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.

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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
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.
What Limits the Distribution of Liriomyza huidobrensis and Its Congener Liriomyza sativae in Their Native Niche : When Temperature and Competition Affect Species' Distribution Range in Guatemala
Rodríguez-Castañeda, Genoveva ; MacVean, C. ; Cardona, C. ; Hof, A.R. - \ 2017
Journal of Insect Science 17 (2017)4. - ISSN 1536-2442 - 13 p.
introduced species - Liriomyza huidobrensis - Liriomyza sativae - native niche - physiological limit

Factors limiting distribution range for most species are generally unknown regardless of whether they are native or invasive. We studied factors that could enable or restrict the distribution of two cosmopolitan invasive leafminer fly species, Liriomyza huidobrensis (Blanchard) and Liriomyza sativae (Blanchard) in their native niche. In order to test which ecological and environmental factors affect leafminer distribution we conducted thermal tolerance assays, sampled along elevation gradients and modeled species distribution. Findings from the field and rearing chambers showed a physiological restriction due to high temperatures for L. huidobrensis at 28-29 °C, above which adult emergence is compromised. We also found that maximum temperatures below 22 °C, typical of tropical highlands, favored L. huidobrensis. L. sativae was found across a wider temperature range (i.e., from 21 to 36 °C) in Guatemala. Our finding of a physiological threshold in temperature for L. huidobrensis may enable us to predict its invasive risk when combined with the environmental conditions at horticultural ports of entry and the global agricultural landscape. Further, it strengthens our predictions on shifts in distribution of the leafminer fly under future climate. We also found a temperature mediated competitive exclusion interaction between the two herbivore species, where L. sativae occurred at temperatures < 22 °C only in the absence of L. huidobrensis. We show that parasitoids had a negative effect on the leafminer flies, which varied with host plant. Finally, we show the importance of taking a multiaspect approach when investigating what limits distribution and invasiveness of a species.

Current challenges facing the assessment of the allergenic capacity of food allergens in animal models
Bøgh, Katrine Lindholm ; Bilsen, Jolanda van; Głogowski, Robert ; López-Expósito, Iván ; Bouchaud, Grégory ; Blanchard, Carine ; Bodinier, Marie ; Smit, Joost ; Pieters, Raymond ; Bastiaan-Net, Shanna ; Wit, Nicole de; Untersmayr, Eva ; Adel-Patient, Karine ; Knippels, Leon ; Epstein, Michelle M. ; Noti, Mario ; Nygaard, Unni Cecilie ; Kimber, Ian ; Verhoeckx, Kitty ; O'Mahony, Liam - \ 2016
Clinical and Translational Allergy 6 (2016). - ISSN 2045-7022
Animal models - Food allergy - Hazard identification - Novel allergens

Food allergy is a major health problem of increasing concern. The insufficiency of protein sources for human nutrition in a world with a growing population is also a significant problem. The introduction of new protein sources into the diet, such as newly developed innovative foods or foods produced using new technologies and production processes, insects, algae, duckweed, or agricultural products from third countries, creates the opportunity for development of new food allergies, and this in turn has driven the need to develop test methods capable of characterizing the allergenic potential of novel food proteins. There is no doubt that robust and reliable animal models for the identification and characterization of food allergens would be valuable tools for safety assessment. However, although various animal models have been proposed for this purpose, to date, none have been formally validated as predictive and none are currently suitable to test the allergenic potential of new foods. Here, the design of various animal models are reviewed, including among others considerations of species and strain, diet, route of administration, dose and formulation of the test protein, relevant controls and endpoints measured.

Inter-laboratory study to characterize the detection of serum antibodies against porcine epidemic diarrhoea virus
Strandbygaard, Bertel ; Lavazza, Antonio ; Lelli, Davide ; Blanchard, Yannick ; Grasland, Béatrice ; Poder, Sophie Le ; Rose, Nicolas ; Steinbach, Falko ; Poel, Wim H.M. van der; Widén, Frederik ; Belsham, Graham J. ; Bøtner, Anette - \ 2016
Veterinary Microbiology 197 (2016). - ISSN 0378-1135 - p. 151 - 160.
ELISA - PEDV - Porcine coronavirus - Ring trial - Serology

