner, Eitan ; Husada, Florence ; Roelfs, Martin ; Chung, Sangyoon ; Hohlbein, Johannes ; Weiss, Shimon ; Cordes, Thorben - \ 2016
    Scientific Reports 6 (2016). - ISSN 2045-2322

    Advanced microscopy methods allow obtaining information on (dynamic) conformational changes in biomolecules via measuring a single molecular distance in the structure. It is, however, extremely challenging to capture the full depth of a three-dimensional biochemical state, binding-related structural changes or conformational cross-Talk in multi-protein complexes using one-dimensional assays. In this paper we address this fundamental problem by extending the standard molecular ruler based on Förster resonance energy transfer (FRET) into a two-dimensional assay via its combination with protein-induced fluorescence enhancement (PIFE). We show that donor brightness (via PIFE) and energy transfer efficiency (via FRET) can simultaneously report on e.g., the conformational state of double stranded DNA (dsDNA) following its interaction with unlabelled proteins (BamHI, EcoRV, and T7 DNA polymerase gp5/trx). The PIFE-FRET assay uses established labelling protocols and single molecule fluorescence detection schemes (alternating-laser excitation, ALEX). Besides quantitative studies of PIFE and FRET ruler characteristics, we outline possible applications of ALEX-based PIFE-FRET for single-molecule studies with diffusing and immobilized molecules. Finally, we study transcription initiation and scrunching of E. coli RNA-polymerase with PIFE-FRET and provide direct evidence for the physical presence and vicinity of the polymerase that causes structural changes and scrunching of the transcriptional DNA bubble.

    A Quantitative Theoretical Framework for Protein-Induced Fluorescence Enhancement-Förster-Type Resonance Energy Transfer (PIFE-FRET)
    Lerner, Eitan ; Ploetz, Evelyn ; Hohlbein, Johannes ; Cordes, Thorben ; Weiss, Shimon - \ 2016
    The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 120 (2016)26. - ISSN 1520-6106 - p. 6401 - 6410.

    Single-molecule, protein-induced fluorescence enhancement (PIFE) serves as a molecular ruler at molecular distances inaccessible to other spectroscopic rulers such as Förster-type resonance energy transfer (FRET) or photoinduced electron transfer. In order to provide two simultaneous measurements of two distances on different molecular length scales for the analysis of macromolecular complexes, we and others recently combined measurements of PIFE and FRET (PIFE-FRET) on the single molecule level. PIFE relies on steric hindrance of the fluorophore Cy3, which is covalently attached to a biomolecule of interest, to rotate out of an excited-state trans isomer to the cis isomer through a 90° intermediate. In this work, we provide a theoretical framework that accounts for relevant photophysical and kinetic parameters of PIFE-FRET, show how this framework allows the extraction of the fold-decrease in isomerization mobility from experimental data, and show how these results provide information on changes in the accessible volume of Cy3. The utility of this model is then demonstrated for experimental results on PIFE-FRET measurement of different protein-DNA interactions. The proposed model and extracted parameters could serve as a benchmark to allow quantitative comparison of PIFE effects in different biological systems.

    Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida
    Bombarely, Aureliano ; Moser, Michel ; Amrad, Avichai ; Bao, Manzhu ; Bapaume, Laure ; Barry, Cornelius S. ; Bliek, Mattijs ; Boersma, Maaike R. ; Borghi, Lorenzo ; Bruggmann, Rémy ; Bucher, Marcel ; Agostino, Nunzio D'; Davies, Kevin ; Druege, Uwe ; Dudareva, Natalia ; Egea-Cortines, Marcos ; Delledonne, Massimo ; Fernandez-Pozo, Noe ; Franken, Philipp ; Grandont, Laurie ; Heslop-Harrison, J.S. ; Hintzsche, Jennifer ; Johns, Mitrick ; Koes, Ronald ; Lv, Xiaodan ; Lyons, Eric ; Malla, Diwa ; Martinoia, Enrico ; Mattson, Neil S. ; Morel, Patrice ; Mueller, Lukas A. ; Muhlemann, Joëlle ; Nouri, Eva ; Passeri, Valentina ; Pezzotti, Mario ; Qi, Qinzhou ; Reinhardt, Didier ; Rich, Melanie ; Richert-Pöggeler, Katja R. ; Robbins, Tim P. ; Schatz, Michael C. ; Schranz, Eric ; Schuurink, Robert C. ; Schwarzacher, Trude ; Spelt, Kees ; Tang, Haibao ; Urbanus, Susan L. ; Vandenbussche, Michiel ; Vijverberg, Kitty ; Villarino, Gonzalo H. ; Warner, Ryan M. ; Weiss, Julia ; Yue, Zhen ; Zethof, Jan ; Quattrocchio, Francesca ; Sims, Thomas L. ; Kuhlemeier, Cris - \ 2016
    Nature Plants 2 (2016). - ISSN 2055-026X

    Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization: the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral colour patterns and pollination systems. The high-quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms.

