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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Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies
Ulaszewska, Marynka M. ; Weinert, Christoph H. ; Trimigno, Alessia ; Portmann, Reto ; Andres Lacueva, Cristina ; Badertscher, René ; Brennan, Lorraine ; Brunius, Carl ; Bub, Achim ; Capozzi, Francesco ; Cialiè Rosso, Marta ; Cordero, Chiara E. ; Daniel, Hannelore ; Durand, Stéphanie ; Egert, Bjoern ; Ferrario, Paola G. ; Feskens, Edith J.M. ; Franceschi, Pietro ; Garcia-Aloy, Mar ; Giacomoni, Franck ; Giesbertz, Pieter ; González-Domínguez, Raúl ; Hanhineva, Kati ; Hemeryck, Lieselot Y. ; Kopka, Joachim ; Kulling, Sabine E. ; Llorach, Rafael ; Manach, Claudine ; Mattivi, Fulvio ; Migné, Carole ; Münger, Linda H. ; Ott, Beate ; Picone, Gianfranco ; Pimentel, Grégory ; Pujos-Guillot, Estelle ; Riccadonna, Samantha ; Rist, Manuela J. ; Rombouts, Caroline ; Rubert, Josep ; Skurk, Thomas ; Sri Harsha, Pedapati S.C. ; Meulebroek, Lieven Van; Vanhaecke, Lynn ; Vázquez-Fresno, Rosa ; Wishart, David ; Vergères, Guy - \ 2018
Molecular Nutrition & Food Research 63 (2018)1. - ISSN 1613-4125
GC–MS - LC–MS - metabolomics - NMR - nutrition
The life sciences are currently being transformed by an unprecedented wave of developments in molecular analysis, which include important advances in instrumental analysis as well as biocomputing. In light of the central role played by metabolism in nutrition, metabolomics is rapidly being established as a key analytical tool in human nutritional studies. Consequently, an increasing number of nutritionists integrate metabolomics into their study designs. Within this dynamic landscape, the potential of nutritional metabolomics (nutrimetabolomics) to be translated into a science, which can impact on health policies, still needs to be realized. A key element to reach this goal is the ability of the research community to join, to collectively make the best use of the potential offered by nutritional metabolomics. This article, therefore, provides a methodological description of nutritional metabolomics that reflects on the state-of-the-art techniques used in the laboratories of the Food Biomarker Alliance (funded by the European Joint Programming Initiative “A Healthy Diet for a Healthy Life” (JPI HDHL)) as well as points of reflections to harmonize this field. It is not intended to be exhaustive but rather to present a pragmatic guidance on metabolomic methodologies, providing readers with useful “tips and tricks” along the analytical workflow.
Predicting flowering behavior and exploring its genetic determinism in an apple multi-family population based on statistical indices and simplified phenotyping
Durand, Jean Baptiste ; Allard, Alix ; Guitton, Baptiste ; Weg, Eric van de; Bink, Marco C.A.M. ; Costes, Evelyne - \ 2017
Frontiers in Plant Science 8 (2017). - ISSN 1664-462X - 15 p.
Bayes factor - Biennial bearing - Entropy - Malus × domestica - Markov models - Pedigree based analysis

Irregular flowering over years is commonly observed in fruit trees. The early prediction of tree behavior is highly desirable in breeding programmes. This study aims at performing such predictions, combining simplified phenotyping and statistics methods. Sequences of vegetative vs. floral annual shoots (AS) were observed along axes in trees belonging to five apple related full-sib families. Sequences were analyzed using Markovian and linear mixed models including year and site effects. Indices of flowering irregularity, periodicity and synchronicity were estimated, at tree and axis scales. They were used to predict tree behavior and detect QTL with a Bayesian pedigree-based analysis, using an integrated genetic map containing 6,849 SNPs. The combination of a Biennial Bearing Index (BBI) with an autoregressive coefficient (γg) efficiently predicted and classified the genotype behaviors, despite few misclassifications. Four QTLs common to BBIs and γg and one for synchronicity were highlighted and revealed the complex genetic architecture of the traits. Irregularity resulted from high AS synchronism, whereas regularity resulted from either asynchronous locally alternating or continual regular AS flowering. A relevant and time-saving method, based on a posteriori sampling of axes and statistical indices is proposed, which is efficient to evaluate the tree breeding values for flowering regularity and could be transferred to other species.

