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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    Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls
    Bodkhe, Rahul ; Shetty, Sudarshan A. ; Dhotre, Dhiraj P. ; Verma, Anil K. ; Bhatia, Khushbo ; Mishra, Asha ; Kaur, Gurvinder ; Pande, Pranav ; Bangarusamy, Dhinoth K. ; Santosh, Beena P. ; Perumal, Rajadurai C. ; Ahuja, Vineet ; Shouche, Yogesh S. ; Makharia, Govind K. - \ 2019
    Frontiers in Microbiology 10 (2019). - ISSN 1664-302X
    Recent studies on celiac disease (CeD) have reported alterations in the gut microbiome. Whether this alteration in the microbial community is the cause or effect of the disease is not well understood, especially in adult onset of disease. The first-degree relatives (FDRs) of CeD patients may provide an opportunity to study gut microbiome in pre-disease state as FDRs are genetically susceptible to CeD. By using 16S rRNA gene sequencing, we observed that ecosystem level diversity measures were not significantly different between the disease condition (CeD), pre-disease (FDR) and control subjects. However, differences were observed at the level of amplicon sequence variant (ASV), suggesting alterations in specific ASVs between pre-disease and diseased condition. Duodenal biopsies showed higher differences in ASVs compared to fecal samples indicating larger disruption of the microbiota at the disease site. The duodenal microbiota of FDR was characterized by significant abundance of ASVs belonging to Parvimonas, Granulicatella, Gemella, Bifidobacterium, Anaerostipes, and Actinomyces genera. The duodenal microbiota of CeD was characterized by higher abundance of ASVs from genera Megasphaera and Helicobacter compared to the FDR microbiota. The CeD and FDR fecal microbiota had reduced abundance of ASVs classified as Akkermansia and Dorea when compared to control group microbiota. In addition, predicted functional metagenome showed reduced ability of gluten degradation by CeD fecal microbiota in comparison to FDRs and controls. The findings of the present study demonstrate differences in ASVs and predicts reduced ability of CeD fecal microbiota to degrade gluten compared to the FDR fecal microbiota. Further research is required to investigate the strain level and active functional profiles of FDR and CeD microbiota to better understand the role of gut microbiome in pathophysiology of CeD.
    Hydrodynamically Coupled Brownian Dynamics : A coarse-grain particle-based Brownian dynamics technique with hydrodynamic interactions for modeling self-developing flow of polymer solutions
    Ahuja, V.R. ; Gucht, J. Van Der; Briels, W.J. - \ 2018
    Journal of Chemical Physics 148 (2018)3. - ISSN 0021-9606
    We present a novel coarse-grain particle-based simulation technique for modeling self-developing flow of dilute and semi-dilute polymer solutions. The central idea in this paper is the two-way coupling between a mesoscopic polymer model and a phenomenological fluid model. As our polymer model, we choose Responsive Particle Dynamics (RaPiD), a Brownian dynamics method, which formulates the so-called "conservative" and "transient" pair-potentials through which the polymers interact besides experiencing random forces in accordance with the fluctuation dissipation theorem. In addition to these interactions, our polymer blobs are also influenced by the background solvent velocity field, which we calculate by solving the Navier-Stokes equation discretized on a moving grid of fluid blobs using the Smoothed Particle Hydrodynamics (SPH) technique. While the polymers experience this frictional force opposing their motion relative to the background flow field, our fluid blobs also in turn are influenced by the motion of the polymers through an interaction term. This makes our technique a two-way coupling algorithm. We have constructed this interaction term in such a way that momentum is conserved locally, thereby preserving long range hydrodynamics. Furthermore, we have derived pairwise fluctuation terms for the velocities of the fluid blobs using the Fokker-Planck equation, which have been alternatively derived using the General Equation for the Non-Equilibrium Reversible-Irreversible Coupling (GENERIC) approach in Smoothed Dissipative Particle Dynamics (SDPD) literature. These velocity fluctuations for the fluid may be incorporated into the velocity updates for our fluid blobs to obtain a thermodynamically consistent distribution of velocities. In cases where these fluctuations are insignificant, however, these additional terms may well be dropped out as they are in a standard SPH simulation. We have applied our technique to study the rheology of two different concentrations of our model linear polymer solutions. The results show that the polymers and the fluid are coupled very well with each other, showing no lag between their velocities. Furthermore, our results show non-Newtonian shear thinning and the characteristic flattening of the Poiseuille flow profile typically observed for polymer solutions.
