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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    Vraag en antwoord over verpakkingen in relatie tot houdbaarheid en duurzaamheid
    Thoden van Velzen, E.U. ; Pereira da Silva, F.I.D.G. ; Paillart, M.J.M. ; Immink, V.M. ; Bos-Brouwers, H.E.J. ; Hetterscheid, S. - \ 2020
    Wageningen : Wageningen Food & Biobased Research (Wageningen Food & Biobased Research report 2045) - 39
    Alleles to Enhance Antioxidant Content in Maize-A Genome-Wide Association Approach
    Alves, Mara Lisa ; Bento-Silva, Andreia ; Carbas, Bruna ; Gaspar, Daniel ; Paulo, Manuel ; Brites, Claúdia ; Mendes-Moreira, Pedro ; Brites, Carla Moita ; Bronze, Maria Do Rosário ; Malosetti, Marcos ; Eeuwijk, Fred Van; Vaz Patto, Maria Carlota - \ 2020
    Journal of Agricultural and Food Chemistry 68 (2020)13. - ISSN 0021-8561 - p. 4051 - 4061.
    carotenoids - color - phenolic compounds - quantitative trait loci - tocopherols

    The interest in antioxidant compound breeding in maize (Zea mays L.), a major food crop, has increased in recent years. However, breeding of antioxidant compounds in maize can be hampered, given the complex genetic nature of these compounds. In this work, we followed a genome-wide association approach, using a unique germplasm collection (containing Portuguese germplasm), to study the genetic basis of several antioxidants in maize. Sixty-seven genomic regions associated with seven antioxidant compounds and two color-related traits were identified. Several significant associations were located within or near genes involved in the carotenoid (Zm00001d036345) and tocopherol biosynthetic pathways (Zm00001d017746). Some indications of a negative selection against α-tocopherol levels were detected in the Portuguese maize germplasm. The strongest single nucleotide polymorphism (SNP)-trait associations and the SNP alleles with larger effect sizes were pinpointed and set as priority for future validation studies; these associations detected now constitute a benchmark for developing molecular selection tools for antioxidant compound selection in maize.

    Frozen evolution of an RNA virus suggests accidental release as a potential cause of arbovirus re-emergence
    Pascall, David J. ; Nomikou, Kyriaki ; Bréard, Emmenuel ; Zientara, Stephan ; Silva Filipe, Ana da; Hoffmann, Bernd ; Jacquot, Maude ; Singer, Joshua B. ; Clercq, Kris De; Botner, Anette ; Sailleau, Corinne ; Viarouge, Cyril ; Batten, Carrie ; Puggioni, Giantonella ; Ligios, Ciriaco ; Savini, Giovanni ; Rijn, P.A. van; Mertens, Peter P.C. ; Biek, Roman ; Palmarini, Massimo - \ 2020
    PloS Biology (2020). - ISSN 1545-7885
    Sources and fates of perchlorate in soils in Chile : A case study of perchlorate dynamics in soil-crop systems using lettuce (Lactuca sativa) fields.
    Calderon, R. ; Rajendiran, Karthikraj ; Kim, U.J. ; Palma, P. ; Arancibia-Miranda, N. ; Silva-Moreno, E. ; Corradini, F. - \ 2020
    Environmental Pollution 264 (2020). - ISSN 0269-7491
    Fertilizers - Food safety - Perchlorate - Soil contamination

