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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    Fluctuations in populations of subsurface methane oxidizers in coordination with changes in electron acceptor availability
    Magnabosco, C. ; Timmers, P.H.A. ; Lau, M.C.Y. ; Borgonie, G. ; Linage-Alvarez, B. ; Kuloyo, O. ; Alleva, R. ; Kieft, T.L. ; Slater, G.F. ; Heerden, E. van; Sherwood Lollar, B. ; Onstott, T.C. - \ 2018
    FEMS microbiology ecology 94 (2018)7. - ISSN 0168-6496
    Archaea - Metagenomics - Methane oxidation - Subsurface

    The concentrations of electron donors and acceptors in the terrestrial subsurface biosphere fluctuate due to migration and mixing of subsurface fluids, but the mechanisms and rates at which microbial communities respond to these changes are largely unknown. Subsurface microbial communities exhibit long cellular turnover times and are often considered relatively static-generating just enough ATP for cellular maintenance. Here, we investigated how subsurface populations of CH4 oxidizers respond to changes in electron acceptor availability by monitoring the biological and geochemical composition in a 1339 m-below-land-surface (mbls) fluid-filled fracture over the course of both longer (2.5 year) and shorter (2-week) time scales. Using a combination of metagenomic, metatranscriptomic, and metaproteomic analyses, we observe that the CH4 oxidizers within the subsurface microbial community change in coordination with electron acceptor availability over time. We then validate these findings through a series of 13C-CH4 laboratory incubation experiments, highlighting a connection between composition of subsurface CH4 oxidizing communities and electron acceptor availability.

    Mechanism and structural diversity of exoribonuclease-resistant RNA structures in flaviviral RNAs
    Macfadden, Andrea ; O’Donoghue, Zoe ; Silva, Patricia A.G.C. ; Chapman, Erich G. ; Olsthoorn, René C. ; Sterken, Mark G. ; Pijlman, Gorben P. ; Bredenbeek, Peter J. ; Kieft, Jeffrey S. - \ 2018
    Nature Communications 9 (2018)1. - ISSN 2041-1723
    Flaviviruses such as Yellow fever, Dengue, West Nile, and Zika generate disease-linked viral noncoding RNAs called subgenomic flavivirus RNAs. Subgenomic flavivirus RNAs result when the 5′–3′ progression of cellular exoribonuclease Xrn1 is blocked by RNA elements called Xrn1-resistant RNAs located within the viral genome’s 3′-untranslated region that operate without protein co-factors. Here, we show that Xrn1-resistant RNAs can halt diverse exoribonucleases, revealing a mechanism in which they act as general mechanical blocks that ‘brace’ against an enzyme’s surface, presenting an unfolding problem that confounds further enzyme progression. Further, we directly demonstrate that Xrn1-resistant RNAs exist in a diverse set of flaviviruses, including some specific to insects or with no known arthropod vector. These Xrn1-resistant RNAs comprise two secondary structural classes that mirror previously reported phylogenic analysis. Our discoveries have implications for the evolution of exoribonuclease resistance, the use of Xrn1-resistant RNAs in synthetic biology, and the development of new therapies.
    Shortening of Microtubule overlap regions defines membrane delivery sites during plant cytokinesis
    Keijzer, J. de; Kieft, H. ; Ketelaar, T. ; Goshima, G. ; Janson, M.E. - \ 2017
    Current Biology 27 (2017)4. - ISSN 0960-9822 - p. 514 - 520.
    plant cytokinesis, microtubule, moss
    Plants and animals synthesize and move large amounts of membraneous material to construct a division plane for cell division. We define short stretches of antiparallel microtubule overlap as membrane accumulation sites in moss plants. Dimensions of the dividing cell plate are set by kinesin-4-mediated shortening of these overlaps.
