# 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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 Renaissance of traditional DNA transfer strategies for improvement of industrial lactic acid bacteriaBron, Peter A. ; Marcelli, Barbara ; Mulder, Joyce ; Els, Simon van der; Morawska, Luiza P. ; Kuipers, Oscar P. ; Kok, Jan ; Kleerebezem, Michiel - \ 2019Current Opinion in Biotechnology 56 (2019). - ISSN 0958-1669 - p. 61 - 68. The ever-expanding genomic insight in natural diversity of lactic acid bacteria (LAB) has revived the industrial interest in traditional and natural genetic mobilization methodologies. Here, we review recent advances in horizontal gene transfer processes in LAB, including natural competence, conjugation, and phage transduction. In addition, we envision the possibilities for industrial strain improvement arising from the recent discoveries of molecular exchanges between bacteria through nanotubes and extracellular vesicles, as well as the constantly expanding genome editing possibilities using the CRISPR-Cas technology. Functional diversity in nematode communities across terrestrial ecosystemsSechi, Valentina ; Goede, Ron G.M. De; Rutgers, Michiel ; Brussaard, Lijbert ; Mulder, Christian - \ 2019Basic and Applied Ecology 30 (2019). - ISSN 1439-1791 - p. 76 - 86. Body-size distribution - Functional divergence - Functional evenness - Functional richness - Functional trait - Trophic groups Functional diversity can be defined as the distribution of trait values within a community. Hence, functional diversity can be an indicator of habitat filtering and a reliable environmental predictor of ecosystem functioning. However, there is a serious lack of studies that test how functional diversity indices change depending on the environmental conditions. The aim of this study is to provide such evidence by analyzing the distribution and variation of continuous body-mass values (i.e. functional diversity) and related shifts in body length and width in a nematode community. We used a large online dataset on nematode traits to analyze: (i) the distribution of body mass using three functional diversity indices, i.e. functional richness, functional divergence and functional evenness; (ii) the shifts in body-size traits (length and width); and (iii) the body-mass distributions of five trophic groups and of the entire nematode community. Managed grasslands exhibited the widest range of body-mass values while body-mass distribution in arable fields covered the greatest area in comparison to the other ecosystem types. The shift in body size revealed environmental filters that could not have been identified by the study of functional diversity indices per se. We found low values of functional evenness to be associated with high values of functional richness. We provide novel empirical evidence that body-mass distribution within a trophic group mirrors the effects of habitat filtering more than the distribution in the community as a whole. Hence, our trait-based approach, more than functional diversity itself, disclosed soil food-web structure and identified community responses. Gene-editing nog niet de kip met gouden eierenBastiaansen, John ; Bovenhuis, Henk ; Mulder, Herman - \ 2018 Inge van Drie Quantitative genetics of environmental variance and resilience: analyses in livestock and aquaculture populationsMulder, Herman - \ 2018 IOWA STATE University Quantitative genetics of environmental variance and resilience: analyses in livestock and aquaculture populationsMulder, Herman - \ 2018 IOWA STATE University Use of AMS data in dairy cattle breedingMulder, Herman - \ 2018 more info ... Modelling the Plant Microtubule CytoskeletonDeinum, Eva E. ; Mulder, Bela M. - \ 2018In: Mathematical Modelling in Plant Biology / Morris, Richard J., Springer International Publishing - ISBN 9783319990699 - p. 53 - 67. The physical shape and structure of plants are manifestations of the actions of gene products and their concerted responses to their environment. In this chapter we introduce the plant cortical microtubule array. This structure is both a nexus in the control of plant cell shape and function, and a fascinating out-of-equilibrium system for state-of-the-art physics research. We describe how analytical and computational approaches complement each other in the study of the array, and highlight some recent results and open research questions Students’ online argumentative peer feedback, essay writing, and content learning : does gender matter?Noroozi, Omid ; Hatami, Javad ; Bayat, Arash ; Ginkel, Stan van; Biemans, Harm J.A. ; Mulder, Martin - \ 2018Interactive Learning Environments (2018). - ISSN 1049-4820 - 16 p. Argumentative essay - gender - learning - online peer feedback - writing Whilst the importance of online peer feedback and writing argumentative essays for students in higher education is unquestionable, there is a need for further research into whether and the extent to which female and male students differ with regard to their argumentative feedback, essay writing, and content learning in online settings. The current