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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Rassenbericht Grasland 2019
Schoot, Jan Rinze van der; Schilder, Henk - \ 2019
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1209) - 9
Rapportage van proefveldresultaten van het rassenonderzoek aan Engels raaigras in de periode 2011-2018.
Real-Time Assembly of Viruslike Nucleocapsids Elucidated at the Single-Particle Level
Marchetti, Margherita ; Kamsma, Douwe ; Cazares Vargas, Ernesto ; Hernandez García, Armando ; Schoot, Paul van der; Vries, Renko de; Wuite, Gijs J.L. ; Roos, Wouter H. - \ 2019
Nano Letters 19 (2019)8. - ISSN 1530-6984 - p. 5746 - 5753.
acoustic force spectroscopy - artificial virus - biophysics - optical tweezers - physical virology - Self-assembly

While the structure of a multitude of viral particles has been resolved to atomistic detail, their assembly pathways remain largely elusive. Key unresolved issues are particle nucleation, particle growth, and the mode of genome compaction. These issues are difficult to address in bulk approaches and are effectively only accessible by the real-time tracking of assembly dynamics of individual particles. This we do here by studying the assembly into rod-shaped viruslike particles (VLPs) of artificial capsid polypeptides. Using fluorescence optical tweezers, we establish that small oligomers perform one-dimensional diffusion along the DNA. Larger oligomers are immobile and nucleate VLP growth. A multiplexed acoustic force spectroscopy approach reveals that DNA is compacted in regular steps, suggesting packaging via helical wrapping into a nucleocapsid. By reporting how real-time assembly tracking elucidates viral nucleation and growth principles, our work opens the door to a fundamental understanding of the complex assembly pathways of both VLPs and naturally evolved viruses.

Combining agro-ecological functions in grass-clover mixtures
Haas, Brechtje R. de; Hoekstra, Nyncke J. ; Schoot, Jan R. van der; Visser, Eric J.W. ; Kroon, Hans de; Eekeren, Nick van - \ 2019
AIMS Agriculture and Food 4 (2019)3. - ISSN 2471-2086 - p. 547 - 567.
Agrobiodiversity - Lolium multiflorum - Lolium perenne - Regenerative agriculture - Trifolium pratense - Trifolium repens

Grass-clover mixtures show many benefits for sustainable agriculture. In the Netherlands, organic farmers often work together in a so-called partner farm concept, with the aim to close nutrient cycles on a regional level. In this system, arable farms grow one-year grass-clover leys, as fodder for a livestock farm, in exchange for, e.g., manure. This practice could also be used in the transition of conventional farms towards a more circular regenerative and nature inclusive agriculture. In the current experiment we assessed the effect of a range of grass (Lolium perenne: Lp, Lolium multiflorum: Lm) and clover (Trifolium pratense: Tp and Trifolium repens: Tr) monocultures and mixtures on both below- and aboveground parameters in light of benefits for livestock and arable farms, and biodiversity. The grass monocultures showed good weed suppression, high root density, and especially Lp had a positive effect on soil structure. Clover, on the other hand, showed high herbage dry matter yield (particularly Tp) and Nitrogen (N) yield, and Tr showed high digestibility. Moreover, clover had a positive effect on the soil mineral N, and earthworm abundance tended to be higher in the clover monocultures. When (some of) the four species were combined in grass-clover mixtures, they combined the positive effects of the species and often even outperformed the (best) monocultures. We concluded that grass-clover mixtures increased agro-ecological functions.