Whole proteome analyses on Ruminiclostridium cellulolyticum show a modulation of the cellulolysis machinery in response to cellulosic materials with subtle differences in chemical and structural properties
Badalato, Nelly ; Guillot, Alain ; Sabarly, Victor ; Dubois, Marc ; Pourette, Nina ; Pontoire, Bruno ; Robert, Paul ; Bridier, Arnaud ; Monnet, Véronique ; Machado de Sousa, Diana ; Durand, Sylvie ; Mazéas, Laurent ; Buléon, Alain ; Bouchez, Théodore ; Mortha, Gerard ; Bize, Ariane - \ 2017
PLoS ONE 12 (2017)1. - ISSN 1932-6203
Lignocellulosic materials from municipal solid waste emerge as attractive resources for anaerobic digestion biorefinery. To increase the knowledge required for establishing efficient bioprocesses, dynamics of batch fermentation by the cellulolytic bacterium Ruminiclostridium cellulolyticum were compared using three cellulosic materials, paper handkerchief, cotton discs and Whatman filter paper. Fermentation of paper handkerchief occurred the fastest and resulted in a specific metabolic profile: it resulted in the lowest acetate-to-lactate and acetate-to-ethanol ratios. By shotgun proteomic analyses of paper handkerchief and Whatman paper incubations, 151 proteins with significantly different levels were detected, including 20 of the 65 cellulosomal components, 8 non-cellulosomal CAZymes and 44 distinct extracytoplasmic proteins. Consistent with the specific metabolic profile observed, many enzymes from the central carbon catabolic pathways had higher levels in paper handkerchief incubations. Among the quantified CAZymes and cellulosomal components, 10 endoglucanases mainly from the GH9 families and 7 other cellulosomal subunits had lower levels in paper handkerchief incubations. An in-depth characterization of the materials used showed that the lower levels of endoglucanases in paper handkerchief incubations could hypothetically result from its lower crystallinity index (50%) and degree of polymerization (970). By contrast, the higher hemicellulose rate in paper handkerchief (13.87%) did not result in the enhanced expression of enzyme with xylanase as primary activity, including enzymes from the "xyl-doc " cluster. It suggests the absence, in this material, of molecular structures that specifically lead to xylanase induction. The integrated approach developed in this work shows that subtle differences among cellulosic materials regarding chemical and structural characteristics have significant effects on expressed bacterial functions, in particular the cellulolysis machinery, resulting in different metabolic patterns and degradation dynamics.
Overview of the PREPARE WP3: management of contaminated goods in post-accidental situation – Synthesis of European stakeholders' panels
Charron, S. ; Lafage, S. ; Asselt, E. Van; Baptista, M. ; Bourgondiën, M. Van; Brandhoff, P. ; Cabianca, T. ; Camps, J. ; Cessac, B. ; Crouail, P. ; Durand, V. ; Gallego, E. ; Gil, O. ; Holmes, S. ; Hourdakis, C. ; Jones, K. ; Kamenopoulou, V. ; Lecomte, J.F. ; Liland, A. ; Lopes, I. ; Madruga, M.J. ; Martins, J.O. ; McMahon, C. ; Montero, M. ; Murith, C. ; Olyslaegers, G. ; Organo, C. ; Paiva, I. ; Peltonen, T. ; Portugal, L. ; Potiriadis, C. ; Prades, A. ; Reis, M. ; Rossignol, N. ; Schneider, T. ; Sala, R. ; Smith, V. ; Tafili, V. ; Teles, P. ; Tomkiv, Y. ; Trueba, C. ; Turcanu, C. ; Turtiainen, T. ; Twenhöfel, C. ; Vaz, P. ; Duranova, Tatiana ; Raskob, Wolfgang ; Schneider, Thierry - \ 2016
Radioprotection 51 (2016). - ISSN 0033-8451 - p. S83 - S91.
Recommendations and requirements for the management of foodstuffs including drinking water and
feedstuffs (but not other commodities) contaminated after a nuclear accident or a radiological event have been developed by
international bodies such as Codex Alimentarius Commission or European Union as well as by individual countries.
However, the experience fromsevere nuclear accidents (Chernobyl,Fukushima) and less serious radiological events, shows
that the implementation of such systems (based on criteria expressed in activity concentration) seems to be not fully suitable
to prevent several difficulties such as, for instance, stigmatization and even rejection attitudes from consumers or retailers
(anticipating the fears of consumers). Tofurther investigate the possible strategies and stakeholder expectations to deal with
this sensitive issue, a study has been launchedwithin the European research projectPREPARE-WP3. The overall objective
of this work, coordinated is to contribute to the development of strategies, guidance and tools for the management of the
contaminated products, taking into account the views of producers, processing and retail industries and consumers. For this
purpose, 10 stakeholder panels from different European countries have been set up. In addition, feedback experience from
the management of contaminated goods following the Fukushima accident has been provided by Japanese stakeholders.
