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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    Late-spring frost risk between 1959 and 2017 decreased in North America but increased in Europe and Asia
    Zohner, Constantin M. ; Mo, Lidong ; Renner, Susanne S. ; Svenning, Jens Christian ; Vitasse, Yann ; Benito, Blas M. ; Ordonez, Alejandro ; Baumgarten, Frederik ; Bastin, Jean François ; Sebald, Veronica ; Reich, Peter B. ; Liang, Jingjing ; Nabuurs, Gert Jan ; De-Migueln, Sergio ; Alberti, Giorgio ; Antón-Fernández, Clara ; Balazy, Radomir ; Brändli, Urs Beat ; Chen, Han Y.H. ; Chisholm, Chelsea ; Cienciala, Emil ; Dayanandan, Selvadurai ; Fayle, Tom M. ; Frizzera, Lorenzo ; Gianelle, Damiano ; Jagodzinski, Andrzej M. ; Jaroszewicz, Bogdan ; Jucker, Tommaso ; Kepfer-Rojas, Sebastian ; Khan, Mohammed Latif ; Kim, Hyun Seok ; Korjus, Henn ; Johannsen, Vivian Kvist ; Laarmann, Diana ; Langn, Mait ; Zawila-Niedzwiecki, Tomasz ; Niklaus, Pascal A. ; Paquette, Alain ; Pretzsch, Hans ; Saikia, Purabi ; Schall, Peter ; Seben, Vladimír ; Svoboda, Miroslav ; Tikhonova, Elena ; Viana, Helder ; Zhang, Chunyu ; Zhao, Xiuhai ; Crowther, Thomas W. - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)22. - ISSN 0027-8424
    Climate change - Freezing damage - Late frost - Phenology - Spring leaf-out

    Late-spring frosts (LSFs) affect the performance of plants and animals across the world's temperate and boreal zones, but despite their ecological and economic impact on agriculture and forestry, the geographic distribution and evolutionary impact of these frost events are poorly understood. Here, we analyze LSFs between 1959 and 2017 and the resistance strategies of Northern Hemisphere woody species to infer trees' adaptations for minimizing frost damage to their leaves and to forecast forest vulnerability under the ongoing changes in frost frequencies. Trait values on leaf-out and leaf-freezing resistance come from up to 1,500 temperate and boreal woody species cultivated in common gardens. We find that areas in which LSFs are common, such as eastern North America, harbor tree species with cautious (late-leafing) leaf-out strategies. Areas in which LSFs used to be unlikely, such as broad-leaved forests and shrublands in Europe and Asia, instead harbor opportunistic tree species (quickly reacting to warming air temperatures). LSFs in the latter regions are currently increasing, and given species' innate resistance strategies, we estimate that ∼35% of the European and ∼26% of the Asian temperate forest area, but only ∼10% of the North American, will experience increasing late-frost damage in the future. Our findings reveal region-specific changes in the spring-frost risk that can inform decision-making in land management, forestry, agriculture, and insurance policy.

    The impact of sensitivity and uncertainty of soil physical parameters on the terms of the water balance: Some case studies with default R packages. Part I: Theory, methods and case descriptions
    Wesseling, Jan ; Kroes, Joop ; Campos Oliveira, Thalita ; Damiano, Francisco - \ 2020
    Computers and Electronics in Agriculture 170 (2020). - ISSN 0168-1699
    HPC - IRS - LHS - Numerical model - R - Sensitivity - Sobol - SWAP - Uncertainty

    These papers (part I and part II) emphasize the need for sensitivity and uncertainty analyses. A number of techniques are applied, e.g. latin hypercube sampling, impact response surfaces and Sobol-analyses. Five examples are presented, four of them concerning the numerical model SWAP. The data generation and analysis is performed with standard R packages. Although the computations can be made on any computer, the most time-consuming examples in this paper have been run on a High Performance Computer Cluster. With the relatively simple Impact Response Surface technique it is shown that variation of the saturated hydraulic conductivity has far less impact than changing the moisture content at saturation. Analyses according to the Sobol-Jansen method show that when the soil physical relationships are described according to Damiano, then the parameter b has a very large influence on the results. If the well-known Mualem - Van Genuchten equations are applied, most variation can be explained by the parameter n.