    Literatuurstudie naar het effect van zoutstress op plantenstoffen en de potentiële toegevoegde waarde
    Arkel, J. van; Meer, I.M. van der - \ 2015
    In: Zilt Perspectief : kennis en kansen voor teelt en verwerking van gewassen op zilte landbouwgrond rond de Wadden, afgestemd op de unieke natuurlijke en landschappelijke kwaliteiten met aandacht voor educatie en kennisverspreiding: eindverslag / Vos, A.C., Rijsselberghe, A.M.J., Kieft, H., Den Burg : Stichting Ziltperspectief - p. 64 - 70.
    Kringlooplandbouw in Noord-Nederland : van marge naar mainstream
    Holster, H.C. ; Opheusden, M. van; Gerritsen, A.L. ; Kieft, H. ; Kros, H. ; Plomp, M. ; Verhoeven, F. ; Vries, W. de; Essen, E. van; Sonneveld, M.P.W. ; Venekamp, A. - \ 2014
    Wageningen : Wageningen UR - ISBN 9789461739940 - 64
    agro-ecologie - melkveehouderij - bemesting - bodemchemie - waterkwaliteit - bodemkwaliteit - fosfaten - stikstof - emissiereductie - friese wouden - drenthe - agroecology - dairy farming - fertilizer application - soil chemistry - water quality - soil quality - phosphates - nitrogen - emission reduction - friese wouden - drenthe
    Sinds 1990 wordt er in Noord-Nederland, waaronder de Noordelijke Friese Wouden en de provincie Drenthe, door melkveehouders, wetenschappers en beleidsmakers geëxperimenteerd om de kringloop van mineralen op het bedrijf zo goed mogelijk te sluiten. Steeds meer agrarisch ondernemers worden zich bewust van het belang van het sluiten van de kringloop ingegeven door aanscherping in mestwetgeving, schaarste van grondstoffen, hogere kosten van kunstmest en belasting van de omgeving. Zij zullen naar de toekomst de nieuwe kringloopboeren kunnen worden. Efficiënt gebruik van grond- en hulpstoffen is de kerngedachte
    Characterization of polarity development through 2- and 3-D imaging during the initial phase of microspore embryogenesis in Brassica napus L.
    Dubas, E. ; Custers, J. ; Kieft, H. ; Wedzony, M. ; Lammeren, A.A.M. van - \ 2014
    Protoplasma 251 (2014)1. - ISSN 0033-183X - p. 103 - 113.
    nuclear-dna synthesis - cv topas - extracellular-matrix - sporophytic development - cultured microspores - actin-filament - heat-shock - in-vitro - induction - pollen
    Isolated microspores of B. napus in culture change their developmental pathway from gametophytic to sporophytic and form embryo-like structures (ELS) upon prolonged heat shock treatment (5 days at 32 °C). ELS express polarity during the initial days of endosporic development. In this study, we focussed on the analysis of polarity development of ELS without suspensor. Fluorescence microscopy and 3-D confocal laser scanning microscopy (CLSM) without tissue interfering enabled us to get a good insight in the distribution of nuclei, mitochondria and endoplasmic reticulum(ER), the architecture of microtubular (MT) cytoskeleton and the places of 5-bromo- 2'-deoxy-uridine (BrdU) incorporation in successive stages of microspore embryogenesis. Scanning electron microscopy (SEM) analysis revealed, for the first time, the appearance of a fibrillar extracellular matrix-like structure (ECM-like structure) in androgenic embryos without suspensor. Two types of endosporic development were distinguished based upon the initial location of the microspore nucleus. The polarity of dividing and growing cells was recognized by the differential distributions of organelles, by the organization of the MT cytoskeleton and by the visualization of DNA synthesis in the cell cycle. The directional location of nuclei, ER, mitochondria and starch grains in relation to theMTs configurations were early polarity indicators. Both exine rupture and ECMlike structure on the outer surfaces of ELS are supposed to stabilize ELS's morphological polarity. As the role of cell polarity during early endosporic microspore embryogenesis in apical–basal cell fate determination remains unclear, microspore culture system provides a powerful in vitro tool for studying the developmental processes that take place during the earliest stages of plant embryogenesis.
