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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    Comparative genomics of virulence towards malaria mosquitoes in Beauveria bassiana
    Valero Jimenez, C.A. ; Spring in 'T Veld, D. ; Smit, Sandra ; Koenraadt, C.J.M. ; Zwaan, B.J. ; Kan, J.A.L. van - \ 2015
    In: Book of Abstracts 28th Fungal Genetics Conference. - - p. 162 - 162.
    Entomopathogenic fungi such as Metarhizium anisopliae and Beauveria bassiana have been proposed as biological control agents to kill malaria mosquitoes. Indeed, it has been shown that these fungi successfully reduce the lifespan of mosquitoes in the laboratory and in the field. Previously, we characterized the natural variation in virulence of 29 isolates of Beauveria bassiana and showed that there were up to 10-fold differences in virulence between the most virulent isolate compared to the least virulent isolate. This natural variation can be used to uncover the genetic mechanisms underpinning virulence, which will provide essential information for (i) further improving fungi as biocontrol agents, and (ii) estimating the likelihood of resistance development in the vector, i.e. mosquitoes. In this study, we sequenced 5 isolates representing the extremes of low/high virulence for further comparative genomic analysis. The genomes were de novo assembled and the draft genome size varied from 35.02 Mb to 38.83 Mb. The predicted encoding proteins were supported with three RNA-Seq libraries, and ranged from 10,283 to 10,831 genes. The core set consisted of 8800 genes shared between all isolates. We focused on the genome differences between isolates with contrasting virulence, with special emphasis on gene gain/loss, single nucleotide polymorphisms (SNPs), and secreted proteins. Our findings are discussed in the context of other sequenced entomopathogenic fungi (Metarhizium anisopliae, M. robertsii and M. acridum) as well as plant pathogenic fungi.
    Principal polynomial analysis
    Laparra, Valero ; Jiménez, Sandra ; Tuia, Devis ; Camps-Valls, Gustau ; Malo, Jesus - \ 2014
    International Journal of Neural Systems 24 (2014)7. - ISSN 0129-0657
    Classification - Coding - Dimensionality reduction - Manifold learning - Principal Polynomial Analysis

    This paper presents a new framework for manifold learning based on a sequence of principal polynomials that capture the possibly nonlinear nature of the data. The proposed Principal Polynomial Analysis (PPA) generalizes PCA by modeling the directions of maximal variance by means of curves, instead of straight lines. Contrarily to previous approaches, PPA reduces to performing simple univariate regressions, which makes it computationally feasible and robust. Moreover, PPA shows a number of interesting analytical properties. First, PPA is a volume-preserving map, which in turn guarantees the existence of the inverse. Second, such an inverse can be obtained in closed form. Invertibility is an important advantage over other learning methods, because it permits to understand the identified features in the input domain where the data has physical meaning. Moreover, it allows to evaluate the performance of dimensionality reduction in sensible (input-domain) units. Volume preservation also allows an easy computation of information theoretic quantities, such as the reduction in multi-information after the transform. Third, the analytical nature of PPA leads to a clear geometrical interpretation of the manifold: it allows the computation of Frenet-Serret frames (local features) and of generalized curvatures at any point of the space. And fourth, the analytical Jacobian allows the computation of the metric induced by the data, thus generalizing the Mahalanobis distance. These properties are demonstrated theoretically and illustrated experimentally. The performance of PPA is evaluated in dimensionality and redundancy reduction, in both synthetic and real datasets from the UCI repository.

    Natural variation in virulence of the entomopathogenic fungus Beauveria bassiana against malaria mosquitoes
    Valero Jimenez, C.A. ; Debets, A.J.M. ; Kan, J.A. van; Schoustra, S.E. ; Takken, W. ; Zwaan, B.J. ; Koenraadt, C.J.M. - \ 2014
    Malaria Journal 13 (2014). - ISSN 1475-2875 - 8 p.
    metarhizium-anisopliae - anopheles-gambiae - infection - agents - susceptibility - degradation - persistence - expression - resistance - behavior
    Background Insecticide resistance is greatly hampering current efforts to control malaria and therefore alternative methods are needed. Entomopathogenic fungi have been proposed as an alternative with a special focus on the cosmopolitan species Beauveria bassiana. However, few studies have analysed the effects of natural variation within fungal isolates on mosquito survival, and the implications and possible exploitation for malaria control. Methods Laboratory bioassays were performed on adult female mosquitoes (Anopheles coluzzii) with spores from 29 isolates of B. bassiana, originating from different parts of the world. In addition, phenotypic characteristics of the fungal isolates such as sporulation, spore size and growth rate were studied to explore their relationship with virulence. Results All tested isolates of B. bassiana killed An. coluzzii mosquitoes, and the rate at which this happened differed significantly among the isolates. The risk of mosquitoes dying was around ten times higher when they were exposed to the most virulent as compared to the least virulent isolate. There was significant variation among isolates in spore size, growth rate and sporulation, but none of these morphological characteristics were correlated, and thus predictive, for the ability of the fungal isolate to kill malaria mosquitoes. Conclusions This study shows that there is a wide natural variation in virulence of isolates of B. bassiana, and that selecting an appropriate fungal isolate is highly relevant in killing and thus controlling malaria mosquitoes, particularly if used as part of an integrated vector management strategy. Also, the wide variation observed in virulence offers the opportunity to better understand the molecular and genetic mechanisms that drive this variation and thus to address the potential development of resistance against entomopathogenic fungi
    Ranking risks posed by composite food products
    Stella, P. ; Cerf, O. ; Koutsoumanis, K.P. ; Nguyen-The, C. ; Sofos, J.N. ; Valero, A. ; Zwietering, M.H. ; Hugas, M. - \ 2013
    In: Conference proceedings 8th International Conference on Predictive Modelling in Food, Paris, France, 16 - 20 September, 2013. - Paris : CNIEL, IFIP - ISBN 9782356700254 - p. 191 - 192.