    Erratum to: Persistent aryl hydrocarbon receptor inducers increase with altitude, and estrogen-like disrupters are low in soils of the Alps
    Levy, Walkiria ; Henkelmann, Bernhard ; Bernhöft, Silke ; Bovee, Toine ; Buegger, Franz ; Jakobi, Gert ; Kirchner, Manfred ; Bassan, Rodolfo ; Kräuchi, Norbert ; Moche, Wolfgang ; Offenthaler, Ivo ; Simončič, Primoz ; Weiss, Peter ; Schramm, Karl Werner - \ 2015
    Environmental Science and Pollution Research 22 (2015)4. - ISSN 0944-1344 - p. 3180 - 3181.
    Impacts of European livestock production : Nitrogen, sulphur, phosphorus and greenhouse gas emissions, land-use, water eutrophication and biodiversity
    Leip, Adrian ; Billen, Gilles ; Garnier, Josette ; Grizzetti, Bruna ; Lassaletta, Luis ; Reis, Stefan ; Simpson, David ; Sutton, M.A. ; Vries, Wim De; Weiss, Franz ; Westhoek, Henk - \ 2015
    Environmental Research Letters 10 (2015)11. - ISSN 1748-9326
    air quality - biodiversity loss - climate change - coastal eutrophication - European Union - livestock production - soil acidification

    Livestock production systems currently occupy around 28% of the land surface of the European Union (equivalent to 65% of the agricultural land). In conjunction with other human activities, livestock production systems affect water, air and soil quality, global climate and biodiversity, altering the biogeochemical cycles of nitrogen, phosphorus and carbon. Here, we quantify the contribution of European livestock production to these major impacts. For each environmental effect, the contribution of livestock is expressed as shares of the emitted compounds and land used, as compared to the whole agricultural sector. The results show that the livestock sector contributes significantly to agricultural environmental impacts. This contribution is 78% for terrestrial biodiversity loss, 80% for soil acidification and air pollution (ammonia and nitrogen oxides emissions), 81% for global warming, and 73% for water pollution (both N and P). The agriculture sector itself is one of the major contributors to these environmental impacts, ranging between 12% for global warming and 59% for N water quality impact. Significant progress in mitigating these environmental impacts in Europe will only be possible through a combination of technological measures reducing livestock emissions, improved food choices and reduced food waste of European citizens.