    The impact of sensitivity and uncertainty of soil physical parameters on the terms of the water balance: Some case studies with default R packages. Part II: Results and discussion
    Wesseling, Jan ; Kroes, Joop ; Campos Oliveira, Thalita ; Damiano, Francisco - \ 2020
    Computers and Electronics in Agriculture 170 (2020). - ISSN 0168-1699
    HPC - IRS - LHS - Numerical model - R - Sensitivity - Sobol - Swap - Uncertainty

    These papers (part I and part II) emphasize the need for sensitivity and uncertainty analyses. A number of techniques are applied, e.g. latin hypercube sampling, impact response surfaces and Sobol-analyses. Five examples are presented, four of them concerning the numerical model Swap. The data generation and analysis is performed with standard R packages. Although the computations can be made on any computer, the most time-consuming examples in this paper have been run on a High Performance Computer Cluster. With the relatively simple Impact Response Surface technique it is shown that variation of the saturated hydraulic conductivity has far less impact than changing the moisture content at saturation. Analyses according to the Sobol-Jansen method show that when the soil physical relationships are described according to Damiano, then the parameter b has a very large influence on the results. If the well-known Mualem - Van Genuchten equations are applied, most variation can be explained by the parameter n.

    An EFR-Cf-9 chimera confers enhanced resistance to bacterial pathogens by SOBIR1- and BAK1-dependent recognition of elf18
    Wu, Jinbin ; Reca, Ida Barbara ; Spinelli, Francesco ; Lironi, Damiano ; Lorenzo, Giulia De; Poltronieri, Palmiro ; Cervone, Felice ; Joosten, Matthieu H.A.J. ; Ferrari, Simone ; Brutus, Alexandre - \ 2019
    Molecular Plant Pathology 20 (2019)6. - ISSN 1464-6722 - p. 751 - 764.
    BAK1 - Cf-9 - EFR - pattern recognition receptors - plant innate immunity - R genes - SOBIR1

    The transfer of well-studied native and chimeric pattern recognition receptors (PRRs) to susceptible plants is a proven strategy to improve host resistance. In most cases, the ectodomain determines PRR recognition specificity, while the endodomain determines the intensity of the immune response. Here we report the generation and characterization of the chimeric receptor EFR-Cf-9, which carries the ectodomain of the Arabidopsis thaliana EF-Tu receptor (EFR) and the endodomain of the tomato Cf-9 resistance protein. Both transient and stable expression of EFR-Cf-9 triggered a robust hypersensitive response (HR) upon elf18 treatment in tobacco. Co-immunoprecipitation and virus-induced gene silencing studies showed that EFR-Cf-9 constitutively interacts with SUPPRESSOR OF BIR1-1 (SOBIR1) co-receptor, and requires both SOBIR1 and kinase-active BRI1-ASSOCIATED KINASE1 (BAK1) for its function. Transgenic plants expressing EFR-Cf-9 were more resistant to the (hemi)biotrophic bacterial pathogens Pseudomonas amygdali pv. tabaci (Pta) 11528 and Pseudomonas syringae pv. tomato DC3000, and mounted an HR in response to high doses of Pta 11528 and P. carotovorum. Taken together, these data indicate that the EFR-Cf-9 chimera is a valuable tool for both investigating the molecular mechanisms responsible for the activation of defence responses by PRRs, and for potential biotechnological use to improve crop disease resistance.

    Agrohydrological analysis of groundwater recharge and land use changes in the Pampas of Argentina
    Kroes, Joop ; Dam, Jos van; Supit, Iwan ; Abelleyra, Diego de; Verón, Santiago ; Wit, Allard de; Boogaard, Hendrik ; Angelini, Marcos ; Damiano, Francisco ; Groenendijk, Piet ; Wesseling, Jan ; Veldhuizen, Ab - \ 2019
    Agricultural Water Management 213 (2019). - ISSN 0378-3774 - p. 843 - 857.
    Argentina - Capillary rise - Groundwater recharge - Land use - Pampas - Soybean - SWAP - WOFOST

