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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    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.

    Conflation of expert and crowd reference data to validate global binary thematic maps
    Waldner, François ; Schucknecht, Anne ; Lesiv, Myroslava ; Gallego, Javier ; See, Linda ; Pérez-Hoyos, Ana ; andrimont, Raphaël D'; Maet, Thomas De; Bayas, Juan Carlos Laso ; Fritz, Steffen ; Leo, Olivier ; Kerdiles, Hervé ; Díez, Mónica ; Tricht, Kristof Van; Gilliams, Sven ; Shelestov, Andrii ; Lavreniuk, Mykola ; Simões, Margareth ; Ferraz, Rodrigo ; Bellón, Beatriz ; Bégué, Agnès ; Hazeu, Gerard ; Stonacek, Vaclav ; Kolomaznik, Jan ; Misurec, Jan ; Verón, Santiago R. ; Abelleyra, Diego De; Plotnikov, Dmitry ; Mingyong, Li ; Singha, Mrinal ; Patil, Prashant ; Zhang, Miao ; Defourny, Pierre - \ 2019
    Remote Sensing of Environment 221 (2019). - ISSN 0034-4257 - p. 235 - 246.
    With the unprecedented availability of satellite data and the rise of global binary maps, the collection of shared reference data sets should be fostered to allow systematic product benchmarking and validation. Authoritative global reference data are generally collected by experts with regional knowledge through photo-interpretation. During the last decade, crowdsourcing has emerged as an attractive alternative for rapid and relatively cheap data collection, beckoning the increasingly relevant question: can these two data sources be combined to validate thematic maps? In this article, we compared expert and crowd data and assessed their relative agreement for cropland identification, a land cover class often reported as difficult to map. Results indicate that observations from experts and volunteers could be partially conflated provided that several consistency checks are performed. We propose that conflation, i.e., replacement and augmentation of expert observations by crowdsourced observations, should be carried out both at the sampling and data analytics levels. The latter allows to evaluate the reliability of crowdsourced observations and to decide whether they should be conflated or discarded. We demonstrate that the standard deviation of crowdsourced contributions is a simple yet robust indicator of reliability which can effectively inform conflation. Following this criterion, we found that 70% of the expert observations could be crowdsourced with little to no effect on accuracy estimates, allowing a strategic reallocation of the spared expert effort to increase the reliability of the remaining 30% at no additional cost. Finally, we provide a collection of evidence-based recommendations for future hybrid reference data collection campaigns.
    Environmental impact assessment of agricultural land use changes
    Kroes, J.G. ; Groenendijk, P. ; Abelleyra, Diego de; Veron, Santiago R. ; Plotnikov, Dmitry ; Bartalev, Sergey ; Yan, Nana ; Wu, Bingfang ; Kussul, Nataliia ; Fritz, Steffen - \ 2017
    SIGMA - 97 p.
    Technical description of crop model (WOFOST) calibration and simulation activities for Argentina, pampas region
    Wit, A.J.W. de; Abelleyra, D. d'; Veron, S. ; Kroes, J.G. ; Supit, I. ; Boogaard, H.L. - \ 2017
    SIGMA - 59 p.
    AF-EU-15035
    Water exchange rate in RAS and dietary inclusion of micro-minerals influence growth, body composition and mineral metabolism in common carp
    Antony Jesu Prabhu, P. ; Kaushik, S.J. ; Geurden, I. ; Stouten, T. ; Fontagné-dicharry, S. ; Veron, V. ; Mariojouls, C. ; Verreth, J.A.J. ; Eding, E.H. ; Schrama, J.W. - \ 2017
    Aquaculture 471 (2017). - ISSN 0044-8486 - p. 8 - 18.
    Recirculation aquaculture system - Minerals - Requirement - Metabolism - Fish
    Recirculation aquaculture systems (RASs) operated at low water exchange rates are known to accumulate minerals in the water. This study examined the dietary mineral requirement and metabolism in common carp reared in RAS of contrasting water exchange rates. Two independent RAS (water exchange rates, 70 vs. 2000 L/kg feed) and five experimental diets with graded levels of micro-mineral premix inclusion (0.0, 0.3, 0.6, 1.0 and 1.5%) were tested in a 2 × 5 factorial arrangement. Common carp fingerlings (8.5 g) were reared in either of the RAS and fed the experimental diets in triplicates for 8 weeks at 24 °C. Water quality, fish growth, body composition, tissue mineral concentrations, blood haemoglobin and haematocrit levels, biochemical and molecular markers of oxidative stress, mineral uptake and metabolism were studied. RAS operated at low water exchange rate showed significantly high conductivity, nitrate, nitrite and dissolved mineral concentrations in water. A tendency for higher growth, significantly higher whole body mineral levels except Cu and Zn were observed in fish reared in RAS with high accumulation of minerals (H-RAS). Of the micro-minerals studied, effect of RAS on the minimal dietary inclusion level was significant only for Se; lower in fish reared in the H-RAS (0.28 mg/kg) compared to L-RAS (0.32 mg/kg). Increasing premix inclusion decreased growth and feed efficiency, increased the whole body concentration of Cu, Se and Zn, while Fe and Mn were unaffected. Plasma P, Ca, K and Mn were higher and haematocrit was lower in H-RAS reared fish; plasma mineral levels were also influenced by premix inclusion. Enzymes involved in micro-mineral uptake and metabolism (ferric reductase, cupric reductase and alkaline phosphatase) and oxidative stress markers (glutathione peroxidase, catalase, glutathione reductase and glutathione S-transferase) were analysed in gill, intestine and liver. In fish reared in H-RAS, reduced glutathione peroxidase (GPx) and increased glutathione reductase (GR) activities were observed in liver and intestine, respectively. Activity of GPx in all the analysed tissues increased with premix supplementation. Differential regulation in mRNA expression of molecular markers related to micro-mineral uptake, metabolism and oxidative stress were observed in the tissues in response to RAS and premix inclusion. To conclude, fish reared in high accumulation RAS had higher mineral levels in whole body and vertebrae, but did not result in a lower estimate of micro-minerals, except for Se. Difference in rearing system had multiple effects on the physiology and metabolism of fish on the whole, apart from mineral balance alone.
    Responses in micro-mineral metabolism in rainbow trout to change in dietary ingredient composition and inclusion of a micro-mineral premix
    Prabhu, Antony Jesu P. ; Geurden, Inge ; Fontagné-Dicharry, Stéphanie ; Veron, Vincent ; Larroquet, Laurence ; Mariojouls, Catherine ; Schrama, Johan W. ; Kaushik, Sadasivam J. - \ 2016
    PLoS ONE 11 (2016)2. - ISSN 1932-6203

