Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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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.
Soil-mediated filtering organizes tree assemblages in regenerating tropical forests
Pinho, Bruno Ximenes ; Melo, Felipe Pimentel Lopes de; Arroyo-Rodríguez, Víctor ; Pierce, Simon ; Lohbeck, Madelon ; Tabarelli, Marcelo - \ 2018
Journal of Ecology 106 (2018)1. - ISSN 0022-0477 - p. 137 - 147.
Atlantic forest - Brazil - Community assembly - Determinants of plant community diversity and structure - Environmental filtering - Forest regeneration - Functional traits - Secondary succession - Soil fertility - Soil nutrients

Secondary forests are increasingly dominant in human-modified tropical landscapes, but the drivers of forest recovery remain poorly understood. Soil conditions influence plant community composition, and are expected to change over a gradient of succession. However, the role of soil conditions as an environmental filter driving community assembly during forest succession has rarely been explicitly assessed. We evaluated the role of stand basal area and soil conditions on community assembly and its consequences for community functional properties along a chronosequence of Atlantic forest regeneration following sugar cane cultivation. Specifically, we tested whether community functional properties are related to stand basal area, soil fertility and soil moisture. Our expectations were that edaphic environmental filters play an increasingly important role along secondary succession by increasing functional trait convergence towards more conservative attributes. We sampled soil and woody vegetation features across 15 second-growth (3-30 years) and 11 old-growth forest plots (300 m2 each). We recorded tree functional traits related to resource-use strategies (specific leaf area, SLA; leaf dry matter content, LDMC; leaf area, LA; leaf thickness, LT; and leaf succulence, LS) and calculated community functional properties using the community-weighted mean (CWM) of each trait and the functional dispersion (FDis) of each trait separately and all traits together. With exception of LA, all leaf traits were strongly associated with stand basal area; LDMC and SLA increased, while LT and LS decreased with forest development. Such changes in LDMC, LT and LS were also related to the decrease in soil nutrient availability and pH along succession, while soil moisture was weakly related to community functional properties. Considering all traits, as well as leaf thickness and succulence separately, FDis strongly decreased with increasing basal area and decreasing soil fertility along forest succession, presenting the lowest values in old-growth forests. Synthesis. Our findings suggest that tropical forest regeneration may be a deterministic process shaped by soil conditions. Soil fertility operates as a key filter causing functional convergence towards more conservative resource-use strategies, such as leaves with higher leaf dry matter content.

Data from: Soil-mediated filtering organizes tree assemblages in regenerating tropical forests
Pinho, Bruno Ximenes ; Melo, Felipe Pimentel Lopes de; Arroyo-Rodríguez, Víctor ; Pierce, Simon ; Lohbeck, M.W.M. ; Tabarelli, Marcelo - \ 2017
determinants of plant community diversity and structure - environmental filtering - forest regeneration - functional traits - limiting similarity - secondary succession - soil fertility - community assembly
1.Secondary forests are increasingly dominant in human-modified tropical landscapes, but the drivers of forest recovery remain poorly understood. Soil conditions influence plant community composition, and are expected to change over a gradient of succession. However, the role of soil conditions as an environmental filter driving community assembly during forest succession has rarely been explicitly assessed. 2.We evaluated the role of stand basal area and soil conditions on community assembly and its consequences for community functional properties along a chronosequence of Atlantic forest regeneration following sugar cane cultivation. Specifically, we tested whether community functional properties are related to stand basal area, soil fertility and soil moisture. Our expectations were that edaphic environmental filters play an increasingly important role along secondary succession by increasing functional trait convergence towards more conservative attributes. 3.We sampled soil and woody vegetation features across 15 second-growth (3-30 years) and 11 old-growth forest plots (300 m² each). We recorded tree functional traits related to resource-use strategies (specific leaf area, SLA; leaf dry matter content, LDMC; leaf area, LA; leaf thickness, LT; and leaf succulence, LS) and calculated community functional properties using the community-weighted mean (CWM) of each trait and the functional dispersion (FDis) of each trait separately and all traits together. 4.With exception of LA, all leaf traits were strongly associated with stand basal area; LDMC and SLA increased, while LT and LS decreased with forest development. Such changes in LDMC, LT and LS were also related to the decrease in soil nutrient availability and pH along succession, while soil moisture was weakly related to community functional properties. Considering all traits, as well as leaf thickness and succulence separately, FDis strongly decreased with increasing basal area and decreasing soil fertility along forest succession, presenting the lowest values in old-growth forests. 5.Synthesis. Our findings suggest that tropical forest regeneration may be a deterministic process shaped by soil conditions. Soil fertility operates as a key filter causing functional convergence towards more conservative resource-use strategies, such as leaves with higher leaf dry mass content.