    Perchlorate occurs naturally in the environment in deposits of nitrate and can be formed in the atmosphere and precipitate into soil. However, little is known about the occurrence and levels of perchlorate in soils and fertilizers in Chile and its impacts on agricultural systems and food safety. In this study, concentrations of perchlorate were determined in 101 surface soils and 17 fertilizers [nitrogenous (n = 8), nitrogen-phosphorous-potassium (NPK; n = 3), phosphate (n = 2) and non-nitrogenous (n = 4)] collected across Chile from 2017 to 2018. Our results show that perchlorate was detected mainly in agricultural soils (mean: 0.32 ng g−1), grassland rotation sites (0.41 ngg−1) and urban locations (0.38 ng g−1). Interestingly, elevated concentrations of perchlorate (9.66 and 54.0 ng g−1) were found in agricultural soils. All fertilizers contained perchlorate: nitrogenous fertilizers (mean: 32.6 mg kg−1), NPK (mean: 12.6 mg kg−1), non-nitrogenous fertilizers (mean: 10.2 mg kg−1) and phosphates (mean: 11.5 mg kg−1). Only one type of nitrogenous fertilizer (KNO3: 95.3 mg kg−1) exceeded the international regulation limit (50 mg kg−1). For two agronomic practices, the content of perchlorate in lettuce increased as the fertilizer application rate increased, with fertigation promoting a more significant accumulation. However, the concentrations generally remained below regulatory values. Our results suggest that fertilizers constitute an important source of perchlorate in soils.

    More frequent droughts slow down litter decomposition across European agroecosystems and increase the importance of earthworm functional diversity
    Silva, Pedro Martins da; Nascimento, Eduardo ; Reis, Filipa ; Briones, Maria J.I. ; Brussaard, Lijbert ; Sousa, José Paulo - \ 2020
    Applied Soil Ecology 153 (2020). - ISSN 0929-1393
    Climate change - Community weighted means - Decomposition - Ecological groups - Land-use - Niche complementarity

    Effects of increasing rainfall variability and weather extremes on litter decomposition are still uncertain, especially in agroecosystems, where the functional structure of soil communities is already affected. We conducted a mesocosm experiment to evaluate the impacts of different rain regimes and land management on litter mass loss and earthworm ecological groups (epigeic, endogeic and anecic) across European agroecosystems. We also tested if the effects of different rainfall regimes (normal, drought, flooding, intermittent) on earthworm functional diversity (FD) or community-weighted mean (CWM) of earthworm ecological groups (particularly anecic species in the case of CWM), affected litter mass loss across land-use types. We found that drought was the main factor retarding litter mass loss across European agroecosystems irrespective of management type. The effects of the rain regime on litter mass loss were coupled with the pedoclimatic conditions that were different among the studied European land-use types. Across land-use types the importance of earthworm communities for litter decomposition was higher under water depletion. These results also suggest that FD, as a proxy of niche complementarity, is crucial for the stability of the decomposition process under environmental disturbances. The FD values under drought regimes strongly indicated that climatic changes may slow down litter decomposition as a result of FD alterations that could compromise the long-term maintenance of litter mass loss. This result may be especially relevant for the European soils that are already under hydric stress, such as in most Mediterranean agroecosystems.

    A global database of soil nematode abundance and functional group composition
    Hoogen, Johan van den; Geisen, Stefan ; Wall, Diana H. ; Wardle, David A. ; Traunspurger, Walter ; Goede, Ron G.M. de; Adams, Byron J. ; Ahmad, Wasim ; Ferris, Howard ; Bardgett, Richard D. ; Bonkowski, Michael ; Campos-Herrera, Raquel ; Cares, Juvenil E. ; Caruso, Tancredi ; Brito Caixeta, Larissa de; Chen, Xiaoyun ; Costa, Sofia R. ; Creamer, Rachel ; Cunha e Castro, José Mauro da; Dam, Marie ; Djigal, Djibril ; Escuer, Miguel ; Griffiths, Bryan S. ; Gutiérrez, Carmen ; Hohberg, Karin ; Kalinkina, Daria ; Kardol, Paul ; Kergunteuil, Alan ; Korthals, Gerard ; Krashevska, Valentyna ; Kudrin, Alexey A. ; Li, Qi ; Liang, Wenju ; Magilton, Matthew ; Marais, Mariette ; Martín, José Antonio Rodríguez ; Matveeva, Elizaveta ; Mayad, El Hassan ; Mzough, E. ; Mulder, Christian ; Mullin, Peter ; Neilson, Roy ; Nguyen, Duong T.A. ; Nielsen, Uffe N. ; Okada, Hiroaki ; Rius, Juan Emilio Palomares ; Pan, Kaiwen ; Peneva, Vlada ; Pellissier, Loïc ; Silva, Julio Carlos Pereira da; Pitteloud, Camille ; Powers, Thomas O. ; Powers, Kirsten ; Quist, Casper W. ; Rasmann, Sergio ; Moreno, Sara Sánchez ; Scheu, Stefan ; Setälä, Heikki ; Sushchuk, Anna ; Tiunov, Alexei V. ; Trap, Jean ; Vestergård, Mette ; Villenave, Cecile ; Waeyenberge, Lieven ; Wilschut, Rutger A. ; Wright, Daniel G. ; Keith, Aidan M. ; Yang, Jiuein ; Schmidt, Olaf ; Bouharroud, R. ; Ferji, Z. ; Putten, Wim H. van der; Routh, Devin ; Crowther, Thomas W. - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463