    Non-alcoholic fatty liver disease (NAFLD) is associated with a distinct fecal microbiome signature–a case control study
    Schulz, C. ; Lerch, M. ; Lahti, L.M. ; Kühn, J. ; Schütte, K. ; Weiss, F. ; Völzke, H. ; Baumeister, S. ; Fuentes Enriquez de Salamanca, S. ; Fluhr, G. ; Vos, W.M. de; Mayerle, J. - \ 2015
    Background: Nonalcoholic fatty liver disease is now being recognized as the most common liver disorder worldwide. The majority of NAFLD patients are characterized by mere liver steatosis but up to one third progresses to non-alcoholic steatohepatitis (NASH). The underlying pathophysiology is poorly understood but changes in the gut microbiome have been suggested to be involved. Design: Using a case control design we recruited 84 subjects with liver steatosis and 83 controls from the population-based Study of Health in Pommerania. Subjects with diabetes mellitus, BMI > 25 kg/m2, immoderate alcohol intake or gallstone disease were excluded. Liver fat content was quantitated by confounder corrected chemical shift encoded MRI sequence at 1.5T. Cases with steatosis were defined as subjects with a mean liver fat content of 24.9% and controls with 2.2%. NAFLD and NASH were distinguished by using the FIB-4 score (Cut-off 1.3). Phylogenetic profiling of fecal samples was performed using the Human intestinal tract Chip (HITChip). For phenotypic correlation of the gut microbiome signature up to 224 host variables, including diet, were available and 38 reached significance. Results: By study design the extent of steatosis on liver MRI differed significantly between cases and controls (p <10 – 6). Hierarchical clustering showed a clustering tendency. Random Forrest analysis revealed 69%± 14% 95CI classification accuracy on 130 genus-level taxa. Diet did not affect the classification accuracy. Reduced Shannon diversity (p = 0.046) and richness (p = 0.007) in cases were detected. PCA cluster analysis identified 4 out of 130 taxa discriminating between cases and controls (Prevotella oralis and P. melaninogenica, Sutterella wadsworthia, Uncultured Clostridiales) all of those with bimodal distribution. NASH cases showed a significantly increased abundancy of Gram-positive taxa as well as several Bacteroides spp. that could be used as a classifier. Conclusion: In the absence of metabolic syndrome NAFLD is associated with a distinct gut microbiome signature, which is unaffected by diet. Decreased abundancy of taxa, previously defined as tipping elements, points to a pathophysiological relevance. Progression to NASH is correlated with additional distinct changes in the microbiome.
    The implementation of Natura 2000 in forests: A trans- and interdisciplinary assessment of challenges and choices.
    Winkel, G. ; Blondet, M. ; Borrass, L. ; Frei, T. ; Geitzenauer, M. ; Gruppe, A. ; Jump, A. ; Koning, J. de; Sotirov, M. ; Weiss, G. ; Winter, S. ; Turnhout, E. - \ 2015
    Environmental Science & Policy 52 (2015). - ISSN 1462-9011 - p. 23 - 32.
    climate-change - biodiversity conservation - european-union - management - science - policy - network - stand
    Natura 2000 is the core of the EU's biodiversity conservation policy. 50% of the overall protected area under Natura 2000 is forest. Yet, comparatively little is known about the implementation of the policy in forests. Building on a rich set of social and natural science data, and an inter- and transdisciplinary discussion process involving scientists from different disciplines as well as EU, national and local stakeholders, this paper identifies five important challenges related to the implementation of Natura 2000 in forests: (1) the balancing of biodiversity conservation and timber production, (2) the integration of conservation (science) and local stakeholders’ demands, (3) climate change, (4) lacking and less effective funding, and (5) conflicts related to other sectoral policies. Subsequently, five possible pathways to tackle these challenges are proposed: (1) a learning approach through better communication and transparency, (2) a pathway emphasizing the role of conservation science in developing management strategies and responding to climate change, (3) an approach of better integrating Europe's citizens in the design and implementation of the policy, (4) an approach highlighting the necessity of an effective funding strategy, and (5) the vision to work towards an integrated European land use and conservation policy. In conclusion, we emphasize, on one hand, the distinct character of the five pathways but, on the other hand, underline that probably all of them need to be followed in order to make the implementation of Natura 2000 in Europe's forests a success story.
    An economics assessment of GHG mitigation policy options for EU agriculture
    Doorslaer, B. van; Witzke, P. ; Huck, I. ; Weiss, F. ; Fellmann, T. ; Salputra, G. ; Jansson, T. ; Drabik, D. ; Leip, A. - \ 2015
    Luxembourg : Publications Office of the European Union (JRC technical reports JC 3434) - ISBN 9789279454165
    europees parlement - europees fonds voor regionale ontwikkeling - landbouwbeleid - mitigatie - landbouwkundig onderzoek - emissiereductie - agrarische economie - european parliament - european regional development fund - agricultural policy - mitigation - agricultural research - emission reduction - agricultural economics
    The report presents an overview of the historical and projected development of agricultural GHG emissions in the EU. The major objective of the report is to present the improvements made in the CAPRI modelling system with respect to GHG emission accounting and especially regarding the implementation of endogenous technological mitigation options. Furthermore, the CAPRI model was applied to provide a quantitative assessment of illustrative GHG mitigation policy options in the agricultural sector, and their production and economic implications.