    Responses in micro-mineral metabolism to changes in dietary ingredient composition and inclusion of a micro-mineral premix (Fe, Cu, Mn, Zn and Se) were studied in rainbow trout. In a 2 × 2 factorial design, triplicate groups of rainbow trout (initial weight: 20g) were fed over 12 weeks at 17°C a fishmeal-based diet (M) or a plant-ingredient based diet (V), with or without inclusion of a mineral premix. Trout fed the V vs. M diet had lower feed intake, growth, hepato-somatic index, apparent availability coefficient (AAC) of Fe, Cu, Mn and Zn and also lower whole body Se and Zn concentration, whereas whole body Fe and Cu and plasma Fe concentrations were higher. Feeding the V diet increased intestinal ferric reductase activity; at transcriptional level, hepatic hepcidin expression was down-regulated and ferroportin 1 was up-regulated. Transcription of intestinal Cu-transporting ATPases and hepatic copper transporter1 were higher in V0 compared to other groups. Among the hepatic metaloenzyme activities assayed, only Se-dependent glutathione peroxidase was affected, being lower in V fed fish. Premix inclusion reduced the AAC of Fe, Cu and Zn; increased the whole body concentration of all micro- minerals; up-regulated hepatic hepcidin and downregulated intestinal ferroportin 1 transcription; and reduced the transcription of Cu-transporting ATPases in the intestine. Overall, the regulation of micro-mineral metabolism in rainbow trout, especially Fe and Cu, was affected both by a change in ingredient composition and micro-mineral premix inclusion.

    Iron absorption and balance in rainbow trout: indication of transcriptional regulation in response to modifications in diet composition
    Antony Jesu Prabhu, P. ; Veron, V. ; Fontagné-Dicharry, S. ; Mariojouls, C. ; Geurden, I. ; Schrama, J.W. ; Kaushik, S.J. - \ 2014
    Evidence of interaction network evolution by whole-genome duplications: A case study in MADS-box proteins
    Veron, A.S. ; Kaufmann, K. ; Bornberg-Bauer, E. - \ 2007
    Molecular Biology and Evolution 24 (2007)3. - ISSN 0737-4038 - p. 670 - 678.
    transcription factor family - gene duplications - flowering plants - floral organ - arabidopsis - history - heterodimerization - organization - eukaryotes - identity
    Recent investigations on metazoan transcription factors (TFs) indicate that single-gene duplication events and the gain and loss of protein domains are 2 crucial factors in shaping their protein¿protein interaction networks. Plant genomes, on the other hand, have a history of polyploidy and whole-genome duplications (WGDs), and thus, their study helps to understand whether WGDs have also had a significant influence on protein network evolution. Here we investigate the evolution of the interaction network in the well-studied MADS domain MIKC-type proteins, a TF family which plays an important role in both the vegetative and the reproductive phases of plant life. We combine phylogenetic reconstruction, protein domain analysis, and interaction data from different species. We show that, unlike previously analyzed interaction networks, the MIKC-type protein network displays a characteristic topology, with overall high inter-subfamily connectivity, shared interactors between paralogs, and conservation of interaction patterns across species. The evaluation of the number of MIKC-type proteins at key time points throughout the evolution of land plants in the lineage leading to Arabidopsis suggested that most duplicates were retained after each round of WGD. We provide evidence that an initial network, formed by 9¿11 homodimerizing proteins interacting with each other, existed in the common ancestor of all seed plants. This basic structure has been conserved after each round of WGD, adding layers of paralogs with similar interaction patterns. We thus present the first model where we can show that a network of eukaryotic TFs has evolved via rounds of WGD. Furthermore, we found that in subfamilies in which the K domain is most diverged, the interactions with other subfamilies have been largely lost. We discuss the possibility that such a high proportion of genes were retained after each WGD because of their capacity to form higher order complexes involving proteins from different subfamilies. The simultaneous duplications allowed for the conservation of the quantitative balance between the constituents and facilitated sub- and neofunctionalization through differential expression of whole units.
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