This paper highlights the key topics tackled by the different European stakeholders’ panels
A statistical analysis of three ensembles of crop model responses to temperature and CO2 concentration
Makowski, D. ; Asseng, S. ; Ewert, F. ; Bassu, S. ; Durand, J.L. ; Li, G. ; Martre, P. ; Adam, M.Y.O. ; Aggarwal, P.K. ; Angulo, C. ; Baron, C. ; Basso, B. ; Bertuzzi, P. ; Biernath, C. ; Boogaard, H.L. ; Boote, K.J. ; Bouman, B. ; Bregaglio, S. ; Brisson, N. ; Buis, S. ; Cammarano, D. ; Challinor, A.J. ; Confalonieri, R. ; Conijn, J.G. ; Corbeels, M. ; Deryng, D. ; Sanctis, G. De; Doltra, J. ; Fumoto, T. ; Gayler, S. ; Gaydon, D. ; Goldberg, R. ; Grant, R.F. ; Grassini, P. ; Hatfield, J.L. ; Hasegawa, T. ; Heng, L. ; Hoek, S.B. ; Hooker, J. ; Hunt, L.A. ; Ingwersen, J. ; Izaurralde, C. ; Jongschaap, R.E.E. ; Jones, J.W. ; Kemanian, R.A. ; Kersebaum, K.C. ; Kim, S.H. ; Lizaso, J. ; Marcaida III, M. ; Müller, C. ; Nakagawa, H. ; Naresh Kumar, S. ; Nendel, C. ; O'Leary, G.J. ; Olesen, J.E. ; Oriol, P. ; Osborne, T.M. ; Palosuo, T. ; Pravia, M.V. ; Priesack, E. ; Ripoche, D. ; Rosenzweig, C. ; Ruane, A.C. ; Ruget, F. ; Sau, F. ; Semenov, M.A. ; Shcherbak, I. ; Singh, B. ; Soo, A.K. ; Steduto, P. ; Stöckle, C.O. ; Stratonovitch, P. ; Streck, T. ; Supit, I. ; Tang, L. ; Tao, F. ; Teixeira, E. ; Thorburn, P. ; Timlin, D. ; Travasso, M. ; Rötter, R.P. ; Waha, K. ; Wallach, D. ; White, J.W. ; Wilkens, P. ; Williams, J.R. ; Wolf, J. ; Ying, X. ; Yoshida, H. ; Zhang, Z. ; Zhu, Y. - \ 2015
Agricultural and Forest Meteorology 214-215 (2015). - ISSN 0168-1923 - p. 483 - 493.
Ensembles of process-based crop models are increasingly used to simulate crop growth for scenarios of temperature and/or precipitation changes corresponding to different projections of atmospheric CO2 concentrations. This approach generates large datasets with thousands of simulated crop yield data. Such datasets potentially provide new information but it is difficult to summarize them in a useful way due to their structural complexities. An associated issue is that it is not straightforward to compare crops and to interpolate the results to alternative climate scenarios not initially included in the simulation protocols. Here we demonstrate that statistical models based on random-coefficient regressions are able to emulate ensembles of process-based crop models. An important advantage of the proposed statistical models is that they can interpolate between temperature levels and between CO2 concentration levels, and can thus be used to calculate temperature and [CO2] thresholds leading to yield loss or yield gain, without re-running the original complex crop models. Our approach is illustrated with three yield datasets simulated by 19 maize models, 26 wheat models, and 13 rice models. Several statistical models are fitted to these datasets, and are then used to analyze the variability of the yield response to [CO2] and temperature. Based on our results, we show that, for wheat, a [CO2] increase is likely to outweigh the negative effect of a temperature increase of +2°C in the considered sites. Compared to wheat, required levels of [CO2] increase are much higher for maize, and intermediate for rice. For all crops, uncertainties in simulating climate change impacts increase more with temperature than with elevated [CO2].
Turbulence vertical structure of the boundary layer during the afternoon transition
Darbieu, C. ; Lohou, F. ; Lothon, M. ; Vilà-Guerau De Arellano, J. ; Couvreux, F. ; Durand, P. ; Pino, D. ; Patton, E.G. ; Nilsson, E. ; Blay-Carreras, E. ; Giolo, B. - \ 2015
Atmospheric Chemistry and Physics 15 (2015). - ISSN 1680-7316 - p. 10071 - 10086.
We investigate the decay of planetary boundary layer (PBL) turbulence in the afternoon, from the time the surface buoyancy flux starts to decrease until sunset. Dense observations of mean and turbulent parameters were acquired during the Boundary Layer Late Afternoon and Sunset Turbulence (BLLAST) field experiment by several meteorological surface stations, sounding balloons, radars, lidars and two aircraft during the afternoon transition. We analysed a case study based on some of these observations and largeeddy simulation (LES) data focusing on the turbulent vertical structure throughout the afternoon transition. The decay of turbulence is quantified through the temporal and vertical evolution of (1) the turbulence kinetic energy (TKE), (2) the characteristic length scales of turbulence and (3) the shape of the turbulence spectra. A spectral analysis of LES data, airborne and surface measurements is performed in order to characterize the variation in the turbulent decay with height and study the distribution of turbulence over eddy size. This study highlights the LES ability to reproduce the turbulence evolution throughout the afternoon. LESs and observations agree that the afternoon transition can be divided in two phases: (1) a first phase during which the TKE decays at a low rate, with no significant change in turbulence characteristics, and (2) a second phase characterized by a larger TKE decay rate and a change in spectral shape, implying an evolution of eddy size distribution and energy cascade from low to high wave number. The changes observed either in TKE decay (during the first phase) or in the vertical wind spectra shape (during the second phase of the afternoon transition) occur first in the upper region of the PBL. The higher within the PBL, the stronger the spectra shape changes.