Porcine epidemic diarrhea virus (PEDV) has caused extensive economic losses to pig producers in many countries. It was recently introduced, for the first time, into North America and outbreaks have occurred again in multiple countries within Europe as well. To assess the properties of various diagnostic assays for the detection of PEDV infection, multiple panels of porcine sera have been shared and tested for the presence of antibodies against PEDV in an inter-laboratory ring trial. Different laboratories have used a variety of “in house” ELISAs and also one commercial assay. The sensitivity and specificity of each assay has been estimated using a Bayesian analysis applied to the ring trial results obtained with the different assays in the absence of a gold standard. Although different characteristics were found, it can be concluded that each of the assays used can detect infection of pigs at a herd level by either the early European strains of PEDV or the recently circulating strains (INDEL and non-INDEL). However, not all the assays seem suitable for demonstrating freedom from disease in a country. The results from individual animals, especially when the infection has occurred within an experimental situation, show more variation.

Assumptions behind size-based ecosystem models are realistic
Andersen, Ken H. ; Blanchard, Julia L. ; Fulton, Elizabeth A. ; Gislason, Henrik ; Jacobsen, Nis Sand ; Kooten, Tobias van - \ 2016
ICES Journal of Marine Science 73 (2016)6. - ISSN 1054-3139 - p. 1651 - 1655.
Balanced harvesting - Cohort biomass - Size-spectrum model

A recent publication about balanced harvesting (Froese et al., ICES Journal of Marine Science; 73: 1640-1650) contains several erroneous statements about size-spectrum models. We refute the statements by showing that the assumptions pertaining to size-spectrum models discussed by Froese et al. are realistic and consistent. We further show that the assumption about density-dependence being described by a stock recruitment relationship is responsible for determining whether a peak in the cohort biomass of a population occurs late or early in life. Finally, we argue that there is indeed a constructive role for a wide suite of ecosystem models to evaluate fishing strategies in an ecosystem context.