    As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.

    In vitro toxicological characterisation of the antifungal compound soybean toxin (SBTX)
    Arantes, Mariana Reis ; Peijnenburg, Ad ; Hendriksen, Peter J.M. ; Stoopen, Geert ; Almeida, Thiago Silva ; Souza, Terezinha Maria ; Farias, Davi Felipe ; Carvalho, Ana Fontenele Urano ; Rocha, Talita Magalhães ; Leal, Luzia Kalyne Almeida Moreira ; Vasconcelos, Ilka Maria ; Oliveira, Jose Tadeu Abreu - \ 2020
    Toxicology in Vitro 65 (2020). - ISSN 0887-2333
    Antifungal agent - Cytotoxicity - SBTX - Toxicogenomics

    Soybean toxin (SBTX) is a protein isolated from soybean seeds and composed of two polypeptide subunits (17 and 27 kDa). SBTX has in vitro activity against phytopathogenic fungi such as Cercospora sojina, Aspergillus niger, and Penicillium herguei, and yeasts like Candida albicans, C. parapsilosis, Kluyveromyces marxiannus, and Pichia membranifaciens. The present study aimed to analyze in vitro whether SBTX causes any side effects on non-target bacterial and mammalian cells that could impede its potential use as a novel antifungal agent. SBTX at 100 μg/mL and 200 μg/mL did not hinder the growth of the bacteria Salmonella enterica (subspecies enterica serovar choleraesuis), Bacillus subtilis (subspecies spizizenii) and Staphylococcus aureus. Moreover, SBTX at concentrations up to 500 μg/mL did not significantly affect the viability of erythrocytes, neutrophils, and human intestinal Caco-2 cells. To study whether SBTX could induce relevant alterations in gene expression, in vitro DNA microarray experiments were conducted in which differentiated Caco-2 cells were exposed for 24 h to 100 μg/mL or 200 μg/mL SBTX. SBTX up-regulated genes involved in cell cycle and immune response pathways, but down-regulated genes that play a role in cholesterol biosynthesis and platelet degranulation pathways. Thus, although SBTX did not affect bacteria, nor induced cytotoxity in mammalian cells, it affected some biological pathways in the human Caco-2 cell line that warrants further investigation.