    Natura 2000 et les forêts de l’Europe : Comprendre et relever les defies de la mise en oeuvre
    Winkel, Georg ; Blondet, Marieke ; Borrass, Lars ; Geitzenauer, Maria ; Gruppe, Axel ; Jump, Alistair ; Koning, Jessica De; Sotirov, Metodi ; Weiss, Gerhard ; Winter, Susanne ; Turnhout, Esther - \ 2014
    Revue Forestiere Francaise 66 (2014)6. - ISSN 0035-2829 - p. 743 - 750.

    The BiodivERsA-funded BeFoFu project has investigated both ecological challenges related to management of protected forests and governance challenges related to the implementation of Natura 2000. This Policy Brief describes these socio-ecological challenges, presents key research results, and outlines policy solution pathways towards improving the effectiveness of Natura 2000 with regards to the conservation and sustainable management of Europe’s forests.

    Contribution of Dynamic Vegetation Phenology to Decadal Climate Predictability
    Weiss, M. ; Miller, P.A. ; Hurk, B.J.J.M. van den; Noije, T. van; Stefanescu, S. ; Haarsma, R. ; Ulft, L.H. van; Hazeleger, W. ; Sager, P. Le; Smith, B. ; Schurgers, G. - \ 2014
    Journal of Climate 27 (2014)22. - ISSN 0894-8755 - p. 8563 - 8577.
    leaf-area index - ensemble forecasts - data assimilation - soil-moisture - model - prediction - system - impact - skill - oscillation
    In this study, the impact of coupling and initializing the leaf area index from the dynamic vegetation model Lund-Potsdam-Jena General Ecosystem Simulator (LPJ-GUESS) is analyzed on skill of decadal predictions in the fully coupled atmosphere-land-ocean-sea ice model, the European Consortium Earth System Model (EC-Earth). Similar to the impact of initializing the model with the observed oceanic state, initializing the leaf area index (LAI) fields obtained from an offline LPJ-GUESS simulation forced by the observed atmospheric state leads to a systematic drift. A different treatment of the water and soil moisture budget in LPJ-GUESS is a likely cause of this drift. The coupled system reduces the cold bias of the reference model over land by reducing LAI (and the associated evaporative cooling), particularly outside the growing season. The coupling with the interactive vegetation module implies more degrees of freedom in the coupled model, which generates more noise that can mask a portion of the extra signal that is generated. The forecast reliability improves marginally, particularly early in the forecast. Ranked probability skill scores are also improved slightly in most areas analyzed, but the signal is not fully coherent over the forecast interval because of the relatively low number of ensemble members. Methods to remove the LAI drift and allow coupling of other variables probably need to be implemented before significant forecast skill can be expected.
    Trends in Soil, Sediment and Groundwater Quality Management
    Rijnaarts, H. ; Weiss, H. - \ 2014
    Science of the Total Environment 485-486 (2014). - ISSN 0048-9697 - p. 701 - 704.
    site - germany
    Soil, groundwater, surface water and sediment systems play an important role in quality of life. The harmful effects of chemical pollution of such systems have been a concern for politicians, the public and scientists for decades. More than half a century of experience in soil and groundwater quality management gives the opportunity to abstract some interesting trends in societal responses, and how these relate to cost effective research and management approaches.
    Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
    Schoch, C.L. ; Robbertse, B. ; Robert, V. ; Vu, D. ; Cardinali, G. ; Irinyi, L. ; Meyer, W. ; Nilsson, R.H. ; Hughes, K. ; Miller, A.N. ; Kirk, P.M. ; Abarenkov, K. ; Aime, M.C. ; Ariyawansa, H.A. ; Bidartondo, M. ; Boekhout, T. ; Buyck, B. ; Cai, Q. ; Chen, J. ; Crespo, A. ; Crous, P.W. ; Damm, U. ; Beer, Z.W. de; Dentinger, B.T.M. ; Divakar, P.K. ; Duenas, M. ; Feau, N. ; Fliegerova, K. ; Garcia, M.A. ; Ge, Z.W. ; Griffith, G.W. ; Groenewald, J.Z. ; Groenewald, M. ; Grube, M. ; Gryzenhout, M. ; Gueidan, C. ; Guo, L. ; Hambleton, S. ; Hamelin, R. ; Hansen, K. ; Hofstetter, V. ; Hong, S.B. ; Houbraken, J. ; Hyde, K.D. ; Inderbitzin, P. ; Johnston, P.A. ; Karunarathna, S.C. ; Koljalg, U. ; Kovacs, G.M. ; Kraichak, E. ; Krizsan, K. ; Kurtzman, C.P. ; Larsson, K.H. ; Leavitt, S. ; Letcher, P.M. ; Liimatainen, K. ; Liu, J.K. ; Lodge, D.J. ; Luangsa-ard, J.J. ; Lumbsch, H.T. ; Maharachchikumbura, S.S.N. ; Manamgoda, D. ; Martin, M.P. ; Minnis, A.M. ; Moncalvo, J.M. ; Mule, G. ; Nakasone, K.K. ; Niskanen, T. ; Olariaga, I. ; Papp, T. ; Petkovits, T. ; Pino-Bodas, R. ; Powell, M.J. ; Raja, H.A. ; Redecker, D. ; Sarmiento-Ramirez, J.M. ; Seifert, K.A. ; Shrestha, B. ; Stenroos, S. ; Stielow, B. ; Suh, S.O. ; Tanaka, K. ; Tedersoo, L. ; Telleria, M.T. ; Udayanga, D. ; Untereiner, W.A. ; Dieguez Uribeondo, J. ; Subbarao, K.V. ; Vagvolgyi, C. ; Visagie, C. ; Voigt, K. ; Walker, D.M. ; Weir, B.S. ; Weiss, M. ; Wijayawardene, N.N. ; Wingfield, M.J. ; Xu, J.P. ; Yang, Z.L. ; Zhang, N. ; Zhuang, W.Y. ; Federhen, S. - \ 2014
    Database : the Journal of Biological Databases and Curation 2014 (2014). - ISSN 1758-0463 - 21 p.
    internal transcribed spacer - arbuscular mycorrhizal fungi - ribosomal dna - interspecific hybridization - sequence analyses - species complex - identification - evolution - barcode - life
    DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
    Assessing the importance of technological non-CO2 GHG emission mitigation options in EU agriculture with the CAPRI model
    Witzke, P. ; Doorslaer, B. Van; Huck, I. ; Salputra, G. ; Fellmann, T. ; Drabik, D. ; Weiss, F. ; Leip, A. - \ 2014
    - p. 1 - 15.
    The European Commission started to reflect on a new policy framework on climate and energy for 2030. Identifying the best options for agriculture to contribute to future GHG emission reductions in the EU requires a comprehensive analysis of a wide range of possible policies, technological and management measures. In this context the CAPRI model has been further improved with respect to GHG emission accounting and especially regarding the endogenous implementation of technological mitigation options. In this paper we present the methodology of the new model features and highlight the importance of including endogenous technological GHG emission mitigation options in the model analysis. Results of illustrative emission mitigation scenarios show that different assumptions on the availability and uptake of technologies alter the scenario outcome significantly. The analysis indicates that possible negative impacts of mitigation policies on agricultural production and trade can drastically be reduced when technological mitigation options are available to farmers. This is a strong signal for enhanced research and development in the area of technological mitigation options, as well as policies that promote their diffusion.
    The nitrogen footprint of food products in the European Union
    Leip, A. ; Weiss, F. ; Lesschen, J.P. ; Westhoek, H. - \ 2014
    The Journal of Agricultural Science 152 (2014)S1. - ISSN 0021-8596 - p. 20 - 33.
    greenhouse-gas emissions - water footprint - agriculture - land - budgets - carbon - capri
    Nitrogen (N) is an essential element for plants and animals. Due to large inputs of mineral fertilizer, crop yields and livestock production in Europe have increased markedly over the last century, but as a consequence losses of reactive N to air, soil and water have intensified as well. Two different models (CAPRI and MITERRA) were used to quantify the N flows in agriculture in the European Union (EU27), at country-level and for EU27 agriculture as a whole, differentiated into 12 main food categories. The results showed that the N footprint, defined as the total N losses to the environment per unit of product, varies widely between different food categories, with substantially higher values for livestock products and the highest values for beef (c. 500 g N/kg beef), as compared to vegetable products. The lowest N footprint of c. 2 g N/kg product was calculated for sugar beet, fruits and vegetables, and potatoes. The losses of reactive N were dominated by N leaching and run-off, and ammonia volatilization, with 0·83 and 0·88 due to consumption of livestock products. The N investment factors, defined as the quantity of new reactive N required to produce one unit of N in the product varied between 1·2 kg N/kg N in product for pulses to 15–20 kg N for beef.