Study of a prototypical convective boundary layer observed during BLLAST: contributions by large-scale forcings
Pietersen, H.P. ; Vilà-Guerau De Arellano, J. ; Augustin, P. ; Boer, A. van de; Coster, O. de; Delbarre, H. ; Durand, P. ; Fourmentin, M. ; Gioli, B. ; Hartogensis, O.K. ; Lohou, F. ; Lothon, M. ; Ouwersloot, H.G. ; Pino, D. ; Reuder, J. - \ 2015
Atmospheric Chemistry and Physics 15 (2015). - ISSN 1680-7316 - p. 4241 - 4257.
large-eddy simulation - turbulence - entrainment - transition - radiation - decay
We study the influence of the large-scale atmospheric contribution to the dynamics of the convective boundary layer (CBL) in a situation observed during the Boundary Layer Late Afternoon and Sunset Turbulence (BLLAST) field campaign. We employ two modeling approaches, the mixed-layer theory and large-eddy simulation (LES), with a complete data set of surface and upper-air atmospheric observations, to quantify the contributions of the advection of heat and moisture, and subsidence. We find that by only taking surface and entrainment fluxes into account, the boundary-layer height is overestimated by 70 %. Constrained by surface and upper-air observations, we infer the large-scale vertical motions and horizontal advection of heat and moisture. Our findings show that subsidence has a clear diurnal pattern. Supported by the presence of a nearby mountain range, this pattern suggests that not only synoptic scales exert their influence on the boundary layer, but also mesoscale circulations. LES results show a satisfactory correspondence of the vertical structure of turbulent variables with observations. We also find that when large-scale advection and subsidence are included in the simulation, the values for turbulent kinetic energy are lower than without these large-scale forcings. We conclude that the prototypical CBL is a valid representation of the boundary-layer dynamics near regions characterized by complex topography and small-scale surface heterogeneity, provided that surface- and large-scale forcings are representative for the local boundary layer.
Statistical Analysis of Large Simulated Yield Datasets for Studying Climate Effects
Makowski, D. ; Asseng, S. ; Ewert, F. ; Bassu, S. ; Durand, J.L. ; Martre, P. ; Adam, M. ; Aggarwal, P.K. ; Angulo, C. ; Baron, C. ; Basso, B. ; Bertuzzi, P. ; Biernath, C. ; Boogaard, H. ; Boote, K.J. ; Brisson, N. ; Cammarano, D. ; Challinor, A.J. ; Conijn, J.G. ; Corbeels, M. ; Deryng, D. ; Sanctis, G. De; Doltra, J. ; Gayler, S. ; Goldberg, R. ; Grassini, P. ; Hatfield, J.L. ; Heng, L. ; Hoek, S.B. ; Hooker, J. ; Hunt, L.A. ; Ingwersen, J. ; Izaurralde, C. ; Jongschaap, R.E.E. ; Jones, J.W. ; Kemanian, R.A. ; Kersebaum, K.C. ; Kim, S.H. ; Lizaso, J. ; Müller, C. ; Naresh Kumar, S. ; Nendel, C. ; O'Leary, G.J. ; Olesen, J.E. ; Osborne, T.M. ; Palosuo, T. ; Pravia, M.V. ; Priesack, E. ; Ripoche, D. ; Rosenzweig, C. ; Ruane, A.C. ; Sau, F. ; Semenov, M.A. ; Shcherbak, I. ; Steduto, P. ; Stöckle, C.O. ; Stratonovitch, P. ; Streck, T. ; Supit, I. ; Tao, F. ; Teixeira, E. ; Thorburn, P. ; Timlin, D. ; Travasso, M. ; Roetter, R.P. ; Waha, K. ; Wallach, D. ; White, J.W. ; Williams, J.R. ; Wolf, J. - \ 2015
In: Handbook of Climate Change and Agroecosystems: The Agricultural Model Intercomparison and Improvement Project (AgMIP) / Hillel, D., Rosenzweig, C., - 1100 p.