    Arabidopsis VILLIN2 and VILLIN3 are required for the generation of thick actin filament bundles and for directional organ growth.
    Honing, H.S. van der; Kieft, H. ; Emons, A.M.C. ; Ketelaar, T. - \ 2012
    Plant Physiology 158 (2012)3. - ISSN 0032-0889 - p. 1426 - 1438.
    pollen-tube growth - elongation-factor 1-alpha - root hair-cells - f-actin - binding-sites - plant villin - tip growth - severing protein - cytoskeleton - morphogenesis
    In plant cells, actin filament bundles serve as tracks for myosin-dependent organelle movement and play a role in the organization of the cytoplasm. Although virtually all plant cells contain actin filament bundles, the role of the different actin-bundling proteins remains largely unknown. In this study, we investigated the role of the actin-bundling protein villin in Arabidopsis (Arabidopsis thaliana). We used Arabidopsis T-DNA insertion lines to generate a double mutant in which VILLIN2 (VLN2) and VLN3 transcripts are truncated. Leaves, stems, siliques, and roots of vln2 vln3 double mutant plants are twisted, which is caused by local differences in cell length. Microscopy analysis of the actin cytoskeleton showed that in these double mutant plants, thin actin filament bundles are more abundant while thick actin filament bundles are virtually absent. In contrast to full-length VLN3, truncated VLN3 lacking the headpiece region does not rescue the phenotype of the vln2 vln3 double mutant. Our results show that villin is involved in the generation of thick actin filament bundles in several cell types and suggest that these bundles are involved in the regulation of coordinated cell expansion.
    Gametophytic development of Brassica napus pollen in vitro enables examination of cytoskeleton and nuclear movements
    Dubas, E. ; Wedzony, M. ; Custers, J.B.M. ; Kieft, H. ; Lammeren, A.A.M. van - \ 2012
    Protoplasma 249 (2012)2. - ISSN 0033-183X - p. 369 - 377.
    microspore embryogenesis - cv topas - induction - actin - cells - microtubules - differentiation - organization - arabidopsis - behavior
    Isolated microspores and pollen suspension of Brassica napus “Topas” cultured in NLN-13 medium at 18°C follow gametophytic pathway and develop into pollen grains closely resembling pollen formed in planta. This culture system complemented with whole-mount immunocytochemical technology and novel confocal laser scanning optical technique enables detailed studies of male gametophyte including asymmetric division, cytoskeleton, and nuclear movements. Microtubular cytoskeleton configurationally changed in successive stages of pollen development. The most prominent role of microtubules (MTs) was observed just before and during nuclear migration at the early and mid-bi-cellular stage. At the early bi-cellular stage, parallel arrangement of cortical and endoplasmic MTs to the long axis of the generative cell (GC) as well as MTs within GC under the plasmalemma bordering vegetative cell (VC) were responsible for GC lens shape. At the beginning of the GC migration, endoplasmic microtubules (EMTs) of the VC radiated from the nuclear envelope. Most cortical and EMTs of the VC were found near the sporoderm. At the same time, pattern of MTs observed in GC was considerably different. Multiple EMTs of the GC, previously parallel aligned, reorganized, and start to surround GC, forming a basket-like structure. These results suggest that EMTs of GC provoke changes in GC shape, its detachment from the sporoderm, and play an important role in GC migration to the vegetative nucleus (VN). During the process of migration of the GC to the VC, multiple and thick bundles of MTs, radiating from the cytoplasm near GC plasma membrane, arranged perpendicular to the narrow end of the GC and organized into a “comet-tail” form. These GC “tail” MTs became shortened and the generative nucleus (GN) took a ball shape. The dynamic changes of MTs accompanied polarized distribution pattern of mitochondria and endoplasmic reticulum. In order to confirm the role of MTs in pollen development, a “whole-mount” immunodetection technique and confocal laser-scanning microscopy was essential.