    This paper studies the changes of groundwater, climate and land use in the Pampas of Argentina. These changes offer opportunities and threats. Lowering groundwater without irrigation causes drought and successive crop and yield damage. Rising groundwater may alleviate drought as capillary rise supports root water uptake and crop growth, thus narrowing the difference between potential and actual yields. However, rising groundwater may also limit soil water storage, cause flooding in metropolitan areas and have a negative impact on crop yields. Changing land use from continuous soy bean into crop rotations or natural vegetation may decrease groundwater recharge and thus decrease groundwater levels. In case of crop rotation however, leaching of nutrients like nitrate may increase. We quantified these impacts using integrated dynamic crop growth and soil hydrology modelling. The models were tested at field scale using a local dataset from Argentina. We applied distributed modelling at regional scale to evaluate the impacts on groundwater recharge and crop yields using long term weather data. The experiments showed that threats arise from continuous monotone land use. Opportunities are created when a proper balance is found between supply and demand of soil water using a larger differentiation of land use. Increasing the areas of land use types with higher evapotranspiration, like permanent grassland and trees, will contribute to a more stable hydrologic system with more water storage capacities in the soil system and lower groundwater levels. Modelling tools clearly support the evaluation of the impact of land use and climate change on groundwater levels and crop yields.

    Water-Food-Energy Nexus under Climate Change in Sardinia
    Trabucco, Antonio ; Sušnik, Janez ; Vamvakeridou-Lyroudia, Lydia ; Evans, Barry ; Masia, Sara ; Blanco, Maria ; Roson, Roberto ; Sartori, Martina ; Alexandri, Eva ; Brouwer, Floor ; Spano, Donatella ; Damiano, Alfonso ; Virdis, Andrea ; Sistu, Giovanni ; Pulino, Daniele ; Statzu, Vania ; Madau, Fabio ; Strazzera, Elisabetta ; Mereu, Simone - \ 2018
    BMC Proceedings 2 (2018)11. - ISSN 1753-6561
    Land, food, energy, water and climate are linked and interconnected into a Nexus, characterized by complexity and feedbacks. An integrated management of the Nexus is critical to understand conflicts/synergies and secure efficient and sustainable use of resources, especially under climate change. The Nexus perspective is applied to Sardinia, as regional case study, to better understand and improve integrated resource management and relevant policy initiatives. Vulnerability of Sardinia Nexus is assessed under several climate projections by articulated balances of resources (water, energy) availability and sustainable development goals, at regional and sub-regional scales, accounting for demands and conflicts among key economic sectors (agriculture, hydro-power, tourism).
    Potential and limitations of inferring ecosystem photosynthetic capacity from leaf functional traits
    Musavi, Talie ; Migliavacca, Mirco ; Weg, Martine Janet van de; Kattge, Jens ; Wohlfahrt, Georg ; Bodegom, Peter M. van; Reichstein, Markus ; Bahn, Michael ; Carrara, Arnaud ; Domingues, Tomas F. ; Gavazzi, Michael ; Gianelle, Damiano ; Gimeno, Cristina ; Granier, André ; Gruening, Carsten ; Havránková, Kateřina ; Herbst, Mathias ; Hrynkiw, Charmaine ; Kalhori, Aram ; Kaminski, Thomas ; Klumpp, Katja ; Kolari, Pasi ; Longdoz, Bernard ; Minerbi, Stefano ; Montagnani, Leonardo ; Moors, Eddy ; Oechel, Walter C. ; Reich, Peter B. ; Rohatyn, Shani ; Rossi, Alessandra ; Rotenberg, Eyal ; Varlagin, Andrej ; Wilkinson, Matthew ; Wirth, Christian ; Mahecha, Miguel D. - \ 2016
    Ecology and Evolution 6 (2016)20. - ISSN 2045-7758 - p. 7352 - 7366.
    FLUXNET - Ecosystem functional property - Eddy covariance - Interannual variability - Photosynthetic capacity - Plant traits - Spatiotemporal variability - TRY database

