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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Modeling water quality in the Anthropocene: directions for the next-generation aquatic ecosystem models
Mooij, W.M. ; Wijk, Dianneke van; Beusen, A.H.W. ; Brederveld, R.J. ; Chang, M. ; Cobben, Marleen M.P. ; DeAngelis, D.L. ; Downing, A.S. ; Janssen, A.B.G. ; Hengeveld, G.M. - \ 2019
Current Opinion in Environmental Sustainability 36 (2019). - ISSN 1877-3435 - p. 85 - 95.
Everything changes and nothing stands still” (Heraclitus). Here we review three major improvements to freshwater aquatic ecosystem models — and ecological models in general — as water quality scenario analysis tools towards a sustainable future. To tackle the rapid and deeply connected dynamics characteristic of the Anthropocene, we argue for the inclusion of eco-evolutionary, novel ecosystem and social-ecological dynamics. These dynamics arise from adaptive responses in organisms and ecosystems to global environmental change and act at different integration levels and different time scales. We provide reasons and means to incorporate each improvement into aquatic ecosystem models. Throughout this study we refer to Lake Victoria as a microcosm of the evolving novel social-ecological systems of the Anthropocene. The Lake Victoria case clearly shows how interlinked eco-evolutionary, novel ecosystem and social-ecological dynamics are, and demonstrates the need for transdisciplinary research approaches towards global sustainability.
Deep Learning for Agro-Food Robotics
Barth, Ruud - \ 2018
Breeding API (BrAPI)
Verouden, Maikel - \ 2018
Last Frontier of Agricultural BigData in Rotation?
Keizer, Paul - \ 2018
Kohonen 3.0: Improvements of the Kohonen R package for application of self-organising maps on large data sets
Kruisselbrink, Johannes - \ 2018
Accounting for differences in costs among sampling locations in optimal stratification
Brus, D.J. ; Yang, L. ; Zhu, A.X. - \ 2018
European Journal of Soil Science (2018). - ISSN 1351-0754

In areas with marked differences in accessibility, the cost efficiency of design-based sampling strategies for estimating the population mean or total can be increased by accounting for these differences in the selection of the sampling locations. This can be achieved by stratified random sampling. The question then is how to construct the strata. Existing optimal stratification methods such as cum (Formula presented.) stratification assume a constant cost among the sampling units, and therefore can be suboptimal when this assumption is violated. A simulated annealing algorithm is proposed for simultaneous optimization of the stratum breaks and the sample size under optimal allocation of the sample size, given a chosen maximum for the expected total costs. The proposed stratification method is tested in a study area of 5900 km2 in Anhui province, China. Optimal stratum breaks were computed for estimating the population mean of the soil organic matter content (SOM). Predictions of SOM from a multiple linear regression model were used as a stratification variable. The optimal stratum breaks differed markedly from the cum (Formula presented.) breaks. The variance of the estimated mean of SOM using the optimal stratification was about 8 to 29% smaller than with the cum (Formula presented.) stratification, depending on the number of strata. This large gain in precision can be explained by the moderately strong correlation of the point-wise costs and the stratification variable. Smaller gains are expected when this correlation is weaker or the variation in costs among the units are smaller. The proposed algorithm can also be used when no ancillary variable related to the variable of interest is available, accounting for differences in costs among the sampling units only. An R script with functions is provided as supporting information. Highlights: A method is proposed to compute optimal strata that accounts for differences in costs among sampling locations Simulated annealing is used to optimize stratum breaks and total sample size under a total costs constraint The variance of estimated mean of SOM with proposed method was 8 to 29% smaller than with cum (Formula presented.) method Proposed algorithm can also be used when no stratification variable is available (optimal costs stratification).

Integrating spatial and phylogenetic information in the fourth-corner analysis to test trait–environment relationships
Braga, João ; Braak, Cajo J.F. ter; Thuiller, Wilfried ; Dray, Stéphane - \ 2018
Ecology (2018). - ISSN 0012-9658 - p. 2667 - 26764.
community ecology - fourth-corner analysis - functional ecology - Moran's spectral randomization - null models - type I error