    Arabidopsis myrosinases link the glucosinolate-myrosinase system and the cuticle
    Ahuja, Ishita ; Vos, Ric C.H. de; Rohloff, Jens ; Stoopen, Geert M. ; Halle, Kari K. ; Ahmad, Samina Jam Nazeer ; Hoang, Linh ; Hall, Robert D. ; Bones, Atle M. - \ 2016
    Scientific Reports 6 (2016). - ISSN 2045-2322

    Both physical barriers and reactive phytochemicals represent two important components of a plant's defence system against environmental stress. However, these two defence systems have generally been studied independently. Here, we have taken an exclusive opportunity to investigate the connection between a chemical-based plant defence system, represented by the glucosinolate-myrosinase system, and a physical barrier, represented by the cuticle, using Arabidopsis myrosinase (thioglucosidase; TGG) mutants. The tgg1, single and tgg1 tgg2 double mutants showed morphological changes compared to wild-type plants visible as changes in pavement cells, stomatal cells and the ultrastructure of the cuticle. Extensive metabolite analyses of leaves from tgg mutants and wild-type Arabidopsis plants showed altered levels of cuticular fatty acids, fatty acid phytyl esters, glucosinolates, and indole compounds in tgg single and double mutants as compared to wild-type plants. These results point to a close and novel association between chemical defence systems and physical defence barriers.

    Coarse-grained simulations for flow of complex soft matter fluids in the bulk and in the presence of solid interfaces
    Ahuja, V.R. ; Gucht, J. van der; Briels, W.J. - \ 2016
    Journal of Chemical Physics 145 (2016)19. - ISSN 0021-9606

    We present a coarse-grained particle-based simulation technique for modeling flow of complex soft matter fluids such as polymer solutions in the presence of solid interfaces. In our coarse-grained description of the system, we track the motion of polymer molecules using their centers-of-mass as our coarse-grain co-ordinates and also keep track of another set of variables that describe the background flow field. The coarse-grain motion is thus influenced not only by the interactions based on appropriate potentials used to model the particular polymer system of interest and the random kicks associated with thermal fluctuations, but also by the motion of the background fluid. In order to couple the motion of the coarse-grain co-ordinates with the background fluid motion, we use a Galilean invariant, first order Brownian dynamics algorithm developed by Padding and Briels [J. Chem. Phys. 141, 244108 (2014)], which on the one hand draws inspiration from smoothed particle hydrodynamics in a way that the motion of the background fluid is efficiently calculated based on a discretization of the Navier-Stokes equation at the positions of the coarse-grain coordinates where it is actually needed, but also differs from it because of the inclusion of thermal fluctuations by having momentum-conserving pairwise stochastic updates. In this paper, we make a few modifications to this algorithm and introduce a new parameter, viz., a friction coefficient associated with the background fluid, and analyze the relationship of the model parameters with the dynamic properties of the system. We also test this algorithm for flow in the presence of solid interfaces to show that appropriate boundary conditions can be imposed at solid-fluid interfaces by using artificial particles embedded in the solid walls which offer friction to the real fluid particles in the vicinity of the wall. We have tested our method using a model system of a star polymer solution at the overlap concentration.

    Brassicacea-based management strategies as an alternative to combat nematode pests : A synopsis
    Fourie, Hendrika ; Ahuja, Preeti ; Lammers, Judith ; Daneel, Mieke - \ 2016
    Crop Protection 80 (2016). - ISSN 0261-2194 - p. 21 - 41.
    Biofumigation - Brassicaceae - Cover/green manure crop - PPN - Resistance - Soil amendments

    Nematode pests parasitise and cause substantial crop yield and quality losses to a wide range of crops worldwide. To minimize such damage, the exploitation and development of alternative nematode control strategies are becoming increasingly important, particularly as a result of global efforts to conserve the ozone layer as well as our soil and water substrates. Inclusion of Brassicaceae crops in cropping systems is one such alternative and has been demonstrated in most cases to be effective in managing the top-three rated economically important nematode pests, viz. root-knot (Meloidogyne), cyst (Heterodera and Globodera) and lesion (Pratylenchus) nematodes as well as others. In the past nematode pests were and still are generally managed successfully by the use of synthetically-derived nematicides, which are progressively being removed from world markets. However, fragmented and limited information about the use of Brassicaceae crops as a nematode management tool exists in various countries. The need thus arose to summarize, compare and discuss the vast amount of information that has been generated on this topic in a concise article. This paper therefore represents a comprehensive, practical and critical review of the use and effect(s) of Brassicaceae-based management strategies and the biofumigation and cover-crop/rotation characteristics of Brassicaceae in reducing nematode-pest population levels in global cropping systems.