The links between Biodiversity and Ecosystem Services
Balvanera, P. ; Quijas, S. ; Martin-Lopez, B. ; Barrios, E. ; Dee, L. ; Isbell, F. ; Durance, I. ; White, P. ; Blanchard, R. ; Groot, R.S. de - \ 2015
In: Handbook of Ecosystems Services / Potchin, M., Haines-Young, R., Turner, K., Earthscan - 640 p.
From farm scale synergies to village scale trade-offs: Cereal crop residues use in an agro-pastoral system of the Sudanian zone of Burkina Faso
Andrieu, N. ; Vayssières, J. ; Corbeels, M. ; Blanchard, M. ; Vall, E. ; Tittonell, P.A. - \ 2015
Agricultural Systems 134 (2015). - ISSN 0308-521X - p. 84 - 96.
west-african savanna - sub-saharan africa - livestock systems - conservation agriculture - fertility management - phosphorus budget - soil fertility - spatial carbon - nitrogen - flows
Traditionally, cereal crop harvest residues are communally grazed by the ruminant herds of villagers and transhumant pastoralists in the agro-pastoral systems which predominate in the savannah zone of West Africa. We analysed the impact of the private use of crop residues by individual farmers on crop and livestock productivity at three scales: the field, farm, and village. We collected data in the village of Koumbia, located in the Sudanian region of Burkina Faso. Three types of farmers were identified: resource-poor farmers, predominantly livestock farmers, and resource-rich farmers. The trade-offs between different uses and users of cereal crop residues at the three scales were analysed through field surveys and a simple model of biomass flows. We considered current communal use practices and two alternative scenarios of private cereal crop residue use: (i) for composting (fertility scenario) and (ii) as fodder (fodder scenario). Our analysis of current practices confirmed that farmers left around 80% of cereal crop residues on their fields. Soil fertility for cereal production therefore could be improved through crop residue management at the farm scale. We also found that communal grazing benefited farmers with high numbers of livestock. Maize grain production at the farm scale was improved in both of the simulated scenarios. Yet these scenarios had a negative impact on fodder self-sufficiency at the village scale, and on the N balance of the savannah-derived rangelands. The negative impact was greater in the fertility scenario than the fodder stock scenario. Increasing cereal productivity at the farm scale cannot be achieved without considering the trade-offs involved at the village scale. Changes in practices will require negotiations between the different types of farmers involved. Participatory innovation platforms with discussion support tools like the model presented in our study can facilitate such negotiations.
Evaluating targets and trade-offs among fisheries and conservation objectives using a multispecies size spectrum model
Blanchard, J.L. ; Andersen, K.H. ; Scott, F. ; Hintzen, N.T. ; Piet, G.J. ; Jennings, S. - \ 2014
Journal of Applied Ecology 51 (2014)3. - ISSN 0021-8901 - p. 612 - 622.
large fish indicator - north-sea - ecosystem models - marine ecosystems - trophic cascades - celtic sea - community - management - abundance - climate
Marine environmental management policies seek to ensure that fishing impacts on fished populations and other components of the ecosystem are sustainable, to simultaneously meet objectives for fisheries and conservation. For example, in Europe, targets for (i) biodiversity, (ii) food web structure as indicated by the proportion of large fish and (iii) fishing mortality rates for exploited species that lead to maximum sustainable yield, F-MSY,F- are being proposed to support implementation of the Marine Strategy Framework Directive. Efforts to reconcile any trade-offs among objectives need to be informed by knowledge on the consequences of alternate management actions. We develop, calibrate and apply a multispecies size spectrum model of the North Sea fish community to assess the response of populations and the community to fishing. The model predicts species' size distributions, abundance, productivity and interactions and therefore provides a single framework for evaluating trade-offs between population status, community and food web structure, biodiversity and fisheries yield. We show that the model can replicate realistic fish population and community structure and past responses to fishing. We assess whether meeting management targets for exploited North Sea populations (fishing species at F-MSY) will be sufficient to meet proposed targets for biodiversity and food web indicators under two management scenarios (status quo and F-MSY). The recovery in biodiversity indicators is 60% greater when fishing populations at F-MSY than if status quo (2010) fishing rates are maintained. The probability of achieving a food web target was 60% under both scenarios in spite of major community restructuring revealed by other indicators of community size structure. Synthesis and applications. Our model can be applied to evaluate indicator targets and trade-offs among fisheries and conservation objectives. There is a significant probability that reductions in fishing mortality below F-MSY would be needed in Europe if managers make a binding commitment to a proposed large fish indicator target, with concomitant reductions in fisheries yield.
Standard methods for virus research in Apis mellifera
Miranda, J.R. ; Bailey, L. ; Ball, B.V. ; Blanchard, P. ; Budge, G.E. ; Chejanovsky, N. ; Chen, Y.P. ; Gauthier, L. ; Genersch, E. ; Graaf, D.C. de; Ribiere, M. ; Ryabov, E. ; Smet, L. de; Steen, J.J.M. van der - \ 2013