    Fresh on Demand
    Pereira da Silva, Fatima - \ 2020
    Fresh on Demand
    Pereira da Silva, F.I.D.G. - \ 2020
    Wageningen University & Research - 4 p.
    Fresh on Demand
    Pereira da Silva, F.I.D.G. - \ 2020
    Wageningen University & Research - 4 p.
    S-Fruit Transformation - 2020
    Pereira da Silva, Fatima - \ 2020
    Effects of exogenous compound sprays on cherry cracking: skin properties and gene expression
    Correia, Sofia ; Santos, Marlene ; Glińska, Sława ; Gapińska, Magdalena ; Matos, Manuela ; Carnide, Valdemar ; Schouten, Rob ; Silva, Ana Paula ; Gonçalves, Berta - \ 2020
    Journal of the Science of Food and Agriculture 100 (2020)7. - ISSN 0022-5142 - p. 2911 - 2921.
    BACKGROUND Cherry fruit cracking is a costly problem for cherry growers. The effect of repeated sprayings (gibberellic acid – GA3; abscisic acid – ABA; salicylic acid – SA; glycine betaine – GB, and Ascophyllum nodosum – AN) combined with CaCl2, on ‘Sweetheart’ cherry fruit‐cracking characteristics was investigated. Cracking was quantified in terms of cracking incidence, crack morphology, confocal scanning laser microscopy, cuticular wax content, cell‐wall modification, and cuticular wax gene expression.RESULTS All spray treatments reduced cracking compared with an untreated control (H2O), with fewer cheek cracks. The least cracking incidence was observed for ABA + CaCl2‐ and GB + CaCl2‐treated fruits, indicating an added benefit compared to spraying with CaCl2 alone. In addition, GB + CaCl2‐treated fruits showed higher fruit diameter. ABA + CaCl2 and GB + CaCl2 sprays showed higher wax content and higher cuticle and epidermal thickness compared with the control, including increased expression of wax synthase (ABA + CaCl2) and expansin 1 (GB + CaCl2). CONCLUSION In general, factors that improve the cuticle thickness appear to be important at the fruit‐coloring stage. At the fruit‐ripening stage, larger cell sizes of the epidermis, hypodermis, and parenchyma cells lower cracking incidence, indicating the importance of flexibility and elasticity of the epidermis. © 2020 Society of Chemical Industry
    CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes
    Silva, Vinicius da; Ramos, Marcel ; Groenen, Martien ; Crooijmans, Richard ; Johansson, Anna ; Regitano, Luciana ; Coutinho, Luiz ; Zimmer, Ralf ; Waldron, Levi ; Geistlinger, Ludwig - \ 2020
    Bioinformatics 36 (2020)3. - ISSN 1367-4803 - p. 972 - 973.

    SUMMARY: Copy number variation (CNV) is a major type of structural genomic variation that is increasingly studied across different species for association with diseases and production traits. Established protocols for experimental detection and computational inference of CNVs from SNP array and next-generation sequencing data are available. We present the CNVRanger R/Bioconductor package which implements a comprehensive toolbox for structured downstream analysis of CNVs. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and genome-wide association analysis with gene expression and quantitative phenotypes. AVAILABILITY AND IMPLEMENTATION: http://bioconductor.org/packages/CNVRanger.

    Assessing specialized metabolite diversity of Alnus species by a digitized LC–MS/MS data analysis workflow
    Kang, Kyo Bin ; Woo, Sunmin ; Ernst, Madeleine ; Hooft, Justin J.J. van der; Nothias, Louis Félix ; Silva, Ricardo R. da; Dorrestein, Pieter C. ; Sung, Sang Hyun ; Lee, Mina - \ 2020
    Phytochemistry 173 (2020). - ISSN 0031-9422
    Alnus spp. - Betulaceae - Chemical diversity - Data analysis - LC–MS/MS - Specialized metabolites

    Alnus spp. (Betulaceae) have been used for treatments of hemorrhage, burn injuries, antipyretic fever, diarrhea, and alcoholism in traditional medicines. In this study, a digitized LC–MS/MS data analysis workflow was applied to provide an overview on chemical diversity of 15 Alnus extracts prepared from bark, twigs, leaves, and fruits of A. japonica, A. firma, A. hirsuta, and A. hirsuta var. sibirica. Most of the MS/MS spectra could be putatively annotated based on library matching, in silico fragmentation, and substructural topic modeling. The putative annotation allowed us to discriminate the extracts into three chemotypes based on dominant chemical scaffolds: diarylheptanoids, flavonoids or tannins. This high-throughput chemical annotation was correlated with α-glucosidase inhibition data of extracts, and it allowed us to identify gallic acid as the major active compound of A. firma.