study used a pre-test, post-test design to explore the extent to which female and male students differ regarding their argumentative feedback quality, essay writing and content learning in an online environment. Participants were 201 BSc biotechnology students who wrote an argumentative essay, engaged in argumentative peer feedback with learning partners in the form of triads and finally revised their original argumentative essay. The findings revealed differences between females and males in terms of the quality of their argumentative feedback. Female students provided higher-quality argumentative feedback than male students. Although all students improved their argumentative essay quality and also knowledge content from pre-test to post-test, these improvements were not significantly different between females and males. Explanations for these findings and recommendations are provided. Competence and knowledge development in competence-based vocational education in IndonesiaMisbah, Zainun ; Gulikers, Judith ; Mulder, Martin - \ 2018Learning Environments Research (2018). - ISSN 1387-1579 - 22 p. Agriculture vocational education - Competence development - Competence-based education - Indonesia - Knowledge development Theory and research in the field of competence-based vocational education (CBVE) have advanced enormously during the last decades, although empirical research on CBVE lags far behind. CBVE researchers have complained about the lack of evidence that CBVE results in better competence development, the decreasing attention for knowledge development in CBVE practice, and the cross-sectional nature of much CBVE research. This study addresses these issues by reviewing a worldwide competence-based education literature and comparing competence and knowledge development of students in vocational schools in Indonesia that have implemented principles of CBVE to a higher or lesser degree. The study involved 506 students majoring in food processing and technology and 32 teachers from 11 agricultural secondary vocational schools. Teachers and students rated student competence levels. Student knowledge was assessed with a multiple-choice test. Longitudinal data were collected during one school year at three points of time. Student competence development in high-CBVE was higher than in low-CBVE, suggesting that the implementation of CBVE was successful and had a motivating effect of both students and teachers in Indonesian vocational schools. However, knowledge development was indeed lower in high-CBVE than in low-CBVE, which needs further attention. Quantitative land evaluation implemented in Dutch water managementHack-ten Broeke, M.J.D. ; Mulder, H.M. ; Bartholomeus, R.P. ; Dam, J.C. van; Holshof, G. ; Hoving, I.E. ; Walvoort, D.J.J. ; Heinen, M. ; Kroes, J.G. ; Bakel, P.J.T. van; Supit, I. ; Wit, A.J.W. de; Ruijtenberg, R. - \ 2018Geoderma (2018). - ISSN 0016-7061 - 10 p. Agro-hydrology - Crop yield assessment - Land use - Meta-model - Simulation modelling - Soil management Both in land evaluation and in water management quantitative methods, GIS and simulation modelling are well-known techniques for quantifying the effects of changes, such as land use or climate change. For hydrological management decisions information is often required on the effect of those decisions on agricultural production. To serve the needs of different types of users, like water authorities, provinces, drinking water companies and the National Department of Infrastructure and Water Management we developed a toolbox named WaterVision Agriculture as an instrument that can determine effects on crop yield and the farm economy as a result of drought, too wet or too saline conditions for both current and future climatic conditions. WaterVision Agriculture is based on the hydrological simulation model SWAP, the crop growth model WOFOST and farm management and economic assessments such as DairyWise for dairy farming. The WaterVision Agriculture (WVA) project resulted in two products, namely i) an easily applicable tool (also called the WVA-table) and ii) the operational models for hydrology and crop growth SWAP and WOFOST for calculating effects on field scale combined with calculating farm economic results and indirect effects. SWAP simulates water transport in the unsaturated zone using meteorological data, boundary conditions (like groundwater level or drainage) and soil parameters. WOFOST simulates crop growth as a function of meteorological conditions and crop parameters. Using the combination of these process-based models and methods for describing crop management and economic value we derived a meta-model, i.e. a set of easily applicable simplified relations for assessing crop growth as a function of soil type and groundwater level. These relations are based on multiple model runs for at least 72 soil units and the possible groundwater regimes in the Netherlands. The easily applicable tool (WVA-table) uses this meta-model. Applying the meta-model of WaterVision Agriculture should allow for better decisions on land use or soil and water management because