Journal of Apicultural Research 52 (2013)4. - ISSN 0021-8839
deformed-wing-virus - bee-paralysis-virus - queen-cell-virus - adult honey-bees - real-time pcr - reverse-transcriptase pcr - picorna-like virus - rhopalosiphum-padi virus - quantitative rt-pcr - messenger-rna quantification
Honey bee virus research is an enormously broad area, ranging from subcellular molecular biology through physiology and behaviour, to individual and colony-level symptoms, transmission and epidemiology. The research methods used in virology are therefore equally diverse. This article covers those methods that are very particular to virological research in bees, with numerous cross-referrals to other BEEBOOK papers on more general methods, used in virology as well as other research. At the root of these methods is the realization that viruses at their most primary level inhabit a molecular, subcellular world, which they manipulate and interact with, to produce all higher order phenomena associated with virus infection and disease. Secondly, that viruses operate in an exponential world, while the host operates in a linear world and that much of the understanding and management of viruses hinges on reconciling these fundamental mathematical differences between virus and host. The article concentrates heavily on virus propagation and methods for detection, with minor excursions into surveying, sampling management and background information on the many viruses found in bees.
The SMILING project: A North–South–South collaborative action to prevent micronutrient deficiencies in women and young children in Southeast Asia
Berger, J. ; Blanchard, G. ; Doets, E.L. ; Fahmida, U. ; Hulshof, P.J.M. - \ 2013
Food and Nutrition Bulletin 34 (2013)2. - ISSN 0379-5721 - p. S133 - S139.
undernutrition - consequences - health
BACKGROUND: The "Sustainable Micronutrient Interventions to Control Deficiencies and Improve Nutritional Status and General Health in Asia" project (SMILING), funded by the European Commission, is a transnational collaboration of research institutions and implementation agencies in five Southeast Asian countries--Cambodia, Indonesia, Laos PDR, Thailand, and Vietnam--with European partners, to support the application of state-of-the art knowledge to alleviate micronutrient malnutrition in Southeast Asia. OBJECTIVE: The major expected outcomes are to improve micronutrient status on a large scale, to identify priority interventions in each Southeast Asian country, and to develop a road map for decision makers and donors for inclusion of these priority interventions into the national policy. METHODS: SMILING has been built around a strong project consortium that works on a constant and proactive exchange of data and analyses between partners and allows for the differences in contexts and development stages of the countries, as well as a strong North-South-South collaboration and colearning. RESULTS: The selection of Southeast Asian countries considered the range of social and economic development, the extent of micronutrient malnutrition, and capacity and past success in nutrition improvement efforts. SMILING is applying innovative tools that support nutrition policy-making and programming. The mathematical modeling technique combined with linear programming will provide insight into which food-based strategies have the potential to provide essential (micro) nutrients for women and young children. Multicriteria mapping will offer a flexible decision-aiding tool taking into account the variability and uncertainty of opinions from key stakeholders. The lessons learned throughout the project will be widely disseminated.
The Cyst Nematode SPRYSEC Protein RBP-1 Elicits Gpa2- and RanGAP2-Dependent Plant Cell Death
Sacco, M.A. ; Koropacka, K.B. ; Grenier, E. ; Jaubert, M.J. ; Blanchard, A. ; Goverse, A. ; Smant, G. ; Moffett, P. - \ 2009
PLoS Pathogens 5 (2009)8. - ISSN 1553-7366
disease resistance genes - rich repeat protein - nb-lrr protein - globodera-pallida - downy mildew - sequence alignment - avirulence genes - virus-resistance - potato - arabidopsis
Plant NB-LRR proteins confer robust protection against microbes and metazoan parasites by recognizing pathogen-derived avirulence (Avr) proteins that are delivered to the host cytoplasm. Microbial Avr proteins usually function as virulence factors in compatible interactions; however, little is known about the types of metazoan proteins recognized by NB-LRR proteins and their relationship with virulence. In this report, we demonstrate that the secreted protein RBP-1 from the potato cyst nematode Globodera pallida elicits defense responses, including cell death typical of a hypersensitive response (HR), through the NB-LRR protein Gpa2. Gp-Rbp-1 variants from G. pallida populations both virulent and avirulent to Gpa2 demonstrated a high degree of polymorphism, with positive selection detected at numerous sites. All Gp-RBP-1 protein variants from an avirulent population were recognized by Gpa2, whereas virulent populations possessed Gp-RBP-1 protein variants both recognized and non-recognized by Gpa2. Recognition of Gp-RBP-1 by Gpa2 correlated to a single amino acid polymorphism at position 187 in the Gp-RBP-1 SPRY domain. Gp-RBP-1 expressed from Potato virus X elicited Gpa2-mediated defenses that required Ran GTPase-activating protein 2 (RanGAP2), a protein known to interact with the Gpa2 N terminus. Tethering RanGAP2 and Gp-RBP-1 variants via fusion proteins resulted in an enhancement of Gpa2-mediated responses. However, activation of Gpa2 was still dependent on the recognition specificity conferred by amino acid 187 and the Gpa2 LRR domain. These results suggest a two-tiered process wherein RanGAP2 mediates an initial interaction with pathogen-delivered Gp-RBP-1 proteins but where the Gpa2 LRR determines which of these interactions will be productive