    Ranking the microbiological safety of foods: A new tool and its application to composite products
    Stella, P. ; Cerf, O. ; Hugas, M. ; Koutsoumanis, K.P. ; Nguyen-The, C. ; Sofos, J.N. ; Valero, A. ; Zwietering, M.H. - \ 2013
    Trends in Food Science and Technology 33 (2013)2. - ISSN 0924-2244 - p. 124 - 138.
    quantitative risk-assessment - yersinia-enterocolitica - escherichia-coli - moisture transfer - water - infection - outbreak - storage - virus
    A methodology based on the combination of two complementary approaches to rank microbiological risks in foods is presented. In the forward approach data on the pathogenicity of hazards and their behaviour in food during processing and following steps, up to consumption, are used in decision trees to qualitatively estimate the risk associated with foods. In the backward approach risks are evaluated based on the analysis of data available on the past occurrence of hazards and foodborne outbreaks. The categorisation of foods using the forward approach should prevail, and whenever it leads to a likely risk for a given food, the risk can be further qualified with the results from the backward approach. The methodology developed was applied to rank the public health risk posed by certain composite products, which contain both processed products of animal origin and products of plant origin (e.g., bread, cakes, chocolate). Despite limitations in the data available for these foods, valuable results were obtained. The method is therefore considered suitable for application with success to other types of food, and is proposed as a tool for risk managers to rank foods based on their potential food safety risks
    Scientific opinion on public health risks represented by certain composite products containing food of animal origin
    Cerf, O. ; Koutsoumanis, K. ; Nguyen-The, C. ; Sofos, J. ; Valero, A. ; Zwietering, M.H. - \ 2012
    EFSA Journal 10 (2012)5. - 132 p.
    This Opinion reviews the factors that affect microbial survival and growth in composite products, and in foods in general. It concludes that the main factors to be considered are: water activity, pH, temperature and duration of storage, processing, and intensity and duration of other non-thermal physical processes applied. Prevalence and concentration of the pathogens in food are important to determine the risk for consumers. The opinion presents a review of the quantitative microbiology models and databases that can be used to provide quantitative estimations of the impact of the above factors on the survival and growth of the main bacterial pathogens. In composite products, migration and diffusion of moisture and substances among the ingredients may change their physico-chemical parameters, particularly at the interfaces. Therefore, the assessment of the risk posed by composite products needs to consider the combinations of parameters most permissive to survival and growth of pathogens. Two complementary approaches are proposed for the identification and profiling of microbiological hazards in different specific composite products. The first one is based on past outbreaks and prevalence of hazards in the products and leads to the conclusion that the most frequent hazard-composite product combinations are Salmonella in cakes and bakery products. The second one consists in decision tools based on the impact on the pathogens of food composition and food processing. Categorisation of the risk for composite products requires information on their composition, processing and further handling, which can largely differ for foods belonging to the same category. Further conditions may influence the risk and should be verified, i.e. hygienic conditions during preparation of the composite products and their ingredients, shelf-life conditions, and reliability of cooking by consumers to inactivate pathogens. The decision tools developed apply to all composite products considered by the mandate, as well as to all other foods. © European Food Safety Authority, 2012
    Farm Seed Opportunities a project to promote landrace use and renew biodiversity.
    Chable, V. ; Goldringer, I. ; Dawson, J. ; Bocci, R. ; Lammerts Van Bueren, E. ; Serpolay, E. ; Gonzalez, J.M. ; Valero, A. ; Levillain, T. ; Burg, W.J. van der; Pimbert, M. ; Pino, S. ; Kik, C. - \ 2009
    In: European landraces onfarm conservation, management and use / Negri, V., Maxted, N., Vetlainen, M., Rome : Bioversity International (Bioversity Technical Bulletin 15) - ISBN 9789290438052 - p. 266 - 274.
    Electroporation of cells in microfluidic devices: a review
    Fox, M.B. ; Esveld, D.C. ; Valero, A. ; Luttge, R. ; Mastwijk, H.C. ; Bartels, P.V. ; Berg, A.B.A. van den; Boom, R.M. - \ 2006
    Analytical and Bioanalytical Chemistry 385 (2006)3. - ISSN 1618-2642 - p. 474 - 485.
    pulsed-electric-field - dielectrophoretic impedance measurement - capillary-electrophoresis - high-intensity - biological cells - single cells - microfabricated devices - analysis systems - mass-transfer - patch-clamp
    In recent years, several publications on microfluidic devices have focused on the process of electroporation, which results in the poration of the biological cell membrane. The devices involved are designed for cell analysis, transfection or pasteurization. The high electric field strengths needed are induced by placing the electrodes in close proximity or by creating a constriction between the electrodes, which focuses the electric field. Detection is usually achieved through fluorescent labeling or by measuring impedance. So far, most of these devices have only concerned themselves solely with the electroporation process, but integration with separation and detection processes is expected in the near future. In particular, single-cell content analysis is expected to add further value to the concept of the microfluidic chip. Furthermore, if advanced pulse schemes are employed, such microdevices can also enhance research into intracellular electroporation.
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