    Contribution of anthropology to the study of climate change
    Barnes, Jessica ; Dove, Michael ; Lahsen, Myanna ; Mathews, Andrew ; McElwee, Pamela ; McIntosh, Roderick ; Moore, Frances ; O'Reilly, Jessica ; Orlove, Ben ; Puri, Rajindra ; Weiss, Harvey ; Yager, Karina - \ 2013
    Nature Climate Change 3 (2013)6. - ISSN 1758-678X - p. 541 - 544.

    Understanding the challenge that climate change poses and crafting appropriate adaptation and mitigation mechanisms requires input from the breadth of the natural and social sciences. Anthropology's in-depth fieldwork methodology, long engagement in questions of society-environment interactions and broad, holistic view of society yields valuable insights into the science, impacts and policy of climate change. Yet the discipline's voice in climate change debates has remained a relatively marginal one until now. Here, we identify three key ways that anthropological research can enrich and deepen contemporary understandings of climate change.

    Metabolic Activation of Nonpolar Sediment Extracts Results in enhanced Thyroid Hormone Disrupting Potency
    Montano, M. ; Weiss, J. ; Hoffmann, L. ; Gutleb, A.C. ; Murk, A.J. - \ 2013
    Environmental Science and Technology 47 (2013)15. - ISSN 0013-936X - p. 8878 - 8886.
    persistent organic pollutants - brominated flame retardants - effect-directed analysis - halogenated aromatic-hydrocarbons - polybrominated diphenyl ethers - in-vitro - polychlorinated-biphenyls - endocrine disruption - estrogenic activity - hepatic microsomes
    Traditional sediment risk assessment predominantly considers the hazard derived from legacy contaminants that are present in nonpolar sediment extracts, such as polychlorinated biphenyls (PCBs), dioxins, furans (PCDD/Fs), and polyaromatic hydrocarbons (PAHs). Although in vivo experiments with these compounds have shown to be thyroid hormone disrupting (THD), in vitro their THD potency is not observed in nonpolar sediment extracts. This is hypothesized to be due to the absence of in vitro biotransformation which will result in bioactivation of the lipophilic compounds into THD hydroxyl metabolites. This study reveals that indeed metabolically activated nonpolar contaminants in sediments can competitively bind to thyroid hormone transport proteins. Sediment fractions were incubated with S9 rat microsomes, and the metabolites were extracted with a newly developed method that excludes most of the lipids to avoid interference in the applied nonradioactive 96-well plate TTR competitive binding assay. Metabolic activation increased the TTR binding potency of nonpolar fractions of POP-polluted sediments up to 100 times, resulting in potencies up to 240 nmol T4 equivalents/g sediment equivalent (nmol T4-Eq/g SEQ). This demonstrates that a more realistic in vitro sediment THD risk characterization should also include testing of both polar and medium polar sediment extracts for THD, as well as bioactivated nonpolar sediment fractions to prevent underestimation of its toxic potency.
    Ex vivo transcriptional profiling reveals a common set of genes important for the adaptation of Pseudomonas aeruginosa to chronically infected host sites
    Bielecki, P. ; Komor, U. ; Bielecka, A. ; Müsken, M. ; Puchalka, J. ; Pletz, M.W. ; Ballmann, M. ; Martins Dos Santos, V.A.P. ; Weiss, S. ; Häussler, S. - \ 2013
    Environmental Microbiology 15 (2013)2. - ISSN 1462-2912 - p. 570 - 587.