Many simulation studies have been carried out to predict the effect of climate change on crop yield. Typically, in such study, one or several crop models are used to simulate series of crop yield values for different climate scenarios corresponding to different hypotheses of temperature, CO2 concentration, and rainfall changes. These studies usually generate large datasets including thousands of simulated yield data. The structure of these datasets is complex because they include series of yield values obtained with different mechanistic crop models for different climate scenarios defined from several climatic variables (temperature, CO2 etc.). Statistical methods can play a big part for analyzing large simulated crop yield datasets, especially when yields are simulated using an ensemble of crop models. A formal statistical analysis is then needed in order to estimate the effects of different climatic variables on yield, and to describe the variability of these effects across crop models. Statistical methods are also useful to develop meta-models i.e., statistical models summarizing complex mechanistic models. The objective of this paper is to present a random-coefficient statistical model (mixed-effects model) for analyzing large simulated crop yield datasets produced by the international project AgMip for several major crops. The proposed statistical model shows several interesting features; i) it can be used to estimate the effects of several climate variables on yield using crop model simulations, ii) it quantities the variability of the estimated climate change effects across crop models, ii) it quantifies the between-year yield variability, iv) it can be used as a meta-model in order to estimate effects of new climate change scenarios without running again the mechanistic crop models. The statistical model is first presented in details, and its value is then illustrated in a case study where the effects of climate change scenarios on different crops are compared. See more from this Division: Special Sessions See more from this Session: Symposium--Perspectives on Climate Effects on Agriculture: The International Efforts of AgMIP
A new name for Gloriosa grandiflora (Colchicaceae) from the Democratic Republic of Congo (Kinshasa)
Maroyi, A. ; Maesen, L.J.G. van der - \ 2014
Phytotaxa 183 (2014)2. - ISSN 1179-3155 - p. 119 - 119.
In a recent contribution, Vinnersten & Manning (2007) transferred Littonia Hooker (1853: t. 4723) species to Gloriosa Linnaeus (1753: 305), making 7 new combinations. Unfortunately, the combination Gloriosa grandiflora (De Wildeman & Durand 1901: 34) J.C.Manning & Vinnersten in Vinnersten & Manning (2007: 178) is illegitimate since it is preoccupied by Gloriosa grandiflora (Hooker 1860: t. 5216) O’Brien (1904: 188), now known as Gloriosa simplex Linnaeus (1767: 62) (Maroyi, 2012). We hereby correct this matter by providing a new epithet:
How do various maize crop models vary in their responses to climate change factors?
Bassu, S. ; Brisson, N. ; Durand, J. ; Boote, K.J. ; Lizaso, J. ; Jones, J.W. ; Rosenzweig, C. ; Ruane, A.C. ; Adam, M. ; Baron, C. ; Basso, B. ; Biernath, C. ; Boogaard, H.L. ; Conijn, S. ; Corbeels, M. ; Deryng, D. ; Sanctis, G. De; Gayler, S. ; Grassini, P. ; Hatfield, J.L. ; Hoek, S.B. ; Izaurralde, C. - \ 2014
Global Change Biology 20 (2014)7. - ISSN 1354-1013 - p. 2301 - 2320.
water-use efficiency - air co2 enrichment - simulation-model - elevated co2 - systems simulation - nitrogen dynamics - carbon-dioxide - yield - wheat - agriculture
Potential consequences of climate change on crop production can be studied using mechanistic crop simulation models. While a broad variety of maize simulation models exist, it is not known whether different models diverge on grain yield responses to changes in climatic factors, or whether they agree in their general trends related to phenology, growth, and yield. With the goal of analyzing the sensitivity of simulated yields to changes in temperature and atmospheric carbon dioxide concentrations [CO2], we present the largest maize crop model intercomparison to date, including 23 different models. These models were evaluated for four locations representing a wide range of maize production conditions in the world: Lusignan (France), Ames (USA), Rio Verde (Brazil) and Morogoro (Tanzania). While individual models differed considerably in absolute yield simulation at the four sites, an ensemble of a minimum number of models was able to simulate absolute yields accurately at the four sites even with low data for calibration, thus suggesting that using an ensemble of models has merit. Temperature increase had strong negative influence on modeled yield response of roughly -0.5 Mg ha-1 per °C. Doubling [CO2] from 360 to 720 µmol mol-1 increased grain yield by 7.5% on average across models and the sites. That would therefore make temperature the main factor altering maize yields at the end of this century. Furthermore, there was a large uncertainty in the yield response to [CO2] among models. Model responses to temperature and [CO2] did not differ whether models were simulated with low calibration information or, simulated with high level of calibration information.
Management, regulation and environmental impacts of nitrogen fertilization in northwestern Europe under the Nitrates Directive; a benchmark study
Grinsven, H.J.M. van; Berge, H.F.M. ten; Dalgaard, T. ; Fraters, B. ; Durand, P. ; Hart, A. ; Hofman, G. ; Jacobsen, B.H. ; Lalor, S.T.J. ; Lesschen, J.P. ; Osterburg, B. ; Richards, K.G. ; Techen, A.K. ; Vertes, F. ; Webb, J. ; Willems, W.J. - \ 2012
Biogeosciences 9 (2012)12. - ISSN 1726-4170 - p. 5143 - 5160.