Perspective: Evolution and detection of genetic robustness
Visser, J.A.G.M. de; Hermisson, J. ; Wagner, G.P. ; Ancel Meyers, L. ; Bagheri-Chaichian, H. ; Blanchard, J.L. ; Chao, L. ; Cheverud, J.M. ; Elena, S.F. ; Fontana, W. ; Gibson, G. ; Hansen, T.F. ; Krakauer, D. ; Lewontin, R.C. ; Ofria, C. ; Rice, S.H. ; Dassow, G. von; Wagner, A. ; Whitlock, M.C. - \ 2003
Evolution 57 (2003)9. - ISSN 0014-3820 - p. 1959 - 1972.
drosophila-melanogaster - developmental stability - deleterious mutations - fitness components - heat-shock - canalization - dominance - epistasis - selection - plasticity
Robustness is the invariance of phenotypes in the face of perturbation. The robustness of phenotypes appears at various levels of biological organization, including gene expression, protein folding, metabolic flux, physiological homeostasis, development, and even organismal fitness. The mechanisms underlying robustness are diverse, ranging from thermodynamic stability at the RNA and protein level to behavior at the organismal level. Phenotypes can be robust either against heritable perturbations (e.g., mutations) or nonheritable perturbations (e.g., the weather). Here we primarily focus on the first kind of robustness-genetic robustness-and survey three growing avenues of research: (1) measuring genetic robustness in nature and in the laboratory; (2) understanding the evolution of genetic robustness; and (3) exploring the implications of genetic robustness for future evolution.
The contribution of biotic and abiotic processes during azo dye reduction in anaerobic sludge
Zee, F.P. van der; Bisschops, I.A.E. ; Blanchard, V.G. ; Bouwman, R.H.M. ; Lettinga, G. ; Field, J.A. - \ 2003
Water Research 37 (2003)13. - ISSN 0043-1354 - p. 3098 - 3109.
rioolafvalwater - anaërobe behandeling - azoverbindingen - kleurstoffen (dyes) - redoxreacties - afvalwaterbehandeling - sewage effluent - anaerobic treatment - azo compounds - dyes - redox reactions - waste water treatment - redox mediators - decolorization - bacteria - system
Azo dye reduction results from a combination of biotic and abiotic processes during the anaerobic treatment of dye containing effluents. Biotic processes are due to enzymatic reactions whereas the chemical reaction is due to sulfide. In this research, the relative impact of the different azo dye reduction mechanisms was determined by investigating the reduction of Acid Orange 7 (AO7) and Reactive Red 2 (RR2) under different conditions. Reduction rates of two azo dyes were compared in batch assays over a range of sulphide concentrations in the presence of living or inactivated anaerobic granular sludge
Azo dye reduction results from a combination of biotic and abiotic processes during the anaerobic treatment of dye containing effluents. Biotic processes are due to enzymatic reactions whereas the chemical reaction is due to sulfide. In this research, the relative impact of the different azo dye reduction mechanisms was determined by investigating the reduction of Acid Orange 7 (AO7) and Reactive Red 2 (RR2) under different conditions. Reduction rates of two azo dyes were compared in batch assays over a range of sulphide concentrations in the presence of living or inactivated anaerobic granular sludge. Biological dye reduction followed zero order kinetics and chemical dye reduction followed second-order rate kinetics as a function of sulfide and dye concentration. Chemical reduction of the dyes was greatly stimulated in the presence of autoclaved sludge; whereas chemical dye reduction was not affected by living or gamma-irradiated-sludge. Presumably redox-mediating enzyme cofactors released by cell lysis contributed to the stimulatory effect. This hypothesis was confirmed in assays evaluating the chemical reduction of AO7 utilizing riboflavin, representative of the heat stable redox-mediating moieties of common occurring flavin enzyme cofactors. Sulfate influenced dye reduction in accordance to biogenic sulfide formation from sulfate reduction. In assays lacking sulfur compounds, dye reduction only readily occurred in the presence of living granular sludge, demonstrating the importance of enzymatic mechanisms. Both chemical and biological mechanisms of dye reduction were greatly stimulated by the addition of the redox-mediating compound, anthraquinone-disulfonate. Based on an analysis of the kinetics and demonstration in lab-scale upward-flow anaerobic sludge bed reactors, the relative importance of chemical dye reduction mechanisms in high rate anaerobic bioreactors was shown to be small due to the high biomass levels in the reactors. (C) 2003 Elsevier Science Ltd. All rights reserved.
Diminishing returns from mutation supply rate in asexual populations
Visser, J.A.G.M. de; Zeyl, C.W. ; Gerrish, P.J. ; Blanchard, J.L. ; Lenski, R.E. - \ 1999
Science 283 (1999). - ISSN 0036-8075 - p. 404 - 406.
Recensie van: I. Blanchard (ed.) Labour and leisure in historical perspective, thirteenth to twentieth centuries. Franz Steiner, Stuttgart 1994.
Schuurman, A. - \ 1996
Tijdschrift voor Geschiedenis 109 (1996). - ISSN 0040-7518 - p. 284 - 284.
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