the instrument can help to quantify the effects of changes in climate, land use, hydrological conditions or combinations of these effects on agricultural production. Removal of soil biota alters soil feedback effects on plant growth and defense chemistryWang, Minggang ; Ruan, Weibin ; Kostenko, Olga ; Carvalho, Sabrina ; Hannula, S.E. ; Mulder, Patrick P.J. ; Bu, Fengjiao ; Putten, Wim H. van der; Bezemer, T.M. - \ 2018New Phytologist (2018). - ISSN 0028-646X fractionation - Jacobaea vulgaris - plant–soil feedback (PSF) - pyrrolizidine alkaloids (PAs) - soil biota - spectral reflectance We examined how the removal of soil biota affects plant–soil feedback (PSF) and defense chemistry of Jacobaea vulgaris, an outbreak plant species in Europe containing the defense compounds pyrrolizidine alkaloids (PAs). Macrofauna and mesofauna, as well as fungi and bacteria, were removed size selectively from unplanted soil or soil planted with J. vulgaris exposed or not to above- or belowground insect herbivores. Wet-sieved fractions, using 1000-, 20-, 5- and 0.2-μm mesh sizes, were added to sterilized soil and new plants were grown. Sieving treatments were verified by molecular analysis of the inocula. In the feedback phase, plant biomass was lowest in soils with 1000- and 20-μm inocula, and soils conditioned with plants gave more negative feedback than without plants. Remarkably, part of this negative PSF effect remained present in the 0.2-μm inoculum where no bacteria were present. PA concentration and composition of plants with 1000- or 20-μm inocula differed from those with 5- or 0.2-μm inocula, but only if soils had been conditioned by undamaged plants or plants damaged by aboveground herbivores. These effects correlated with leaf hyperspectral reflectance. We conclude that size-selective removal of soil biota altered PSFs, but that these PSFs were also influenced by herbivory during the conditioning phase. Waterwijzer Landbouw : instrumentarium voor kwantificeren van effecten van waterbeheer en klimaat op landbouwproductieMulder, Martin ; Hack-ten Broeke, Mirjam ; Bartholomeus, Ruud ; Dam, Jos van; Heinen, Marius ; Bakel, Jan van; Walvoort, Dennis ; Kroes, Joop ; Hoving, Idse ; Holshof, Gertjan ; Schaap, Joris ; Spruijt, Joanneke ; Supit, Iwan ; Wit, Allard de; Hendriks, Rob ; Haan, Janjo de; Voort, Marcel van der; Walsum, Paul van - \ 2018Amersfoort : Stowa (Stowa rapport 2018-48) - ISBN 9789057738128 - 71 Harnessing longitudinal information to identify genetic variation in tolerance of pigs to Porcine Reproductive and Respiratory Syndrome virus infectionLough, Graham ; Hess, Andrew ; Hess, Melanie ; Rashidi, Hamed ; Matika, Oswald ; Lunney, Joan K. ; Rowland, Raymond R.R. ; Kyriazakis, Ilias ; Mulder, Han A. ; Dekkers, Jack C.M. ; Doeschl-Wilson, Andrea - \ 2018Genetics, Selection, Evolution 50 (2018). - ISSN 0999-193X Background: High resistance (the ability of the host to reduce pathogen load) and tolerance (the ability to maintain high performance at a given pathogen load) are two desirable host traits for producing animals that are resilient to infections. For Porcine Reproductive and Respiratory Syndrome (PRRS), one of the most devastating swine diseases worldwide, studies have identified substantial genetic variation in resistance of pigs, but evidence for genetic variation in tolerance has so far been inconclusive. Resistance and tolerance are usually considered as static traits. In this study, we used longitudinal viremia measurements of PRRS virus infected pigs to define discrete stages of infection based on viremia profile characteristics. These were used to investigate host genetic effects on viral load (VL) and growth at different stages of infection, to quantify genetic variation in tolerance at these stages and throughout the entire 42-day observation period, and to assess whether the single nucleotide polymorphism (SNP) WUR10000125 (WUR) with known large effects on resistance confers significant differences in tolerance. Results: Genetic correlations between resistance and growth changed considerably over time. Individuals that expressed high genetic resistance early in infection tended to grow slower during that time-period, but were more likely to experience lower VL and recovery in growth by the later stage. The WUR genotype was most strongly associated with VL at early- to mid-stages of infection, and with growth at mid- to late-stages of infection. Both, single-stage and repeated measurements random regression models identified significant genetic variation in tolerance. The WUR SNP was significantly associated only with the overall tolerance slope fitted through all stages of infection, with the genetically more resistant AB pigs for the WUR SNP being also more tolerant to PRRS. Conclusions: The results suggest that genetic selection for improved tolerance of pigs to PRRS is possible in principle, but may be feasible only with genomic selection, requiring intense recording schemes that involve repeated measurements to reliably estimate genetic effects. In the absence of such records, consideration of the WUR