The fourth-corner analysis aims to quantify and test for relationships between species traits and site-specific environmental variables, mediated by site-specific species abundances. Since there is no common unit of observation, the significance of the relationships is tested using a double permutation procedure (site based and species based). This method implies that all species and sites are independent of each other. However, this fundamental hypothesis might be flawed because of phylogenetic relatedness between species and spatial autocorrelation in the environmental data. Here, using a simulation-based experiment, we demonstrate how the presence of spatial and phylogenetic autocorrelations can, in some circumstances, lead to inflated type I error rates, suggesting that significant associations can be misidentified. As an alternative, we propose a new randomization approach designed to avoid this issue, based on Moran's spectral randomization. In this approach, standard permutations are replaced by constrained randomizations so that the distribution of the statistic under the null hypothesis is built with additional constraints to preserve the phylogenetic and spatial structures of the observed data. The inclusion of this new randomization approach provides total control over type I error rates and should be used in real studies where spatial and phylogenetic autocorrelations often occur.

An analysis of characterized plant sesquiterpene synthases
Durairaj, Janani ; Girolamo, Alice Di; Bouwmeester, Harro J. ; Ridder, Dick de; Beekwilder, Jules ; Dijk, Aalt D.J. van - \ 2018
Phytochemistry (2018). - ISSN 0031-9422 - 9 p.
Database - Enzyme - Product specificity - Sesquiterpene - Sesquiterpene synthase - Terpene synthase

Plants exhibit a vast array of sesquiterpenes, C15 hydrocarbons which often function as herbivore-repellents or pollinator-attractants. These in turn are produced by a diverse range of sesquiterpene synthases. A comprehensive analysis of these enzymes in terms of product specificity has been hampered by the lack of a centralized resource of sufficient functionally annotated sequence data. To address this, we have gathered 262 plant sesquiterpene synthase sequences with experimentally characterized products. The annotated enzyme sequences allowed for an analysis of terpene synthase motifs, leading to the extension of one motif and recognition of a variant of another. In addition, putative terpene synthase sequences were obtained from various resources and compared with the annotated sesquiterpene synthases. This analysis indicated regions of terpene synthase sequence space which so far are unexplored experimentally. Finally, we present a case describing mutational studies on residues altering product specificity, for which we analyzed conservation in our database. This demonstrates an application of our database in choosing likely-functional residues for mutagenesis studies aimed at understanding or changing sesquiterpene synthase product specificity.

Salt marsh response to 32 years of relative increase in sea level
Bruls, Anne ; Limpens, J. ; Kuiters, A.T. ; Slim, P.A. - \ 2018
QSAR of 1,4-benzoxazin-3-one antimicrobials and their drug design perspectives
Bruijn, Wouter J.C. de; Hageman, Jos A. ; Araya-Cloutier, Carla ; Gruppen, Harry ; Vincken, Jean Paul - \ 2018
Bioorganic and Medicinal Chemistry 26 (2018)23-24. - ISSN 0968-0896 - p. 6105 - 6114.
2H-1,4-benzoxazin-3(4H)-one - Antibacterial - Antifungal - Benzoxazinoid - Benzoxazinone - Drug design - QSAR - SAR

Synthetic derivatives of 1,4-benzoxazin-3-ones have been shown to possess promising antimicrobial activity, whereas their natural counterparts were found lacking in this respect. In this work, quantitative structure-activity relationships (QSAR) of natural and synthetic 1,4-benzoxazin-3-ones as antimicrobials were established. Data published in literature were curated into an extensive dataset of 111 compounds. Descriptor selection was performed by a genetic algorithm. QSAR models revealed differences in requirements for activity against fungi, gram-positive and gram-negative bacteria. Shape, VolSurf, and H-bonding property descriptors were frequently picked in all models. The models obtained for gram-positive and gram-negative bacteria showed good predictive power (Q2 Ext 0.88 and 0.85, respectively). Based on the models generated, an additional set of 1,4-benzoxazin-3-ones, for which no antimicrobial activity had been determined in literature, were evaluated in silico. Additionally, newly designed lead compounds with a 1,4-benzoxazin-3-one scaffold were generated in silico by varying the positions and combinations of substituents. Two of these were predicted to be up to 5 times more active than any of the compounds in the current dataset. The 1,4-benzoxazin-3-one scaffold was concluded to possess potential for the design of new antimicrobial compounds with potent antibacterial activity, a multitarget mode of action, and possibly reduced susceptibility to gram negatives’ efflux pumps.