agriculture - losses - groundwater - balances - denmark
Implementation of the Nitrates Directive (NiD) and its environmental impacts were compared for member states in the northwest of the European Union (Ireland, United Kingdom, Denmark, the Netherlands, Belgium, Northern France and Germany). The main sources of data were national reports for the third reporting period for the NiD (2004-2007) and results of the MITERRA-EUROPE model. Implementation of the NiD in the considered member states is fairly comparable regarding restrictions for where and when to apply fertilizer and manure, but very different regarding application limits for N fertilization. Issues of concern and improvement of the implementation of the NiD are accounting for the fertilizer value of nitrogen in manure, and relating application limits for total nitrogen (N) to potential crop yield and N removal. The most significant environmental effect of the implementation of the NiD since 1995 is a major contribution to the decrease of the soil N balance (N surplus), particularly in Belgium, Denmark, Ireland, the Netherlands and the United Kingdom. This decrease is accompanied by a modest decrease of nitrate concentrations since 2000 in fresh surface waters in most countries. This decrease is less prominent for groundwater in view of delayed response of nitrate in deep aquifers. In spite of improved fertilization practices, the southeast of the Netherlands, the Flemish Region and Brittany remain to be regions of major concern in view of a combination of a high nitrogen surplus, high leaching fractions to groundwater and tenacious exceedance of the water quality standards. On average the gross N balance in 2008 for the seven member states in EUROSTAT and in national reports was about 20 kg N ha(-1) yr(-1) lower than by MITERRA. The major cause is higher estimates of N removal in national reports which can amount to more than 50 kg N ha(-1) yr(-1). Differences between procedures in member states to assess nitrogen balances and water quality and a lack of cross-boundary policy evaluations are handicaps when benchmarking the effectiveness of the NiD. This provides a challenge for the European Commission and its member states, as the NiD remains an important piece of legislation for protecting drinking water quality in regions with many private or small public production facilities and controlling aquatic eutrophication from agricultural sources.
Comparative mapping in the Fagaceae and beyond with EST-SSRs
Bodenes, C. ; Chancerel, E. ; Gailing, O. ; Vendramin, G.G. ; Bagnoli, F. ; Durand, J. ; Goicoechea, P.G. ; Soliani, C. ; Villani, F. ; Mattioni, C. ; Koelewijn, H.P. ; Murat, F. ; Salse, J. ; Roussel, G. ; Boury, C. ; Alberto, F. ; Kremer, A. ; Plomion, C. - \ 2012
BMC Plant Biology 12 (2012). - ISSN 1471-2229
quantitative trait loci - genetic-linkage map - castanea-sativa mill. - vitis-vinifera l. - quercus-robur l. - microsatellite markers - consensus map - bud burst - segregating populations - sequence alignment
Background: Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species. Results: We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype. Conclusions: This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.
A model for simulating the timelines of field operations at a European scale for use in complex dynamic models
Hutchings, N.J. ; Reinds, G.J. ; Leip, A. ; Wattenbach, M. ; Bienkowski, J. ; Dalgaard, T. ; Dragosits, U. ; Drouet, J. ; Durand, P. ; Maury, O. ; Vries, W. de - \ 2012
Biogeosciences 9 (2012)11. - ISSN 1726-4170 - p. 4487 - 4496.
n2o emissions - nitrogen - climate - soils
Complex dynamic models of carbon and nitrogen are often used to investigate the consequences of climate change on agricultural production and greenhouse gas emissions from agriculture. These models require high temporal resolution input data regarding the timing of field operations. This paper describes the Timelines model, which predicts the timelines of key field operations across Europe. The evaluation of the model suggests that while for some crops a reasonable agreement was obtained in the prediction of the times of field operations, there were some very large differences which need to be corrected. Systematic variations in the date of harvesting and in the timing of the first application of N fertiliser to winter crops need to be corrected and the prediction of soil workability and trafficability might enable the prediction of ploughing and applications of solid manure in preparation for spring crops. The data concerning the thermal time thresholds for sowing and harvesting underlying the model should be updated and extended to a wider range of crops.
On the role of large-scale forcings on the development of the atmospheric boundary layer during the BLLAST field campaign
Pietersen, H.P. ; Vilà-Guerau de Arellano, J. ; Coster, O. de; Boer, A. van de; Hartogensis, O.K. ; Pino, D. ; Gioli, B. ; Durand, P. ; Lothon, M. ; Lohou, F. ; Reuder, J. ; Jonassen, M. ; Faloona, I. - \ 2012
In: 20th Symposium on Boundary Layers and Turbulence/18th Conference on Air-Sea Interaction, American Meteorological Society (9-13 July 2012, Boston, MA). - Boston : American Meteorological Society - p. 14B.2 - 14B.2.