    burn wound infections - biofilm formation - cystic-fibrosis - therapeutic strategies - expression - motility - mutants - protein - system - identification
    The opportunistic bacterium Pseudomonas aeruginosa is a major nosocomial pathogen causing both devastating acute and chronic persistent infections. During the course of an infection, P.¿ aeruginosa rapidly adapts to the specific conditions within the host. In the present study, we aimed at the identification of genes that are highly expressed during biofilm infections such as in chronically infected lungs of patients with cystic fibrosis (CF), burn wounds and subcutaneous mouse tumours. We found a common subset of differentially regulated genes in all three in vivo habitats and evaluated whether their inactivation impacts on the bacterial capability to form biofilms in vitro and to establish biofilm-associated infections in a murine model. Additive effects on biofilm formation and host colonization were discovered by the combined inactivation of several highly expressed genes. However, even combined inactivation was not sufficient to abolish the establishment of an infection completely. These findings can be interpreted as evidence that either redundant traits encode functions that are essential for in vivo survival and chronic biofilm infections and/or bacterial adaptation is considerably achieved independently of transcription levels. Supplemental screens, will have to be applied in order to identify the minimal set of key genes essential for the establishment of chronic infectious diseases
    Developing Conceptual Framework for Ecosystem Mapping
    Banko, G. ; Weiss, M. ; Moser, D. ; Ubach, R. ; Abdul Malak, D. ; Halada, L. ; Roerink, G.J. ; Hazeu, G.W. ; Mucher, C.A. ; Hennekens, S.M. ; Schaminee, J.H.J. ; Brodsky, L. - \ 2013
    Kopenhagen : EEA - European Environment Agency
    Analytical improvements shown over four interlaboratory studies of perfluoroalkyl substances in environmental and food samples
    Weiss, J. ; Veen, I. van der; Leeuwen, S. van; Cofino, W.P. ; Crum, S.J.H. ; Boer, J. de - \ 2013
    TrAC : Trends in Analytical Chemistry 43 (2013). - ISSN 0165-9936 - p. 204 - 216.
    international harmonized protocol - population characteristics - perfluorinated compounds - mass-spectrometry - new-model - exposure - acids - uncertainties - laboratories - inference
    An increasing number of reports confirm the world-wide presence of the perfluoroalkyl substances (PFASs). As a consequence, the demand for qualitative and quantitative environmental occurrence data requires accurate risk assessments. To improve the analytical quality of the determination of PFASs in food and environmental samples, a 4th international interlaboratory study (ILS) was conducted in 2011. A total of 31 partners participated, and, depending on the sample matrix, up to 29 data sets were submitted. The ILS focused on food samples, as it was organized by the PERFOOD consortium in collaboration with QUASIMEME. The results showed that the cumulative experience of the participants has improved their analytical quality over four international ILSs. Several sources of errors were identified and methods to avoid them are suggested.
    Immunoglobulins drive terminal maturation of splenic dendritic cells
    Zietara, N. ; Lyszkiewicz, M. ; Puchalka, J. ; Gutierrez, M.G. ; Lienenklaus, S. ; Hobeika, E. ; Reth, M. ; Martins Dos Santos, V.A.P. ; Krueger, A. ; Weiss, S. - \ 2013
    Proceedings of the National Academy of Sciences of the United States of America 110 (2013)6. - ISSN 0027-8424 - p. 2282 - 2287.
    c-type lectin - cross-presentation - antigen presentation - in-vivo - functional maturation - complement receptors - immune-responses - b-lymphocytes - self-antigens - t-cells
    Nature and physiological status of antigen-presenting cells, such as dendritic cells DCs, are decisive for the immune reactions elicited. Multiple factors and cell interactions have been described that affect maturation of DCs. Here, we show that DCs arising in the absence of immunoglobulins (Ig) in vivo are impaired in cross-presentation of soluble antigen. This deficiency was due to aberrant cellular targeting of antigen to lysosomes and its rapid degradation. Function of DCs could be restored by transfer of Ig irrespective of antigen specificity and isotype. Modulation of cross-presentation by Ig was inhibited by coapplication of mannan and, thus, likely to be mediated by C-type lectin receptors. This unexpected dependency of splenic DCs on Ig to cross-present antigen provides insights into the interplay between cellular and humoral immunity and the immunomodulatory capacity of Ig
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