    Mail goals of the post-harvest processing technologies, improving quality of the crops and reducing losses
    Pereira da Silva, Fatima - \ 2020
    Linking vegetation and soil functions during secondary forest succession in the Atlantic forest
    Teixeira, Heitor Mancini ; Cardoso, Irene Maria ; Bianchi, Felix J.J.A. ; Cruz Silva, Arthur da; Jamme, Delphin ; Peña-Claros, Marielos - \ 2020
    Forest Ecology and Management 457 (2020). - ISSN 0378-1127
    Secondary forest succession can be an effective and low-cost strategy to increase forest cover and the associated biodiversity and soil functions. However, little is known about how soil functions develop during succession, and how vegetation attributes influence soil functions, especially in highly biodiverse and fragmented landscapes in the tropics. Here we assessed a wide range of indicators of taxonomic (e.g. number of tree species), structural (e.g. basal area, canopy openness) and functional diversity (e.g. community weighted means of functional traits) of tree species, as well as indicators for soil functions related to soil organic matter accumulation, nutrient cycling and soil cover in secondary forest patches ranging from 5 to 80 years. Two recently abandoned agricultural fields were included as the starting point of forest succession and two primary forest patches served as references for the end point of forest succession. Four ecological hypotheses, centred around the role of functional diversity, structural diversity and biomass, were tested to explore mechanisms in which forest vegetation may influence soil functions. Most measures of structural, taxonomic and functional diversity converged to values found in primary forests after 25–50 years of succession, whereas functional composition changed from acquisitive to conservative species. Soil carbon and nutrient cycling showed a quick recovery to the levels of primary forests after 15 years of succession. Although soil cover also increased during succession, levels of primary forests were not reached within 80 years. Variation in tree height and trait dominance were identified as aboveground drivers of carbon and nutrient cycling, while aboveground biomass was the main driver of litter accumulation, and the associated soil cover and water retention. Our results indicate that secondary forest succession can lead to a relative fast recovery of nutrient and carbon cycling functions, but not of soil cover. Our findings highlight the essential role of secondary forests in providing multiple ecosystem services. These results can be used to inform management and reforestation programmes targeted at strengthening soil functions, such as soil cover, nutrient and carbon cycling.

    Previou
    Piper anisum as a promising new source of bioactive metabolites
    Batista, Danilo ; Campos, Patrícia ; Silva, Valdenizia R. ; S. Santos, Luciano de; Bezerra, Daniel P. ; Soares, Milena B.P. ; Colepicolo, Pio ; Zambotti-Villela, Leonardo ; Pinto, Ernani ; Araújo, Floricea M. ; Martins, Dirceu ; Fernandez, Luzimar G. ; Ligterink, Wilco ; Canuto, Gisele A.B. ; Cerqueira, Martins Dias de; Ribeiro, Paulo R. - \ 2020
    Chemical Papers 74 (2020). - ISSN 0366-6352 - p. 1505 - 1515.
    Antimicrobial compounds - Antioxidant capacity - Antitumor activity - Bioactive metabolites - Ethnopharmacology - Metabolomics