    Modeling Greenhouse Gas Emissions from Enteric Fermentation
    Kebreab, E. ; Tedeschi, L. ; Dijkstra, J. ; Ellis, J.L. ; Bannink, A. ; France, J. - \ 2016
    In: Synthesis and Modeling of Greenhouse Gas Emissions and Carbon Storage in Agricultural and Forest Systems to Guide Mitigation and Adaptation / Del Grosso, S., Parton, W., Ahuja, L., American Society of Agronomy Inc, Crop Science Society of Americ Inc. and Soil Science Society of America Inc. (Advances in Agricultural Systems Modelling, , Synthesis and Modeling of Greenhouse Gas Emissions and Carbon Storage in Agricultural and Forest Systems to Guide Mitigation and Adaptation 6) - ISBN 9780891183464 - p. 173 - 195.
    Livestock directly contribute to greenhouse gas (GHG) emissions mainly through methane (CH4) and nitrous oxide (N2O) emissions. For cost and practicality reasons, quantification of GHG has been through development of various types of mathematical models. This chapter addresses the utility and limitations of mathematical models used to estimate enteric CH4 emissions from livestock production. Models used in GHG quantification can be broadly classified into either empirical or mechanistic models. Empirical models might be easier to use because they require fewer input variables compared with mechanistic models. However, their applicability in assessing mitigation options such as dietary manipulation may be limited. The major driving variables identified for both types of models include feed intake, lipid and nonstructural carbohydrate content of the feed, and animal variables. Knowledge gaps identified in empirical modeling were that some of the assumptions might not be valid because of geographical location, health status of animals, genetic differences, or production type. In mechanistic modeling, errors related to estimating feed intake, stoichiometry of volatile fatty acid (VFA) production, and acidity of rumen contents are limitations that need further investigation. Model prediction uncertainty was also investigated, and, depending on the intensity and source of the prediction uncertainty, the mathematical model may inaccurately predict the observed values with more or less variability. In conclusion, although there are quantification tools available, global collaboration is required to come to a consensus on quantification protocols. This can be achieved through developing various types of models specific to region, animal, and production type using large global datasets developed through international collaboration.
    Inter-organizational network analysis in synergy parks
    Nuhoff-Isakhanyan, G. ; Wubben, E.F.M. ; Omta, S.W.F. - \ 2014
    Organizational collaborations are important means for organizations to access new resources and enhance the sustainable performance. Recent examples of inter-organizational collaborations towards more sustainable production are synergy parks, such as eco-industrial parks and agroparks. Synergy parks are collaborations among organizations across different sectors, mainly from agriculture and industry, aiming at enhanced economic and environmental performance, sustainable agri-food and bio-energy production through exchanging waste and by-products, creating production synergies. Because synergy parks connect organizations in their non-core business activities, these organizations are not always keen in the realization of synergy parks. A synergy park consists of multiple organizations from various sectors linked through multiple ties, its coordination can be explained by means of organizational network theory (Van de Ven & Fery, 1980). Consequently, a synergy park can be seen as a network where companies are the nodes and their collaborations the ties. Companies with direct ties, can affect the behavior of one another (Rowley, 1997). Recently more and more scholars use network analysis in understanding firms, stakeholders, and their social and behavioral phenomena (Ahuja, 2000; Ahuja, et al., 2009; Corsaro, et al., 2012; Gulati, 2007; Gulati, et al., 2000). Theories that discuss organizational networks, however, pay more attention to relations at dyadic level. Network analysis use in understanding firms, stakeholders, and their social and behavioral phenomena beyond dyadic level is slowly increasing (Ackermann & Eden, 2011; Frooman, 1999; Rowley, 1997). It provides scholars new insights to develop the inter-organizational network theory, to further it from dyadic relationship and examine systems of dyadic interactions capturing the influence of multiple and interdependent relations on network development. The purpose of the study is to understand how the structure of inter-organizational networks impact the realization of synergy parks by analyzing network attributes. In this study we answer the following questions: What is the impact of the network structure attributes (size, type of relation, centrality, and density) on realization of inter-organizational collaborations, such as a synergy park? What alternative network structures are effective in different inter-organizational collaborations? We suggest the following propositions: 1) The relation between the size of the network and the potential of a synergy park realization has an inverse convex shape (n shape) 2) Companies connected with both formal and informal ties have stronger and enduring relationships than the ones connected with formal ties only. 3) Decentralized and dense network structures are more suited for the realization of a synergy park if the set of involved companies are more heterogeneous. We conducted cross-case analysis in three synergy parks through using mixed qualitative and quantitative methods. The