    The aim of this study was to systematically analyze the potential and limitations of using plant functional trait observations from global databases versus in situ data to improve our understanding of vegetation impacts on ecosystem functional properties (EFPs). Using ecosystem photosynthetic capacity as an example, we first provide an objective approach to derive robust EFP estimates from gross primary productivity (GPP) obtained from eddy covariance flux measurements. Second, we investigate the impact of synchronizing EFPs and plant functional traits in time and space to evaluate their relationships, and the extent to which we can benefit from global plant trait databases to explain the variability of ecosystem photosynthetic capacity. Finally, we identify a set of plant functional traits controlling ecosystem photosynthetic capacity at selected sites. Suitable estimates of the ecosystem photosynthetic capacity can be derived from light response curve of GPP responding to radiation (photosynthetically active radiation or absorbed photosynthetically active radiation). Although the effect of climate is minimized in these calculations, the estimates indicate substantial interannual variation of the photosynthetic capacity, even after removing site-years with confounding factors like disturbance such as fire events. The relationships between foliar nitrogen concentration and ecosystem photosynthetic capacity are tighter when both of the measurements are synchronized in space and time. When using multiple plant traits simultaneously as predictors for ecosystem photosynthetic capacity variation, the combination of leaf carbon to nitrogen ratio with leaf phosphorus content explains the variance of ecosystem photosynthetic capacity best (adjusted R2 = 0.55). Overall, this study provides an objective approach to identify links between leaf level traits and canopy level processes and highlights the relevance of the dynamic nature of ecosystems. Synchronizing measurements of eddy covariance fluxes and plant traits in time and space is shown to be highly relevant to better understand the importance of intra- and interspecific trait variation on ecosystem functioning.

    An expanded evaluation of protein function prediction methods shows an improvement in accuracy
    Jiang, Yuxiang ; Oron, Tal Ronnen ; Clark, Wyatt T. ; Bankapur, Asma R. ; Andrea, Daniel D'; Lepore, Rosalba ; Funk, Christopher S. ; Kahanda, Indika ; Verspoor, Karin M. ; Ben-Hur, Asa ; Koo, Da Chen Emily ; Penfold-Brown, Duncan ; Shasha, Dennis ; Youngs, Noah ; Bonneau, Richard ; Lin, Alexandra ; Sahraeian, Sayed M.E. ; Martelli, Pier Luigi ; Profiti, Giuseppe ; Casadio, Rita ; Cao, Renzhi ; Zhong, Zhaolong ; Cheng, Jianlin ; Altenhoff, Adrian ; Skunca, Nives ; Dessimoz, Christophe ; Dogan, Tunca ; Hakala, Kai ; Kaewphan, Suwisa ; Mehryary, Farrokh ; Salakoski, Tapio ; Ginter, Filip ; Fang, Hai ; Smithers, Ben ; Oates, Matt ; Gough, Julian ; Törönen, Petri ; Koskinen, Patrik ; Holm, Liisa ; Chen, Ching Tai ; Hsu, Wen Lian ; Bryson, Kevin ; Cozzetto, Domenico ; Minneci, Federico ; Jones, David T. ; Chapman, Samuel ; BKC, Dukka ; Khan, Ishita K. ; Kihara, Daisuke ; Ofer, Dan ; Rappoport, Nadav ; Stern, Amos ; Cibrian-Uhalte, Elena ; Denny, Paul ; Foulger, Rebecca E. ; Hieta, Reija ; Legge, Duncan ; Lovering, Ruth C. ; Magrane, Michele ; Melidoni, Anna N. ; Mutowo-Meullenet, Prudence ; Pichler, Klemens ; Shypitsyna, Aleksandra ; Li, Biao ; Zakeri, Pooya ; ElShal, Sarah ; Tranchevent, Léon Charles ; Das, Sayoni ; Dawson, Natalie L. ; Lee, David ; Lees, Jonathan G. ; Sillitoe, Ian ; Bhat, Prajwal ; Nepusz, Tamás ; Romero, Alfonso E. ; Sasidharan, Rajkumar ; Yang, Haixuan ; Paccanaro, Alberto ; Gillis, Jesse ; Sedeño-Cortés, Adriana E. ; Pavlidis, Paul ; Feng, Shou ; Cejuela, Juan M. ; Goldberg, Tatyana ; Hamp, Tobias ; Richter, Lothar ; Salamov, Asaf ; Gabaldon, Toni ; Marcet-Houben, Marina ; Supek, Fran ; Gong, Qingtian ; Ning, Wei ; Zhou, Yuanpeng ; Tian, Weidong ; Falda, Marco ; Fontana, Paolo ; Lavezzo, Enrico ; Toppo, Stefano ; Ferrari, Carlo ; Giollo, Manuel ; Piovesan, Damiano ; Tosatto, Silvio C.E. ; Pozo, Angela del; Fernández, José M. ; Maietta, Paolo ; Valencia, Alfonso ; Tress, Michael L. ; Benso, Alfredo ; Carlo, Stefano Di; Politano, Gianfranco ; Savino, Alessandro ; Rehman, Hafeez Ur ; Re, Matteo ; Mesiti, Marco ; Valentini, Giorgio ; Bargsten, Joachim W. ; Dijk, Aalt-Jan van; Gemovic, Branislava ; Glisic, Sanja ; Perovic, Vladmir ; Veljkovic, Veljko ; Veljkovic, Nevena ; Almeida-e-Silva, Danillo C. ; Vencio, Ricardo Z.N. ; Sharan, Malvika ; Vogel, Jörg ; Kansakar, Lakesh ; Zhang, Shanshan ; Vucetic, Slobodan ; Wang, Zheng ; Sternberg, Michael J.E. ; Wass, Mark N. ; Huntley, Rachael P. ; Martin, Maria J. ; O'Donovan, Claire ; Robinson, Peter N. ; Moreau, Yves ; Tramontano, Anna ; Babbitt, Patricia C. ; Brenner, Steven E. ; Linial, Michal ; Orengo, Christine A. ; Rost, Burkhard ; Greene, Casey S. ; Mooney, Sean D. ; Friedberg, Iddo ; Radivojac, Predrag - \ 2016
    Genome Biology 17 (2016)1. - ISSN 1474-7596
    Disease gene prioritization - Protein function prediction

    Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.

    La valutazione dei servizi ecosistemici per la pianificazione territoriale. Esperienze in Europa
    Pedroli, G.B.M. ; Rega, C. - \ 2015
    In: Nuove Sfide per il Suolo / Arcidiacono, Andrea, Di Simine, Damiano, Oliva, Federico, Ronchi, Silvia, Salata, Stefano, Rome : - ISBN 9788876031380 - p. 24 - 30.
    Design According to Liabilities: ACAS X and the Treatment of ADS-B Position Data
    Schebesta, H. ; Contissa, Giuseppe ; Sartor, Giovanni ; Masutti, Anna ; Paola, Tomasello ; Taurino, Damiano - \ 2015
    In: Proceedings of the SESAR Innovation Days (2015) EUROCONTROL. - - 9 p.
    This paper presents the results of the test application
    of the Legal Case on ACAS X, the new generation airborne
    collision avoidance system. The Legal Case is the novel
    methodology, recently developed by the ALIAS project, to
    address liability of innovative systems for aviation and ATM. The
    Legal Case application on ACAS X was conducted in cooperation
    with EUROCONTROL; IATA, air companies and industries.
    Results are meant to inform ACAS X’s future development.
    Effect of Chlorine Dioxide and Ascorbic Acid on Enzymatic Browning and Shelf Life of Fresh-Cut Red Delicious and Granny Smith Apples
    Remorini, Damiano ; Landi, Marco ; Tardelli, Francesca ; Lugani, Arianna ; Massai, Rossano ; Graziani, Giulia ; Fogliano, Vincenzo ; Guidi, Lucia - \ 2015
    Journal of Food Processing and Preservation 39 (2015)6. - ISSN 0145-8892 - p. 2925 - 2934.

    In this work, we tested the hypothesis that ascorbic acid (AA) reduces browning of fresh-cut apples (Red Delicious, RD, and Granny Smith, GS), and we investigated the impact of AA on phenylpropanoid metabolism of RD and GS. Apple slices were dipped in a solution of 100mg/L of chlorine dioxide (ClO2) and ClO2+3% AA and stored at 4C for 96h. Flesh firmness, solid soluble content and browning index, total phenols and flavonoids, and the activity of peroxidase and polyphenol oxidase were monitored upon storage (0, 48 and 96h). Our results demonstrated that GS is less sensitive to browning and thus more suitable for minimally processed produce. Ascorbate reduces the browning index also in RD, a cultivar largely appreciated by consumers but more prone to browning. AA likely contrasts browning appearance by interacting with peroxidase and polyphenol oxidase and/or promoting the regeneration of phenols and flavonoids. Practical Applications: Browning of fresh-cut apple is one of the main problems that limit the shelf life of this type of produce. Given that this produce is highly appreciated by consumers, different antibrowning treatments have been tested to extend the shelf life of fresh-cut apple. We found that treatment with 100mg/L of ClO2+3% of ascorbic acid significantly reduces the browning appearance in apple slices. Browning was also reduced in Red Delicious cultivar that is more prone than Granny Smith to this phenomenon, but that is highly appreciated by consumers.

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