Smart-Logistics Generic Enablers and Architectural Requirements
Vucic, N. ; Reiche, R. ; Sundmaeker, H. ; Verdouw, C.N. ; Robbemond, R.M. ; Koenderink, N.J.J.P. ; Meyer, F. ; Gülcü, N. ; Hernandez, J.G. ; Pimentel, D.Q. ; Bekkum, M. van; Brewster, C. ; Tröger, R. ; Kläser, S. ; Cassing, Y. ; Lehmann, R. ; Schiefer, G. - \ 2012
Wageningen : Smart Agri-Food, EU (WP300 SAF_D300.2) - 134 p.
Locust Control by early identification of breeding sites
Huis, A. van - \ 2007
In: Encyclopedia of Pest Management / Pimentel, D., Taylor & Francis - ISBN 9780824706326 - p. 1 - 3.
Locust outbreaks occur when conditions for breeding become favorable. As a reaction to an increase in density, locusts change their behavior from solitarious to gregarious. When fully gregarious, they are capable of migrating in swarms to agricultural areas, where they can inflict considerable damage. The goal of control is to destroy gregarizing populations in the restricted outbreak areas. The feasibility of this approach will be discussed for different locust species, but in particular for the desert locust.
Opportunities ('costs) matter: a comment on Pimentel and Patzek "Ethanol production using corn, switchgrass, and wood; biodiesel production using soybean and sunflower"
Wesseler, J.H.H. - \ 2007
Energy Policy 35 (2007)2. - ISSN 0301-4215 - p. 1414 - 1416.
The energy balance for different crops reported by Pimentel and Patzek ignores opportunity costs. Including opportunity costs substantially changes the results and leads to different conclusions.
Invasion of Piper aduncum in the shifting cultivation systems of Papua New Guinea: Foreword by David Pimentel
Hartemink, A.E. - \ 2006
Wageningen : ISRIC - World Soil Information - ISBN 9081062816 - 234
piper aduncum - invasies - zwerflandbouw - ecologie - invasie - papoea-nieuw-guinea - invasions - shifting cultivation - ecology - invasion - papua new guinea
Piper aduncum, a shrub native to Central America, arrived in Papua New Guinea before the mid-1930s possibly from West Papua. From the 1970s it started to dominate the secondary fallow vegetation in many parts of the humid lowlands. It invaded grassland areas and it also appeared in the highlands up to 2100 m. The combination of its small and abundant seeds, its high growth rates, and the accidental or intentional spreading has resulted in its presence in most provinces of Papua New Guinea. The spread will continue.