Putative regulatory candidate genes for QTL linked to fruit traits in oil palm (Elaeis guineensis Jacq.)
Ting, Ngoot Chin ; Mayes, Sean ; Massawe, Festo ; Sambanthamurthi, Ravigadevi ; Jansen, Johannes ; Syed Alwee, Sharifah Shahrul Rabiah ; Seng, Tzer Ying ; Ithnin, Maizura ; Singh, Rajinder - \ 2018
Euphytica 214 (2018)11. - ISSN 0014-2336
Deli dura - Marker-assisted selection - Pseudo-chromosome - Yangambi pisifera - Yield components

Palm oil is among the most important vegetable oils, contributing to a quarter of the world’s oils and fats market. The oil palm (Elaeis guineensis Jacq.) fruitlets, which are the source of palm oil, vary from 8 to 20 g in weight. Palm oil content in the fruitlets is approximately 45–50% by weight and an increase in the percentage of mesocarp-to-fruit is likely to have a positive effect on oil yield. In this study, we report a quantitative trait loci (QTL) associated with two yield related components, namely fruit and mesocarp content in a commercial breeding population (Deli dura × Yangambi pisifera). The QTL confidence interval of about 12 cM (~ 6.7 Mbp) was fine-mapped with 31 markers (17 SNPs and 14 SSRs) consisting of 20 nuclear markers derived from the maternal parent, six paternal and five co-segregating markers. Interestingly, inheritance of the paternal alleles leads to a larger difference in both fruit and mesocarp weight, when comparing genotypes in the progeny palms. Candidate genes and transcription factors were mined from the QTL region by positioning markers on the oil palm EG5 genome build. Putative genes and transcription factors involved in various biological processes including flower organ development, flowering, photosynthesis, microtubule formation, nitrogen and lipid metabolism were identified within this QTL interval on pseudo-chromosome 3. This genome-based approach allowed us to identify a number of potential candidate gene markers associated with oil palm fruit and mesocarp weight which can be further evaluated for potential use in marker-assisted breeding.

Evaluation of pest control efficiencies for different banker plant systems with a simple predator–prey model
Yano, Eizi ; Abe, Junichiro ; Hemerik, Lia - \ 2018
Population Ecology 60 (2018)4. - ISSN 1438-3896 - p. 389 - 396.
Biological control - Initial pest density - Mathematical model - Predator immigration - Transient dynamics

The banker plant system has been introduced for the biological control of various pest species in Japanese greenhouses. With the banker plant system, non-crop plants infested with a host insect (a non-commercial crop pest) are placed in the greenhouse to provide alternative resources for the parasitoids or predators. We want to evaluate the effectiveness for controlling pests on the crop in a quantitative way by immigrating predators from the banker plant. Therefore, we developed a simple model for the interaction of the pest and predator in the crop and included the banker plant only as a source for predators. For three different pest-predator systems we parameterised the model and used these models to predict under what conditions biological control in a banker plant system is successful. We defined successful as keeping the pest below the economic injury level of the crop estimated from damage analysis. Because the crop is mostly grown during a period that lasts less than a year our analysis should not only focus on the equilibrium dynamics. In contrast, it should also focus on the transient dynamics. Our main analytical result, from the equilibrium analysis, is that for successful control the maximum lifetime consumption of immigrating predators should exceed the daily prey growth at half the value of the maximum consumption rate. For practical purpose this translates into the fact that the immigration of predators at a low initial pest density is crucial for successful control.

Determining minimal output sets that ensure structural identifiability
Joubert, D. ; Stigter, J.D. ; Molenaar, J. - \ 2018
PLoS One 13 (2018)11. - ISSN 1932-6203

The process of inferring parameter values from experimental data can be a cumbersome task. In addition, the collection of experimental data can be time consuming and costly. This paper covers both these issues by addressing the following question: "Which experimental outputs should be measured to ensure that unique model parameters can be calculated?". Stated formally, we examine the topic of minimal output sets that guarantee a model's structural identifiability. To that end, we introduce an algorithm that guides a researcher as to which model outputs to measure. Our algorithm consists of an iterative structural identifiability analysis and can determine multiple minimal output sets of a model. This choice in different output sets offers researchers flexibility during experimental design. Our method can determine minimal output sets of large differential equation models within short computational times.