Een persistente grasklaver voor de beste bodemkwaliteit
Schoot, Jan Rinze van der - \ 2019
Rassenbericht Grasland 2018
Schoot, Jan Rinze van der; Schilder, Henk - \ 2018
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1136) - 9
'Kwaliteit beoordelen niet simpel'
Schoot, Jan Rinze van der - \ 2018
Kwaliteit gras straks eigenschap op Rassenlijst
Schoot, Jan Rinze van der - \ 2018
Welk grasklavermengsel is het beste?
Schoot, J.R. van der - \ 2018
Ekoland 38 (2018)9. - ISSN 0926-9142 - p. 22 - 23.
Graskwaliteit in de toekomst op de grasrassenlijst
Schoot, Jan Rinze van der - \ 2018
Komt het nog wel goed met dat gele gras? Zo worden onze gazonnen, velden en weilanden weer groen
Schoot, Jan Rinze van der - \ 2018
Opmars van nieuwe grassoort festulolium
Schoot, Jan Rinze van der - \ 2018
WP3 Bodem, teelt en plant-bodem-management interacties: grasland
Schoot, Jan Rinze van der - \ 2017
Rassenbericht Grasland 2017
Schoot, Jan Rinze van der; Schilder, Henk - \ 2017
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1060) - 9
Nieuwsbrief Ruwvoer & Bodem : Hogere draagkracht bodem door dichtere zode bij kurzrasen
Philipsen, A.P. ; Schoot, J.R. van der; Huiting, H.F. ; Schooten, H.A. van; Schils, R.L.M. ; Riemens, M.M. ; Schoutsen, M.A. ; Hoekstra, N.J. ; Eekeren, N.J.M. van - \ 2017
Wageningen University & Research - 5 p.
Illuminating the Reaction Pathways of Viromimetic Assembly
Cingil, Hande E. ; Boz, Emre B. ; Biondaro, Giovanni ; Vries, Renko De; Cohen Stuart, Martien A. ; Kraft, Daniela J. ; Schoot, Paul Van der; Sprakel, Joris - \ 2017
Journal of the American Chemical Society 139 (2017)13. - ISSN 0002-7863 - p. 4962 - 4968.
The coassembly of well-defined biological nanostructures relies on a delicate balance between attractive and repulsive interactions between biomolecular building blocks. Viral capsids are a prototypical example, where coat proteins exhibit not only self-interactions but also interact with the cargo they encapsulate. In nature, the balance between antagonistic and synergistic interactions has evolved to avoid kinetic trapping and polymorphism. To date, it has remained a major challenge to experimentally disentangle the complex kinetic reaction pathways that underlie successful coassembly of biomolecular building blocks in a noninvasive approach with high temporal resolution. Here we show how macromolecular force sensors, acting as a genome proxy, allow us to probe the pathways through which a viromimetic protein forms capsids. We uncover the complex multistage process of capsid assembly, which involves recruitment and complexation, followed by allosteric growth of the proteinaceous coat. Under certain conditions, the single-genome particles condense into capsids containing multiple copies of the template. Finally, we derive a theoretical model that quantitatively describes the kinetics of recruitment and growth. These results shed new light on the origins of the pathway complexity in biomolecular coassembly.
Global methane emission estimates for 2000-2012 from CarbonTracker Europe-CH4 v1.0
Tsuruta, Aki ; Aalto, Tuula ; Backman, Leif ; Hakkarainen, Janne ; Laan-Luijkx, Ingrid T. Van Der; Krol, Maarten C. ; Spahni, Renato ; Houweling, Sander ; Laine, Marko ; Dlugokencky, Ed ; Gomez-Pelaez, Angel J. ; Schoot, Marcel Van Der; Langenfelds, Ray ; Ellul, Raymond ; Arduini, Jgor ; Apadula, Francesco ; Gerbig, Christoph ; Feist, D.G. ; Kivi, Rigel ; Yoshida, Yukio ; Peters, Wouter - \ 2017
Geoscientific Model Development 10 (2017)3. - ISSN 1991-959X - p. 1261 - 1289.

We present a global distribution of surface methane (CH4) emission estimates for 2000-2012 derived using the CarbonTracker Europe-CH4 (CTE-CH4) data assimilation system. In CTE-CH4, anthropogenic and biospheric CH4 emissions are simultaneously estimated based on constraints of global atmospheric in situ CH4 observations. The system was configured to either estimate only anthropogenic or biospheric sources per region, or to estimate both categories simultaneously. The latter increased the number of optimizable parameters from 62 to 78. In addition, the differences between two numerical schemes available to perform turbulent vertical mixing in the atmospheric transport model TM5 were examined. Together, the system configurations encompass important axes of uncertainty in inversions and allow us to examine the robustness of the flux estimates. The posterior emission estimates are further evaluated by comparing simulated atmospheric CH4 to surface in situ observations, vertical profiles of CH4 made by aircraft, remotely sensed dry-air total column-averaged mole fraction (XCH4) from the Total Carbon Column Observing Network (TCCON), and XCH4 from the Greenhouse gases Observing Satellite (GOSAT). The evaluation with non-assimilated observations shows that posterior XCH4 is better matched with the retrievals when the vertical mixing scheme with faster interhemispheric exchange is used. Estimated posterior mean total global emissions during 2000-2012 are 516 ± 51 Tg CH4 yr-1, with an increase of 18 Tg CH4 yr-1 from 2000-2006 to 2007-2012. The increase is mainly driven by an increase in emissions from South American temperate, Asian temperate and Asian tropical TransCom regions. In addition, the increase is hardly sensitive to different model configurations ( < 2 Tg CH4 yr-1 difference), and much smaller than suggested by EDGAR v4.2 FT2010 inventory (33 Tg CH4 yr-1), which was used for prior anthropogenic emission estimates. The result is in good agreement with other published estimates from inverse modelling studies (16-20 Tg CH4 yr-1). However, this study could not conclusively separate a small trend in biospheric emissions (-5 to +6.9 Tg CH4 yr-1) from the much larger trend in anthropogenic emissions (15-27 Tg CH4 yr-1). Finally, we find that the global and North American CH4 balance could be closed over this time period without the previously suggested need to strongly increase anthropogenic CH4 emissions in the United States. With further developments, especially on the treatment of the atmospheric CH4 sink, we expect the data assimilation system presented here will be able to contribute to the ongoing interpretation of changes in this important greenhouse gas budget.