Export of organic carbon in run-off from an Amazonian rainforest blackwater catchment
Waterloo, M.J. ; Oliveira, S.M. ; Drucker, D.P. ; Nobre, A.D. ; Cuartas, L.A. ; Hodnett, M.G. ; Langedijk, I. ; Jans, W.W.P. ; Tomasella, J. ; Araújo, A.C. de; Pimentel, T.P. ; Múnera Estrada, J.C. - \ 2006
Hydrological Processes 20 (2006)12. - ISSN 0885-6087 - p. 2581 - 2597.
tropical forests - rio-negro - fluxes - river - matter - basin - dioxide - brazil - deforestation - variability
Rainfall, run-off and dissolved and particulate organic carbon concentrations were measured to investigate the hydrological export of organic carbon out of the blackwater Igarape Asu rainforest catchment over a two-year period. Annual rainfall was above average (2442 mm) at 2976 mm in 2002 and below average at 2054 mm in 2003. Surface run-off dominated the flow out of the catchment, with groundwater outflow being negligible. Streamflow totals amounted to 1362 mm in 2002 and 780 mm in 2003. Dissolved organic carbon (DOC) concentrations in rainfall were similar to those measured in rainfall elsewhere in the Amazon Basin at 1-2 mg l(-1), leading to atmospheric DOC deposition estimates of 3.5 g m(-2) in 2002 and 2.4 g m(-2) in 2003. Daily average DOC concentrations in run-off ranged from 8 mg l(-1) under low flow conditions to 27 mg l(-1) during large quickflow events. Suspended sediment (10-2000-mu m size fraction) consisted for 28% of carbon and had a median concentration of 4.1 mg l(-1). Daily run-off varied between 1.2-2.5 mm day(-1) during dry periods with corresponding organic carbon exports of 0.009-0.031 g m(-2) day(-1). Exports associated with large storms were much higher, reaching a daily maximum of 1.02 g m(-2) day(-1) for a discharge event of 38.4 mm. Export of carbon during the wet seasons amounted to 70% of the total. Annual exports in river water were different between the years because of differences in run-off, varying between 26.2 g C m(-2) in 2002 and 11.7 g C m(-2) in 2003. Organic carbon exports were dominated by DOC, with exports in sediment constituting 6-8% of the total. Net carbon export, corrected for rainfall inputs, amounted to 22.7 and 9.3 g m(-2) in 2002 and 2003, respectively. The present study indicates that accounting for exports of organic carbon in stream runoff (averaging 19.0 g m(-2) year(-1) over the 2 years) would reduce the rainforest sink strength, estimated at 300-400 g m(-2) year(-1) from eddy covariance measurements, by 5-6% for this blackwater catchment.
Functioning of natural enemies in mixed cropping systems
Bukovinszky, T. ; Lenteren, J.C. van; Vet, L.E.M. - \ 2005
In: Encyclopedia of Pest Management / Pimentel, D., - p. 01 - 04.
Business network connection effects on relationship governance: empirial evidence of the flower sector in the Netherlands
Claro Pimentel, D. ; Hagelaar, J.L.F. ; Kemp, R. - \ 2002
In: IMP conference. - Dijon : [s.n.], 2002
Rede estratégica na selecão e na mantencão de relacionamentos con fornecedores: o caso MONL
Claro Pimentel, D. ; Borin de Oliviera Claro, P. ; Hagelaar, J.L.F. - \ 2002
RA USR revista Administracão 37 (2002)3. - p. 6 - 18.
PCR amplification of the rDNA internal transcribed spacer region for differentiation of Saccharomyces cultures
Valente, R. ; Gouveia, F.C. ; Lemos, G.A. de; Pimentel, D. ; Elsas, J.D. van; Mendonca-Hagler, L.C. ; Hagler, A.N. - \ 1996
FEMS Microbiology Letters 137 (1996). - ISSN 0378-1097 - p. 253 - 256.
The size of the internal transcribed spacer (ITS) region as measured by gel electrophoresis of PCR products, amplified by primers ITS1 and ITS4, was over 800 bp for all Saccharomyces sensu stricto species, but yeasts belonging to other Saccharomyces species had a shorter ITS region, making this characteristic potentially useful in the identification of Saccharomyces isolates. The ITS product length was homogeneous within the species Saccharomyces cerevisiae.
What is durable resistance? A general outline.
Parlevliet, J.E. - \ 1996
In: Techniques for reducing pesticide use / Pimentel, D., - p. 180 - 195.
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