Guided and constrained by a complete data set of surface and upper-air observations taken during the fifth Intensive Observational Period (IOP-05, 25th June 2011) of the Boundary Layer Late Afternoon and Sunset Turbulence (BLLAST) experiment, we reconstruct the evolution of the atmospheric boundary layer (ABL) using mixed-layer theory. The model results are corroborated by UHF radar and multiple profiles done by unmanned and manned aircraft platforms as well as by radiosondes. During the first morning hours, the ABL is mainly controlled by surface forcing, reaching a depth between 500 and 600 meter. At these levels, large-scale subsidence motions become similar in magnitude to the entrainment velocity and the ABL-growth becomes nearly zero. This equilibrium is maintained until the afternoon transition where mixed-layer model results and observations show a decrease of the boundary layer depth in spite of well mixed observed vertical profiles of heat and moisture. We discuss potential explanations to the development of subsidence motions associated to mesoscale flows driven by the proximity of the Pyrenees mountain range and to large-scale forcing. The heat and moisture budgets are also further analyzed with the mixed layer model. We find strong indications of the active role of heat and moisture advection required to reproduce the observed diurnal variability in temperature and specific humidity. By quantifying the budget terms, we are able to obtain a first estimation of the contribution of advection to the heat and moisture budgets. To complete the analysis, we extend the study to examine the turbulent characteristics of the ABL by using aircraft measurements combined with large-eddy simulations. In so doing, we are able to study the role of wind (directional) shear in the development and maintenance of the ABL. IOP05 was characterized by easterly flows within the ABL and westerly winds aloft. Our findings stress the important role of large scale forcing in understanding the ABL development at various stages during BLLAST. The proposed method can also be very useful to support the further interpretation of observations and mesoscale model experiments.
The Boundary Layer Late Afternoon and Sunset Turbulence 2011 field experiment
Lothon, M. ; Lohou, F. ; Durand, P. ; Couvreux, F. ; Hartogensis, O.K. ; Legain, D. ; Pardyjak, E. ; Pino, D. ; Vilà-Guerau de Arellano, J. ; Boer, A. van de; Moene, A.F. ; Steeneveld, G.J. - \ 2012
In: 20th Symposium on Boundary Layers and Turbulence/18th Conference on Air-Sea Interaction, American Meteorological Society (9-13 July 2012, Boston, MA). - Boston : American Meteorological Society - p. 14B.1 - 14B.1.
BLLAST (Boundary Layer Late Afternoon and Sunset Turbulence) aims at better understanding the thermodynamical processes that occur during the late afternoon in the lower troposphere. In direct contact with the Earth surface, the atmospheric boundary layer is governed by buoyant and mechanical turbulence, with a strong diurnal cycle. The late afternoon transition, from the daytime dry convection to the night-time stable boundary layer, still raises a lot of issues and is poorly represented in the meteorological models. Yet, it plays an important role in the transport and diffusion of trace gases, like water vapour, carbon dioxide, pollutants, dusts... How does the afternoon decay in the lower troposphere happen, when the surface sensible heat flux start to sharply decrease ? How do the scales of the motions and transfers change ? What is the impact on the chemical closure and transport of trace gases and aerosols ? How to properly represent those processes in the meteorological models ? An international group is working on those issues by use of observations and numerical simulations, in order to improve our understanding and representation of the turbulent processes of the boundary-layer late afternoon transition. The roles of surface heterogeneity, entrainment at the boundary layer top, large scale subsidence, radiative effects, advection and gravity waves are studied. Due to the large lack of observations during this phase, a field campaign was organized in the vicinity of a 60-m instrumented tower of Laboratoire d'Aérologie, near the Pyrenees ridge in Southwest France, from 14 June to 8 July 2011. This experiment puts together complementary observation resources, in order to obtain an exhaustive description of the boundary-layer dynamical processes, its vertical structure, and the spatial variability related to surface heterogeneity. Continuous measurements (UHF radar and sodar wind profilers, lidars, ground stations), and intensive observations with aircraft, unmanned aerial vehicles, tethered balloons and radiosoundings were used. Particular emphasis was placed to bridge the different spatial scales with an integrated analysis of the observations and a complete numerical model hierarchy. This presentation will give an overview of the field experiment, with an emphasis on specific and innovative instrumental aspects, and with some preliminary results, introducing various contributions of BLLAST participants that will be shown along the 20th BLT conference.
Nitrogen processes in aquatic ecosystems
Durand, P. ; Breuer, L. ; Johnes, P.J. ; Billen, G. ; Klein, J.J.M. de - \ 2011
In: The European nitrogen assessment: sources, effects and policy perspectives Cambridge UK : Cambridge University Press - ISBN 9781107006126 - 664 p.