Data Quality & FAIR
Hengeveld, Geerten - \ 2018
Workshop: What should we ask from data and models used for policy support? The
Kwaliteitsstatus A, A+ and AA checklists
Actual European forest management by region, tree species and owner based on 714,000 re-measured trees in national forest inventories
Schelhaas, Mart-Jan ; Fridman, Jonas ; Hengeveld, Geerten M. ; Henttonen, Helena M. ; Lehtonen, Aleksi ; Kies, Uwe ; Krajnc, Nike ; Lerink, Bas ; Ní Dhubháin, Áine ; Polley, Heino ; Pugh, Thomas A.M. ; Redmond, John J. ; Rohner, Brigitte ; Temperli, Cristian ; Vayreda, Jordi ; Nabuurs, Gert-Jan ; Hanewinkel, Marc - \ 2018
PLoS One 13 (2018)11. - ISSN 1932-6203
Background
European forests have a long record of management. However, the diversity of the current forest management across nations, tree species and owners, is hardly understood. Often when trying to simulate future forest resources under alternative futures, simply the yield table style of harvesting is applied. It is now crucially important to come to grips with actual forest management, now that demand for wood is increasing and the EU Land Use, Land Use Change and Forestry Regulation has been adopted requiring ‘continuation of current management practices’ as a baseline to set the Forest Reference Level carbon sink.
Methods
Based on a large dataset of 714,000 re-measured trees in National Forest inventories from 13 regions, we are now able to analyse actual forest harvesting.
Conclusions
From this large set of repeated tree measurements we can conclude that there is no such thing as yield table harvesting in Europe. We found general trends of increasing harvest probability with higher productivity of the region and the species, but with important deviations related to local conditions like site accessibility, state of the forest resource (like age), specific subsidies, importance of other forest services, and ownership of the forest. As a result, we find a huge diversity in harvest regimes. Over the time period covered in our inventories, the average harvest probability over all regions was 2.4% yr-1 (in number of trees) and the mortality probability was 0.4% yr-1. Our study provides underlying and most actual data that can serve as a basis for quantifying ‘continuation of current forest management’. It can be used as a cornerstone for the base period as required for the Forest Reference Level for EU Member States.
Food for thought: Diedrich Bruns as a researcher
Brink, A. van den; Tobi, H. - \ 2018
In: Diedrich Bruns wird gelehrt haben / Hennecke, Stefanie, Kegler, Harald, Klaczynski, Kirtsen, Münderlein, Daniel, Kassel : University of Kassel - ISBN 9783737650649 - p. 34 - 47.
Health problems of people with intellectual disabilities in Dutch out-of-hours primary care
Heutmekers, Marloes ; Naaldenberg, Jenneken ; Verheggen, Sabine A. ; Assendelft, Willem J.J. ; Schrojenstein Lantman-de Valk, Henny M.J. van; Tobi, Hilde ; Leusink, Geraline L. - \ 2018
Journal of Applied Research in Intellectual Disabilities (2018). - ISSN 1360-2322
after-hours care - electronic health records - general practice - health service utilization - intellectual disability - medical conditions - primary health care

Background: Little is known about the health needs of people with intellectual disabilities who access out-of-hours primary care services, raising concerns about accessibility and quality of care for this group. This study aims to identify commonly presented health problems of people with intellectual disabilities in this specific setting compared with the general population. Method: Cross-sectional study with routine data at two out-of-hours cooperatives with a total of 41,166 persons aged 20–65 requesting outof-hours primary care in 2014, of which 315 persons were identified as having an intellectual disability. Results: Having an intellectual disability was associated with a higher probability of presenting with epilepsy (OR 45.65) and concerns about, and adverse effects of, medical treatment (OR 23.37, and 8.41, respectively). Conclusions: Given the high rates of epilepsy and medication-related concerns of people with intellectual disabilities, this study suggests that these issues require special attention to improve the accessibility and quality of out-of-hours primary care.

Metabolite variation in the lettuce gene pool : towards healthier crop varieties and food
Treuren, Rob van; Eekelen, Henriette D.L.M. van; Wehrens, Ron ; Vos, Ric C.H. de - \ 2018
Metabolomics 14 (2018)11. - ISSN 1573-3882
Crop improvement - Genetic resources - Lettuce - Phytochemical variation - Untargeted metabolomics - Vitamin C