genotype in current selection schemes appears to be a promising strategy to improve simultaneously resistance and tolerance of growing pigs to PRRS. A Plausible Microtubule-Based Mechanism for Cell Division Orientation in Plant EmbryogenesisChakrabortty, Bandan ; Willemsen, Viola ; Zeeuw, Thijs de; Liao, Che Yang ; Weijers, Dolf ; Mulder, Bela ; Scheres, Ben - \ 2018Current Biology 28 (2018)19. - ISSN 0960-9822 - p. 3031 - 3043.e2. arabidopsis - auxin - cell shape - computational modeling - cytokinesis - division orientation - embryogenesis - microtubules - systems biology Oriented cell divisions are significant in plant morphogenesis because plant cells are embedded in cell walls and cannot relocate. Cell divisions follow various regular orientations, but the underlying mechanisms have not been clarified. We propose that cell-shape-dependent self-organization of cortical microtubule arrays is able to provide a mechanism for determining planes of early tissue-generating divisions and may form the basis for robust control of cell division orientation in the embryo. To show this, we simulate microtubules on actual cell surface shapes, from which we derive a minimal set of three rules for proper array orientation. The first rule captures the effects of cell shape alone on microtubule organization, the second rule describes the regulation of microtubule stability at cell edges, and the third rule includes the differential effect of auxin on local microtubule stability. These rules generate early embryonic division plane orientations and potentially offer a framework for understanding patterned cell divisions in plant morphogenesis. Chakrabortty et al. show that a computational model for dynamic self-organization of cortical microtubules on experimentally extracted cell shapes provides a plausible molecular mechanism for division plane orientation in the first four divisions of early stage A. thaliana embryos, in WT as well as two developmental mutants bodenlos and clasp. Methyl Jasmonate Changes the Composition and Distribution Rather than the Concentration of Defence Compounds : a Study on Pyrrolizidine AlkaloidsWei, Xianqin ; Vrieling, Klaas ; Mulder, Patrick P.J. ; Klinkhamer, Peter G.L. - \ 2018Journal of Chemical Ecology (2018). - ISSN 0098-0331 - 10 p. Conversion - Erucifoline - Feeding damage - Herbivory - Induced defense - Jacobaea plants - Reallocation - Seneciphylline In this study we investigated the effect of methyl jasmonate (MeJA) application on pyrrolizidine alkaloid (PA) concentration and composition of two closely related Jacobaea species. In addition, we examined whether MeJA application affected herbivory of the polyphagous leaf feeding herbivore Spodoptera exigua. A range of concentrations of MeJA was added to the medium of Jacobaea vulgaris and J. aquatica tissue culture plants grown under axenic conditions. PA concentrations were measured in roots and shoots using LC-MS/MS. In neither species MeJA application did affect the total PA concentration at the whole plant level. In J. vulgaris the total PA concentration decreased in roots but increased in shoots. In J. aquatica a similar non-significant trend was observed. In both Jacobaea species MeJA application induced a strong shift from senecionine- to erucifoline-like PAs, while the jacobine- and otosenine-like PAs remained largely unaffected. The results show that MeJA application does not necessarily elicits de novo synthesis, but rather leads to PA conversion combined with reallocation of certain PAs from roots to shoots. S. exigua preferred feeding on control leaves of J. aquatica over MeJA treated leaves, while for J. vulgaris both the control and MeJA treated leaves were hardly eaten. This suggests that the MeJA-induced increase of erucifoline-like PAs can play a role in resistance of J. aquatica to S. exigua. In J. vulgaris resistance to S. exigua may already be high due to the presence of jacobine-like PAs or other resistance factors. Ondernemerschap in levensvatbare organisaties: ondernemende werknemers als sleutel tot duurzame inzetbaarheidBaggen, Y. ; Biemans, H.J.A. ; Lans, T. ; Mulder, M. - \ 2018Opleiding en Ontwikkeling (2018). - ISSN 0922-0895 more info ... EditorialMulder, Martin - \ 2018Journal of agricultural education and extension 24 (2018)5. - ISSN 1389-224X - p. 389 - 390. more info ... Determinants of successful lifestyle change during a 6-month preconception lifestyle intervention in women with obesity and infertilityKarsten, Matty D.A. ; Oers, Anne M. van; Groen, Henk ; Mutsaerts, Meike A.Q. ; Poppel, Mireille N.M. van; Geelen, Anouk ; Beek, Cornelieke van de; Painter, Rebecca C. ; Mol, Ben W.J. ; Roseboom, Tessa J. ; Hoek, Annemieke ; Burggraaff, J.M. ; Kuchenbecker, W.K.H. ; Perquin, D.A.M. ; Koks, C.A.M. ; Golde, R. van; Kaaijk, E.M. ; Schierbeek, J.M. ; Oosterhuis, G.J.E. ; Broekmans, F.J. ; Vogel, N.E.A. ; Lambalk, C.B. ; Veen, F. van der; Klijn, N.F. ; Mercelina, P.E.A.M. ; Kasteren, Y.M. van; Nap, A.W. ; Mulder, R.J.A.B. ; Gondrie, E.T.C.M. ; Bruin, J.P. de - \ 2018European Journal of Nutrition (2018). - ISSN 1436-6207 Determinants - Lifestyle intervention - Obesity - Preconception Purpose: To identify demographic, (bio)physical, behavioral, and psychological determinants of successful lifestyle change and program completion by performing a secondary analysis of the intervention arm of a randomized-controlled trial, investigating a preconception lifestyle intervention. Methods: The 6-month lifestyle intervention consisted of dietary counseling, physical activity, and behavioral modification, and was aimed at 5–10% weight loss. We operationalized successful lifestyle change as successful weight loss (≥ 5% weight/BMI ≤ 29 kg/m2), weight loss in kilograms, a reduction in energy intake, and an increase in physical activity during the intervention program. We performed logistic and mixed-effect regression analyses to identify baseline factors that were associated with successful change or program completion. Results: Women with higher external eating behavior scores had higher odds of successful weight loss (OR 1.10, 95% CI 1.05–1.16). Women with the previous dietetic support lost 0.94 kg less during the intervention period (95% CI 0.01–1.87 kg). Women with higher self-efficacy reduced energy intake more than women with lower self-efficacy (p < 0.01). Women with an older partner had an increased energy intake (6 kcal/year older, 95% CI 3–13). A high stage of change towards physical activity was associated with a higher number of daily steps (p = 0.03). A high stage of change towards weight loss was associated with completion of the intervention (p = 0.04). Conclusions: Determinants of lifestyle change and program completion were: higher external eating behavior, not having received previous dietetic support, high stage of change. This knowledge can be used to identify women likely to benefit from lifestyle interventions and develop new interventions for women requiring alternative support. Trial registration: The LIFEstyle study was registered at the Dutch trial registry (NTR 1530; http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=1530). Genomic regions underlying uniformity of yearling weight in Nellore cattle evaluated under different response variablesSouza Iung, Laiza Helena de; Mulder, Herman Arend ; Rezende Neves, Haroldo Henrique de; Carvalheiro, Roberto - \ 2018BMC Genomics 19 (2018). - ISSN 1471-2164 Beef cattle - DHGLM - Genetic heterogeneity of residual variance - Growth traits - GWAS - Micro-environmental sensitivity Background: In livestock, residual variance has been studied because of the interest to improve uniformity of production. Several studies have provided evidence that residual variance is partially under genetic control; however, few investigations have elucidated genes that control it. The aim of this study was to identify genomic regions associated with within-family residual variance of yearling weight (YW; N=423) in Nellore bulls with high density SNP data, using different response variables. For this, solutions from double hierarchical generalized linear models (DHGLM) were used to provide the response variables, as follows: a DGHLM assuming non-null genetic correlation between mean and residual variance (rmv0) to obtain deregressed EBV for mean (dEBVm) and residual variance (dEBVv); and a DHGLM assuming rmv=0 to obtain two alternative response variables for residual variance, dEBVv_r0 and log-transformed variance of estimated residuals (ln_ σ ě 2 $$(\\upsigma)_(\\widehat(\\mathrm(e)))^2$$ ). Results: The dEBVm and dEBVv were highly correlated, resulting in common regions associated with mean and residual variance of YW. However, higher effects on variance than the mean showed that these regions had effects on the variance beyond scale effects. More independent association results between mean and residual variance were obtained when null rmv was assumed. While 13 and 4 single nucleotide polymorphisms (SNPs) showed a strong association (Bayes Factor>20) with dEBVv and ln_ σ ě 2 $$(\\upsigma)_(\\widehat(\\mathrm(e)))^2$$ , respectively, only suggestive signals were found for dEBVv_r0. All overlapping 1-Mb windows among top 20 between dEBVm and dEBVv were previously associated with growth traits. The potential candidate genes for uniformity are involved in metabolism, stress, inflammatory and immune responses, mineralization, neuronal activity and bone formation. Conclusions: It is necessary to use a strategy like assuming null rmv to obtain genomic regions associated with uniformity that are not associated with the mean. Genes involved not only in metabolism, but also stress, inflammatory and immune responses, mineralization, neuronal activity and bone formation were the most promising biological candidates for uniformity of YW. Although no clear evidence of using a specific response variable was found, we recommend consider different response variables to study uniformity to increase evidence on candidate regions and biological mechanisms behind it. Transformations in the editorial team of the JAEEMulder, Martin - \ 2018Journal of agricultural education and extension 24 (2018)4. - ISSN 1389-224X - p. 301 - 305. more info ...