Editorial: Future topics of common interest for EU and SEA partners in food quality, safety and traceability
Montet, D. ; Alldrick, A. ; Bordier, M. ; Bresson, H. ; Chokesajjawatee, N. ; Durand, N. ; Ha, T.T. ; Hariyadi, P. ; Jinap, S. ; Keerratipibul, S. ; Leepipatpiboon, N. ; Luong, H.Q. ; Marvin, H.J.P. ; Medoc, J.M. ; Moustier, P. ; Nitisinprasert, S. ; Phan, T.D. ; Poms, R. ; Prasertvit, S. ; Rakshit, S.K. ; Ruangwises, M.N. ; Siriwatwechakul, W. ; Sparringa, R.A. ; Stouten, P. ; Stroka, J. ; Taharnklaew, R. ; Tayaputch, N. ; Tongpim, S. ; Valyasevi, R. ; Vithayarungruangsri, J. ; Saletes, S. - \ 2010
Quality Assurance and Safety of Crops & Foods 2 (2010)4. - ISSN 1757-8361 - p. 158 - 164.
SEA-EU-NET project is based on the program Capacities under the 7th Framework Program (FP7) of the EU Commission with the strategic objective of Integrating and Strengthening the EU-ASEAN Science and Technology Dialogue through coordination and supporting activities. It is a 4 years program started in January 2008, and is currently supported by 22 institutions from Europe and South-East Asia. The objective is to increase the quality, quantity, profile and impact of bi-regional Science and Technology cooperation between the 10 ASEAN countries and the Members and Associated States of the European Union. Every Thematic Priority of FP7 has to implement dedicated international cooperation activities to achieve the program's goals and to address specific problems of ‘Third Countries/Regions’ (non-EU Members States or non-Associated States). This activity is performed through the organization of annual Thematic Workshops, with the objective to produce a document containing duly justified proposals for Specific International Cooperation Actions. This paper presents the results of the Thematic Workshop on ‘Food Quality, Safety and Traceability’. This expert meeting was done in Thailand in February 2009. Titles for 10 possible themes were identified on the following fields: Bacteria antibioresistance, Mycotoxins, Pathogens (bacteria), Pesticides, Heavy metals, Food traceability, Food Supply Chain, Preserving nutrients, Consumers attitudes, Peri-urban markets.
Effect of carob bean gum, spray dried porcine plasma and sanuinarine on fermentation activity in the gut of weanling pigs
Pellikaan, W.F. ; Andres-Elias, N. ; Durand, A. ; Bongers, L.J.G.M. ; Laar-van Schuppen, S. van; Torrallardona, D. - \ 2010
In: 11th International Symposium on Digestive Physiology of pigs, Part 1. - Elsevier - p. 164 - 168.
growth-performance - animal plasma
Sixty landrace piglets received either a control diet or a control diet with added carob bean gum (CBG), spray dried porcine plasma (SDPP) or sanguinarine, to test the effects on fermentation end-product profiles along the GI tract. After animals were euthanized digesta samples were obtained from the mid-jejunum, distal ileum, caecum, proximal and distal colon at days d0, d1, d2, d6 and d14 post-weaning. Volatile fatty acid (VFA) concentration in the caecum and proximal colon was larger than that in the distal colon, the ileum and mid-jejunum (Pb0.05). At d0 the VFA and NH3 concentration in the ileum, ceacum and proximal colon was higher compared to d1 and d2 (Pb0.05). The molar proportions of acetic (AP), propionic (PP) and butyric (BP) acid in the ileum shifted gradually from d0 (87:6:4) to d14 (70:11:16). The proportion of branched chain VFA (BCP) decreased from d1 to d14 in both the caecum (7.1 to 1.3%) and proximal colon (6.9 to 1.2%). At d1 and d2 the additive treatments gave a numerical decrease in VFA compared to control, ammonia levels showed a differential response, and the BCP was numerically higher for the additive treatments compared to control. Results indicated that at the moment of weaning considerable fermentation activity occurs. During the weaning period fermentation in the ileum, caecum and proximal colon shifted from a proteolytic to a carbohydrate type of fermentation. Addition of CBG, sanguinarine and SDPP only resulted in a numerical decrease of fermentation end-product in the caecum and proximal colon during the first days post-weaning
Carbon stocks and spectroscopic assessment of carbon stability in Kenyan soils
Segnini, A. ; Posadas Durand, A. ; Quiroz, R. ; Claessens, L. ; Gavilan, C. ; Milori, D. ; Martin-Neto, L. - \ 2010
A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study
Durand, J. ; Bodénès, C. ; Chancerel, E. ; Frigerio, J.M. ; Vendramin, G. ; Sebastiani, F. ; Buonamici, A. ; Gailing, O. ; Koelewijn, H.P. ; Villani, F. ; Mattioni, C. ; Cherubini, M. ; Goicoechea, P.G. ; Herrán, A. ; Ikaran, Z. ; Cabané, C. ; Ueno, S. ; Alberto, F. ; Dumoulin, P.Y. ; Guichoux, E. ; Daruvar, A. de; Kremer, A. ; Plomion, C. - \ 2010
BMC Genomics 11 (2010). - ISSN 1471-2164
Background: Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut). Results: A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference fullsib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher. Conclusion: We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.
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