    Microtubule configurations and nuclear DNA synthesis during initiation of suspensor-bearing embryos from Brassica napus cv. Topas microspores
    Dubas, E. ; Custers, J.B.M. ; Kieft, H. ; Wedzony, M. ; Lammeren, A.A.M. van - \ 2011
    Plant Cell Reports 30 (2011)11. - ISSN 0721-7714 - p. 2105 - 2116.
    heat-shock - sporophytic development - cultured microspores - rape embryogenesis - in-vitro - induction - pollen - organization - division - visualization
    In the new Brassica napus microspore culture system, wherein embryos with suspensors are formed, ab initio mimics zygotic embryogenesis. The system provides a powerful in vitro tool for studying the diverse developmental processes that take place during early stages of plant embryogenesis. Here, we studied in this new culture system both the temporal and spatial distribution of nuclear DNA synthesis places and the organization of the microtubular (MT) cytoskeleton, which were visualized with a refined whole mount immunolocalization technology and 3D confocal laser scanning microscopy. A 'mild' heat stress induced microspores to elongate, to rearrange their MT cytoskeleton and to re-enter the cell cycle and perform a predictable sequence of divisions. These events led to the formation of a filamentous suspensor-like structure, of which the distal tip cell gave rise to the embryo proper. Cells of the developing pro-embryo characterized endoplasmic (EMTs) and cortical microtubules (CMTs) in various configurations in the successive stages of the cell cycle. However, the most prominent changes in MT configurations and nuclear DNA replication concerned the first sporophytic division occurring within microspores and the apical cell of the pro-embryo. Microspore embryogenesis was preceded by pre-prophase band formation and DNA synthesis. The apical cell of the proembryo exhibited a random organization of CMTs and, in relation to this, isotropic expansion occurred, mimicking the development of the apical cell of the zygotic situation. Moreover, the apical cell entered the S phase shortly before it divided transversally at the stage that the suspensor was 3-8 celled.
    Education for Sustainable Development: Research overview
    Wals, A.E.J. ; Kieft, G. - \ 2010
    Stockholm : Sida (Sida review / Swedisch International Development Cooperatioen Agency 2010:13) - 54
    onderwijs - ontwikkeling - duurzaamheid (sustainability) - natuur- en milieueducatie - education - development - sustainability - nature and environmental education
    This discussion paper outlines some of the main characteristics of Education for Sustainable Development (ESD), particularly in the context of ‘development’ and ‘globalization’. It addresses the various interpretations and meanings of ESD, shows how these relate to environmental education and emerging educations that overlap with SD-issues and introduces sustainability competence as a key outcome of ESD. The paper also outlines some regional trends that affect the way ESD manifests itself in the various countries and regions around the world. Some key developments affecting ESD are introduced, including globalization, the rise of the information and knowledge society, the utilization of diversity and the need for the inclusion of marginalized groups and perspectives.
    De avifauna van de Engse Wormer 2. de wintergasten
    Noordijk, J. ; Klut, A. ; Belier, J. - \ 2009
    De Kieft 33 (2009)3. - p. 20 - 21.
    Cell proliferation, cell shape, and microtubule and cellulose microfibril organization of tobacco BY-2 cells are not altered by exposure to near weightlessness in space
    Sieberer, B. ; Kieft, H. ; Franssen-Verheijen, M.A.W. ; Emons, A.M.C. ; Vos, J.W. - \ 2009
    Planta 230 (2009)6. - ISSN 0032-0935 - p. 1129 - 1140.