    Piper species are commonly used by indigenous communities to treat several gastrointestinal diseases. In China, they are also used as an active ingredient in formulae to treat cancer. The objective of the study was to perform a large-scale metabolite profiling analysis to identify bioactive compounds in Piper anisum. Antioxidant capacity was assessed by the DPPH assay and total phenolics were assessed by Folin–Ciocalteu’s method. Antimicrobial activity was assessed against several Gram-positive and Gram-negative bacteria, whereas cytotoxicity was assessed against tumor cell lines MCF-7, HCT116, HepG2 and HL-60, and non-tumor cell line MRC-5. The multiplatform metabolite profiling approach encompassed NMR, GC–MS and LC–MS analyses. P. anisum root extract showed the greatest antioxidant capacity and total phenolic content, followed by the stem and leaf extracts. P. anisum extracts showed a highly selective antimicrobial profile, being specifically active against C. albicans (MIC of 500 μg mL−1). Additionally, the root extract (50 μg mL−1) showed the highest cell inhibition percentages against tumor cell lines MCF-7 (59.5%), HCT116 (49.2%), and HepG2 (61.0%). Forty-eight metabolites were annotated by GC–MS and 27 by LC–MS. These included alkaloids, carbohydrates, fatty acids, hydrocarbons, organic acids, phenolic compounds, and terpenes. Taken together, these results showed that P. anisum root extract is a promising source of bioactive compounds.

    Structural variants in the great tit genome and their effect on seasonal timing
    Silva, Vinicius Henrique da - \ 2020
    Wageningen University. Promotor(en): M.A.M. Groenen; M.E. Visser, co-promotor(en): R.P.M.A. Crooijmans; A.M. Johansson. - Wageningen : Wageningen University - ISBN 9789177605201 - 173

    The great tit (Parus major) is a songbird that has been extensively explored in ecological and evolutionary studies, shedding light on the effects of the global warming on nature. Genomic structural variability was never explored in detail in these species. The aim of this thesis was to detect, map, characterize and associate, with seasonal timing, structural variants that are present in the great tit genome such as copy number variations (CNVs) and inversions. First, this thesis presents a genome-wide map of CNV regions in the great tit genome, showing how these variants are associated with genomic architecture underlying their molecular formation. Second, CNVs were associated with breeding timing. Finally, this thesis investigate the genomic complexity of a large inversion in the Chromosome 1A. The inversion is recessive lethal and is inherited twice more than expected from male carriers but are normally inherited from female carriers, suggesting a selfish gene.

    Mass spectrometry searches using MASST
    Wang, Mingxun ; Jarmusch, Alan K. ; Vargas, Fernando ; Aksenov, Alexander A. ; Gauglitz, Julia M. ; Weldon, Kelly ; Petras, Daniel ; Silva, Ricardo da; Quinn, Robert ; Melnik, Alexey V. ; Hooft, Justin J.J. van der; Caraballo-Rodríguez, Andrés Mauricio ; Nothias, Louis Felix ; Aceves, Christine M. ; Panitchpakdi, Morgan ; Brown, Elizabeth ; Ottavio, Francesca Di; Sikora, Nicole ; Elijah, Emmanuel O. ; Labarta-Bajo, Lara ; Gentry, Emily C. ; Shalapour, Shabnam ; Kyle, Kathleen E. ; Puckett, Sara P. ; Watrous, Jeramie D. ; Carpenter, Carolina S. ; Bouslimani, Amina ; Ernst, Madeleine ; Swafford, Austin D. ; Zúñiga, Elina I. ; Balunas, Marcy J. ; Klassen, Jonathan L. ; Loomba, Rohit ; Knight, Rob ; Bandeira, Nuno ; Dorrestein, Pieter C. - \ 2020
    Nature Biotechnology 38 (2020). - ISSN 1087-0156 - p. 23 - 26.
    Correction to: Unravelling the variability and causes of smallholder maize yield gaps in Ethiopia
    Assefa, Banchayehu Tessema ; Chamberlin, Jordan ; Reidsma, Pytrik ; Silva, João Vasco ; Ittersum, Martin K. van - \ 2020
    Food Security 12 (2020). - ISSN 1876-4517 - p. 489 - 490.

    The original version of this article unfortunately contained the following errors. (1) Title of co-author Pytrik Reidsma should be Associate Professor instead of Assistant Professor. (2) In Fig. 6, the explanations in the legend are switched. The corrected figure is shown here. (Figure presented.).

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