Introduction: Lettuce (Lactuca sativa L.) is generally not specifically acknowledged for its taste and nutritional value, while its cultivation suffers from limited resistance against several pests and diseases. Such key traits are known to be largely dependent on the ability of varieties to produce specific phytochemicals. Objectives: We aimed to identify promising genetic resources for the improvement of phytochemical composition of lettuce varieties. Methods: Phytochemical variation was investigated using 150 Lactuca genebank accessions, comprising a core set of the lettuce gene pool, and resulting data were related to available phenotypic information. Results: A hierarchical cluster analysis of the variation in relative abundance of 2026 phytochemicals, revealed by untargeted metabolic profiling, strongly resembled the known lettuce gene pool structure, indicating that the observed variation was to a large extent genetically determined. Many phytochemicals appeared species-specific, of which several are generally related to traits that are associated with plant health or nutritional value. For a large number of phytochemicals the relative abundance was either positively or negatively correlated with available phenotypic data on resistances against pests and diseases, indicating their potential role in plant resistance. Particularly the more primitive lettuces and the closely related wild relatives showed high levels of (poly)phenols and vitamin C, thus representing potential genetic resources for improving nutritional traits in modern crop types. Conclusion: Our large-scale analysis of phytochemical variation is unprecedented in lettuce and demonstrated the ample availability of suitable genetic resources for the development of improved lettuce varieties with higher nutritional quality and more sustainable production.

Cooperation can improve the resilience of common-pool resource systems against over-harvesting
Broeke, G.A. ten; Voorn, G.A.K. van; Ligtenberg, A. ; Molenaar, J. - \ 2018
Ecological Complexity (2018). - ISSN 1476-945X - 22 p.
Agent-based model - Common-pool resource - Cooperation

Currently common-pool resource systems world-wide are under pressure due to overexploitation and environmental change. To ensure that these systems continue to provide vital ecosystem services it is necessary to sustain or increase their resilience against such pressure. One way of doing this may be to improve cooperation among agents who are heavily involved in common-pool resource systems, such as farmers, fishers, managers, and companies. Historical examples suggest that the persistence or collapse of common-pool resource systems may hinge on agents collaborating or not, but cooperation as a mechanism to improve resilience is not commonly included in existing models for studying resilience. Cooperation may be sustained through indirect reciprocity, i.e., cooperative behaviour by one agent that may be repaid by other agents. In this paper we develop a suite of agent-based models that represent an abstract version of a generic spatial common-pool resource system. This suite of models contains various mechanisms for cooperation based on trust. We investigate how the resilience of the models is affected by these mechanisms. The resilience of the models is assessed by applying various shocks which make it more difficult to gather resource, and measuring whether and how fast the agent population can recover from these shocks. The results suggest that although indirect reciprocity positively affects the level of cooperation in the system, cooperation could be common even without indirect reciprocity. It is shown that the presence of cooperation increases the resilience of the models against shocks.

Genomic prediction across populations, using pre-selected markers and differential weight models
Raymond, Biaty ; Bouwman, A.C. ; Schrooten, Chris ; Houwing-Duistermaat, Jeanine J. ; Veerkamp, R.F. - \ 2018
In: Proceedings of the World Congress on Genetics Applied to Livestock Production - 6 p.
Genomic prediction (GP) in numerically small breeds is limited due to the requirement for a large reference set. Across breed prediction has not been very successful either. Our objective was to test alternative models for across breed and multi-breed GP in a small Jersey population, utilizing prior information on marker causality. We used data on 596 Jersey bulls from new Zealand and 5503 Holstein bulls from the Netherlands, all of which had deregressed proofs for stature. Two sets of genotype data were used, one containing 357 potential causal markers identified from a multi-breed meta-GWAS on stature (top markers), while the other contained 48,912 markers on the custom 50k chip, excluding the top markers. We used models in which only one GRM (either top markers, 50k, or top plus 50k markers combined) was fitted, and models in which two GRMs (both the top and 50k) were fitted simultaneously, however with different variance components to weight the GRMs differently. Moreover, we estimated the genetic correlation(s) between the breeds (for each GRM) using a multi-trait GP model, which implicitly weights the contribution of one breed’s information to another. Across breed, we observed low accuracies of GP when the 50k markers were fitted alone (0.06) or when the top markers were added to 50k (0.15). Higher accuracy was obtained when only the top markers were fitted (0.21), whereas the highest accuracy was obtained when fitting 50k and top markers simultaneously as two independent GRMs (0.25). Multi-breed prediction outperformed both within and across breed prediction with accuracies ranging from 0.34 to 0.45, with the same trend as in across breed prediction. Based on our results, the best approach for across and multi-breed GP is to fit models that are able to isolate and differentially weight the most important markers for the trait. Keywords: Across breed genomic prediction, marker pre-selection, multi-trait model, sequence data.
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