    random-positioning machine - cortical microtubules - self-organization - soyuz-missions - plant-cells - arabidopsis - growth - microgravity - gravity - actin
    The microtubule cytoskeleton and the cell wall both play key roles in plant cell growth and division, determining the plant’s final stature. At near weightlessness, tubulin polymerizes into microtubules in vitro, but these microtubules do not self-organize in the ordered patterns observed at 1g. Likewise, at near weightlessness cortical microtubules in protoplasts have difficulty organizing into parallel arrays, which are required for proper plant cell elongation. However, intact plants do grow in space and therefore should have a normally functioning microtubule cytoskeleton. Since the main difference between protoplasts and plant cells in a tissue is the presence of a cell wall, we studied single, but walled, tobacco BY-2 suspension-cultured cells during an 8-day space-flight experiment on board of the Soyuz capsule and the International Space Station during the 12S mission (March–April 2006). We show that the cortical microtubule density, ordering and orientation in isolated walled plant cells are unaffected by near weightlessness, as are the orientation of the cellulose microfibrils, cell proliferation, and cell shape. Likely, tissue organization is not essential for the organization of these structures in space. When combined with the fact that many recovering protoplasts have an aberrant cortical microtubule cytoskeleton, the results suggest a role for the cell wall, or its production machinery, in structuring the microtubule cytoskeleton
    De avifauna van de Engse Wormer. 1. De broedvogels
    Noordijk, J. ; Veer, R. van 't; Jonker, K. - \ 2009
    De Kieft 33 (2009)2. - p. 26 - 27.
    Rapportage onderzoek aantasting van de bast bij laanbomen
    Lammeren, A.A.M. van; Ruiter, N.C.A. ; Kieft, H. - \ 2009
    Wageningen : Wageningen UR, Leerstoelgroep Plantencelbiologie
    straatbomen - afwijkingen, planten - deformiteiten - knobbelvorming - schors - korstmossen - schimmels - landbouwkundig onderzoek - boomverzorging - openbaar groen - street trees - plant disorders - deformities - nodulation - cortex - lichens - fungi - agricultural research - tree care - public green areas
    In dit verslag zijn aantastingen op de stam onderzocht van Carpinus betulus ‘Frans Fontaine’, Fagus sylvatica “ Atropurpurea”, Fraxinus excelsior ‘Atlas’, Quercus palustris, Quercus robur, Sorbus latifolia “Henk Vink” en Ulmus ‘Clusius’ Daarbij is aandacht besteed aan het voorkomen en de aard en ontwikkeling van bastknobbels, baststrepen, bastscheuren, verkleuringen en het effect van epifyten zoals schimmels en korstmossen
    Energetische landbouw: veelbelovend?
    Kieft, H. ; Livestock Research, - \ 2009
    Wageningen : Wageningen UR
    melkveehouderij - agrarische bedrijfsvoering - energetische waarde - netwerken - dairy farming - farm management - energy value - networks
    Een aantal melkveehouders met een energetisch gebalanceerde bedrijfsvoering heeft de handen ineengeslagen en voert samen met Wageningen UR een verkenning uit. Deze verkenning vindt plaats in het netwerk ‘Energetische Kwaliteit Melk’ en richt zich op de vraag of ‘energetisch hoogwaardig voedsel’ een meerwaarde heeft
    Rapportage onderzoek aan bastknobbels en aantasting van bast door korstmossen aantasting van bast door korstmossen
    Lammeren, A.A.M. van; Kieft, H. ; Donkers, J. - \ 2008
    Wageningen : Wageningen Universiteit en Research Centrum
    bomen - fraxinus - afwijkingen - deformiteiten - korstmossen - knobbelvorming - schors, bomen - cedrus - straatbomen - landbouwkundig onderzoek - boomkwekerijen - gemeenten - openbaar groen - trees - fraxinus - abnormalities - deformities - lichens - nodulation - bark - cedrus - street trees - agricultural research - forest nurseries - municipalities - public green areas
    In het hier beschreven onderzoek is nagegaan wat de aard en oorzaak is van het pokdalig uiterlijk van de stam van de es, wat het effect is van korstmosbegroeiing op de essenbast en hoe de reeds eerder beschreven bastknobbels ontstaan. Het is een voortgangsrapportage van een grotere studie naar oorzaak en gevolg van boomaantastingen. Hier worden verschijnselen beschreven maar er is vooralsnog geen uitspraak over hoe de aantastingen zoals bastknobbels zijn veroorzaakt
    Novelties in "energetic agriculture": A strategic niche experiment in dairy farming
    Kieft, H. ; Spoelstra, S.F. ; Roep, D. - \ 2008
    In: Transitions towards sustainable agriculture, food chains and peri-urban areas. - - p. 47 - 48.