unit of analysis is the exchange relationship among the organizations within the networks. We focus on formal, informal, and trust related relations. We identified the boundary spanners in each organization, and asked managers who are the most knowledgeable about the relation of other organizations in the parks. These persons are formally or informally responsible for managing the collaborative relationships with other organizations. The main method of data collection was semi-structured interviews. The network survey has complex design comparing to standard surveys, therefore, we decided to interview each respondent personally by using ONA online survey tools. Concerning to network ties, we gather value and binary data. Each tie among the same companies have been measured and analyzed separately, and compared with one another. The data is coded and analyzed by using UCINET network analysis software (Borgatti, et al., 2002; Hanneman & Riddle, 2005). Networks are framed and analyzed per synergy park separate, which is followed by the analysis across networks. The discussion and the conclusion will be presented in the full paper. Reference Ackermann, F., & Eden, C., 2011. Strategic Management of Stakeholders: Theory and Practice. Long Range Planning, 44(3): 179-196. Ahuja, G., 2000. Collaboration Networks, Structural Holes, and Innovation: A Longitudinal Study. Administrative Science Quarterly, 45(3): 425-455. Ahuja, G., Polidoro, F., & Mitchell, W., 2009. Structural homophily or social asymmetry? The formation of alliances by poorly embedded firms. Strategic Management Journal, 30(9): 941-958. Borgatti, S. P., Everett, M. G., & Freeman, L. C., 2002. UCINET for Windows, Version 6.59: Software for Social Network Analysis. Harvard, MA Analytic Technologies. Corsaro, D., Cantu, C., & Tunisini, A., 2012. Actors' Heterogeneity in Innovation Networks. Industrial Marketing Management, 41(5): 780-789. Frooman, J., 1999. Stakeholder influence strategies. Academy of Management Review, 24(2): 191-205. Gulati, R., 2007. Managing network resources: alliances, affiliations and other relational assets. Oxford: Oxford University Press. Gulati, R., Nohria, N., & Zaheer, A., 2000. Strategic networks. Strategic Management Journal, 21(3): 203-215. Hanneman, R. A., & Riddle, M., 2005. Introduction to Social Network Methods. Riverside CA: University of California. Rowley, T. J., 1997. Moving beyond dyadic ties: A network theory of stakeholder influences. Academy of Management Review, 22(4): 887-910. Van de Ven, A. H., & Fery, D. L., 1980. Measuring and Assessing Organizations: John Wiley & Sons, Inc.
    Modeling winter wheat production across Europe with WOFOST – the effect of two new zonations and two newly calibrated model parameter sets
    Wolf, J. ; Hessel, R. ; Boogaard, H.L. ; Wit, A.J.W. de; Akkermans, W. ; Diepen, C.A. van - \ 2011
    In: Methods of Introducing System Models into Agricultural Research / Ahuja, L.R., Liwang Ma, Madison, WI, USA : American Society of Agronomy, Inc. (Advances in Agricultural Systems Modeling 2) - ISBN 9780891181804 - p. 297 - 326.
    Plant molecular stress responses face climate change. Trends in Plants
    Ahuja, I. ; Vos, R.C.H. de; Bones, A.M. ; Hall, R.D. - \ 2010
    Trends in Plant Science 15 (2010)12. - ISSN 1360-1385 - p. 664 - 674.
    transgenic arabidopsis plants - elevated atmospheric co2 - drought-stress - abiotic stress - transcription factor - gene-expression - heat-stress - systems biology - carbon metabolism - plasma-membrane
    Environmental stress factors such as drought, elevated temperature, salinity and rising CO2 affect plant growth and pose a growing threat to sustainable agriculture. This has become a hot issue due to concerns about the effects of climate change on plant resources, biodiversity and global food security. Plant adaptation to stress involves key changes in the ‘-omic’ architecture. Here, we present an overview of the physiological and molecular programs in stress adaptation focusing on how genes, proteins and metabolites change after individual and multiple environmental stresses. We address the role which ‘-omics’ research, coupled to systems biology approaches, can play in future research on plants seemingly unable to adapt as well as those which can tolerate climatic change.
    A field test of Root Zone Water Quality Model - pesticide and bromide behavior
    Ahuja, L.R. ; Ma, Q.L. ; Rojas, K.W. ; Boesten, J.J.T.I. ; Farahani, H.J. - \ 1996
    Pesticide science : a journal of international research and technology on crop protection and pest control 48 (1996)2. - ISSN 0031-613X - p. 101 - 108.
    colloïdale eigenschappen - persistentie - pesticidenresiduen - pesticiden - gewasbescherming - bodem - bodemkunde - bodemoplossing - colloidal properties - persistence - pesticide residues - pesticides - plant protection - soil - soil science - soil solution
    The Root Zone Water Quality Model is a process-based model that integrates physical, chemical and biological processes to simulate the fate and movement of water and agrochemicals over and through the root zone at a representative point in a field with various management practices. The model was evaluated with field data for the movement of water and bromide, and the transformation and transport of cyanazine and metribuzin in the soil profile. The model reasonably simulated soil water and bromide movement. Pesticide persistence was predicted reasonably well with a two-site sorption model that assumes a rate-limited adsorption-desorption process with the additional assumption of negligible degradation of interaggregate-adsorbed pesticides.
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