Genetic diversity of salt tolerance in Miscanthus
Chen, Charlie ; Schoot, Hanneke van der; Dehghan, Shiva ; Alvim Kamei, Claire L. ; Schwarz, Kai Uwe ; Meyer, Heike ; Visser, Richard G.F. ; Linden, Gerard van der - \ 2017
Frontiers in Plant Science 8 (2017). - ISSN 1664-462X
Ion homeostasis - Ionic stress - Miscanthus - Osmotic stress - Salt tolerance
Miscanthus is a woody rhizomatous C4 grass that can be used as a CO2 neutral biofuel resource. It has potential to grow in marginal areas such as saline soils, avoiding competition for arable lands with food crops. This study explored genetic diversity for salt tolerance in Miscanthus and discovered mechanisms and traits that can be used to improve the yield under salt stress. Seventy genotypes of Miscanthus (including 57 M. sinensis, 5 M. sacchariflorus, and 8 hybrids) were evaluated for salt tolerance under saline (150 mM NaCl) and normal growing conditions using a hydroponic system. Analyses of shoot growth traits and ion concentrations revealed the existence of large variation for salt tolerance in the genotypes. We identified genotypes with potential for high biomass production both under control and saline conditions that may be utilized for growth under marginal, saline conditions. Several relatively salt tolerant genotypes had clearly lower Na+ concentrations and showed relatively high K+/Na+ ratios in the shoots under salt stress, indicating that a Na+ exclusion mechanismwas utilized to prevent Na+ accumulation in the leaves. Other genotypes showed limited reduction in leaf expansion and growth rate under saline conditions, which may be indicative of osmotic stress tolerance. The genotypes demonstrating potentially different salt tolerance mechanisms can serve as starting material for breeding programs aimed at improving salinity tolerance of Miscanthus.
Ethylene and abscisic acid signaling pathways differentially influence tomato resistance to combined powdery mildew and salt stress
Kissoudis, Christos ; Seifi, Alireza ; Yan, Zhe ; Islam, Tanjimul ; Schoot, Hanneke van der; Wiel, Clemens C.M. van de; Visser, Richard G.F. ; Linden, C.G. van der; Bai, Yuling - \ 2017
Frontiers in Plant Science 7 (2017). - ISSN 1664-462X
Abscisic acid - Callose - Cell death - Chitinase - ROS burst - Senescence

There is currently limited knowledge on the role of hormones in plants responses to combinations of abiotic and pathogen stress factors. This study focused on the response of tomato near-isogenic lines (NILs) that carry the Ol-1, ol-2, and Ol-4 loci, conferring resistance to tomato powdery mildew (PM) caused by Oidium neolycopersici, to combined PM and salt stress. These NILs were crossed with the notabilis (ABAdeficient), defenceless1 (JA-deficient), and epinastic (ET overproducer) tomato mutants to investigate possible roles of hormone signaling in response to combined stresses. In the NILs, marker genes for hormonal pathways showed differential expression patterns upon PM infection. The epinastic mutation resulted in breakdown of resistance in NILOl- 1 and NIL-ol-2. This was accompanied by reduced callose deposition, and was more pronounced under combined salt stress. The notabilis mutation resulted in H2O2 overproduction and reduced susceptibility to PM in NIL-Ol-1 under combined stress, but lead to higher plant growth reduction under salinity and combined stress. Resistance in NIL-ol-2 was compromised by the notabilis mutation, which was potentially caused by reduction of callose deposition. Under combined stress the compromised resistance in NIL-ol-2 was restored. PM resistance in NIL-Ol-4 remained robust across all mutant and treatment combinations. Hormone signaling is critical to the response to combined stress and PM, in terms of resistance and plant fitness. ABA appears to be at the crossroads of disease susceptibility/senescence and plant performance under combined stress These gained insights can aid in narrowing down targets for improving crop performance under stress combinations.

Rassenbericht Grasland 2016
Schoot, Jan Rinze van der; Schilder, Henk - \ 2016
Wageningen : Wageningen Livestock Research (Livestock Research rapport 991) - 9
Wandelende maaiers en bemesters in Purmerend : 180 lammeren moeten veldkwaliteit Purmersteijn verbeteren
Schoot, Jan Rinze van der - \ 2016
sports grounds - grazing - lambs - sheep - sward renovation

Al enige tijd liep fieldmanager Jan Butter ermee rond, het idee om de velden te laten begrazen door lammeren. Dit jaar werd die wens werkelijkheid. Op 3 juli werden onder toeziend oog van diverse belangstellenden 180 lammeren losgelaten op complex Purmersteijn. Daar begrazen en bepoepen de beestjes, afkomstig van een plaatselijke boer, zo’n drie weken lang de natuurgrasvelden, in de hoop dat zij de veldkwaliteit helpen verbeteren nog voordat het voetbalseizoen begint

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