    Ecotechnology, refers to existing farm practices lacking scientific underpinning as to their efficacy ( e.g. installing water-vitalizers, techniques to assess vitality). Farmers view these as part of a new integral approach to farm management ( ¿energy balancing¿). With a network of farmers practicing ¿energy balancing¿ a learning process was set up according to the ideas of smart experimentation in strategic niche management. Farmers in this network expressed as their main wish ¿scientific proof of their methods¿ and a financial bonus for their way of farming. From the point of view of systems innovation the case is of interest because: a. The ambitions expressed by the farmers involves a series of innovations with increasing structural systemic resistance: - Break away from the present regime by searching for less intensive forms of farming. - Searching for recognition for the methods and approaches of energetic balancing. - Search for scientific evidence for energetic balancing by today still speculative theories on electromagnetic fields b. The network combines in itself several sources of knowledge. Striking is the presupposition that traditional scientific evidence is more needed for success than new alliances in market or with other groups in the alternative domain.
    Polymer Microcapsules with a Fiber-Reinforced Nanocomposite Shell
    Sagis, L.M.C. ; Ruiter, R. de; Rossier Miranda, F.J. ; Ruiter, J. de; Schroën, C.G.P.H. ; Aelst, A.C. van; Kieft, H. ; Boom, R.M. ; Linden, E. van der - \ 2008
    Langmuir 24 (2008)5. - ISSN 0743-7463 - p. 1608 - 1612.
    human serum-albumin - amyloid fibrils - vesicles - nanocapsules - stability - ph - permeability - fabrication - emulsions - capsules
    Polymer microcapsules can be used as controlled release systems in drugs or in foods. Using layer-by-layer adsorption of common food proteins and polysaccharides, we produced a new type of microcapsule with tunable strength and permeability. The shell consists of alternating layers of pectin and whey protein fibrils, yielding a fiber-reinforced nanocomposite shell. The strength can be tightly controlled by varying the number of layers or the density and length of the fibrils in the protein layers. The mechanical stability of these microcapsules appears to be superior to that of currently available multilayer capsules. The method involves only standard unit operations and has the potential for scaling up to industrial production volumes.
    Netwerk: Energetische Landbouw : Een brug van energetische naar gangbare landbouw
    Kieft, H. ; Vogelzang, T.A. - \ 2007
    alternatieve landbouw - veehouders - samenwerking - communicatie - netwerken - elektromagnetisme - alternative farming - stockmen - cooperation - communication - networks - electromagnetism
    De voortgang van het Netwerk Energetische Landbouw (NEL) wordt beschreven. NEL had het in 2006 niet makkelijk in de publiciteit; ‘Voor kabouters: bel Wageningen’. Er moet daarom gewerkt worden aan een goed en consistent verhaal over de werking van de energetische landbouw, om tevens ook de brug te kunnen slaan naar sceptici en/of de gangbare landbouw. Zie daar het doel voor 2007 van de betrokken veehouders, die vooral idealisten zijn, die wat willen vertellen aan de volgende generaties boeren
    Broedvogels in de Kalverpolder van 2002 tot en met 2005
    Noordijk, J. - \ 2006
    De Kieft 30 (2006)1. - p. 16 - 18.
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