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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    Striga hermonthica MAX2 restores branching but not the Very Low Fluence Response in the Arabidopsis thaliana max2 mutant
    Liu, Q. ; Zhang, Y. ; Matusovaa, R. ; Charnikhova, T. ; Amini, M. ; Jamil, M. ; Fernandez-Aparicio, M. ; Huang, K. ; Timko, M.P. ; Westwood, J.H. ; Ruyter-Spira, C.P. ; Krol, A.R. van der; Bouwmeester, H.J. - \ 2014
    New Phytologist 202 (2014)2. - ISSN 0028-646X - p. 531 - 541.
    arabidopsis seed-germination - box protein max2 - plant hormone - strigolactone - inhibition - photomorphogenesis - stimulants - karrikins - molecule - pathway
    Seed germination of Striga spp. (witchweeds), one of the world’s most destructive parasitic weeds, cannot be induced by light but is specifically induced by strigolactones. It is not known whether Striga uses the same components for strigolactone signaling as host plants, whether it has endogenous strigolactone biosynthesis and whether there is post-germination strigolactone signaling in Striga. Strigolactones could not be detected in in vitro grown Striga, while for host-grown Striga, the strigolactone profile is dominated by a subset of the strigolactones present in the host. Branching of in vitro grown Striga is affected by strigolactone biosynthesis inhibitors. ShMAX2, the Striga ortholog of Arabidopsis MORE AXILLARY BRANCHING 2 (AtMAX2) – which mediates strigolactone signaling – complements several of the Arabidopsis max2-1 phenotypes, including the root and shoot phenotype, the High Irradiance Response and the response to strigolactones. Seed germination of max2-1 complemented with ShMAX2 showed no complementation of the Very Low Fluence Response phenotype of max2-1. Results provide indirect evidence for ShMAX2 functions in Striga. A putative role of ShMAX2 in strigolactone-dependent seed germination of Striga is discussed.
    Immune escape mutants of highly pathogenic avian influenza H5N1 selected using polyclonal sera: Identification of key amino acids in the HA protein
    Sitaras, I. ; Kalthof, D. ; Beer, M. ; Peeters, B.P.H. ; Jong, M.C.M. de - \ 2014
    PLoS ONE 9 (2014)2. - ISSN 1932-6203 - 13 p.
    virus hemagglutinin - antigenic drift - a viruses - monoclonal-antibodies - evolution - poultry - egypt - vaccination - molecule - neutralization
    Evolution of Avian Influenza (AI) viruses – especially of the Highly Pathogenic Avian Influenza (HPAI) H5N1 subtype – is a major issue for the poultry industry. HPAI H5N1 epidemics are associated with huge economic losses and are sometimes connected to human morbidity and mortality. Vaccination (either as a preventive measure or as a means to control outbreaks) is an approach that splits the scientific community, due to the risk of it being a potential driving force in HPAI evolution through the selection of mutants able to escape vaccination-induced immunity. It is therefore essential to study how mutations are selected due to immune pressure. To this effect, we performed an in vitro selection of mutants from HPAI A/turkey/Turkey/1/05 (H5N1), using immune pressure from homologous polyclonal sera. After 42 rounds of selection, we identified 5 amino acid substitutions in the Haemagglutinin (HA) protein, most of which were located in areas of antigenic importance and suspected to be prone to selection pressure. We report that most of the mutations took place early in the selection process. Finally, our antigenic cartography studies showed that the antigenic distance between the selected isolates and their parent strain increased with passage number.
    Silver nanoparticle aggregates as highly efficient plasmonic antennas for fluorescence enhancement
    Gill, R. ; Tian, L. ; Somerville, W.R.C. ; Ru, E.C. Le; Amerongen, H. van; Subramaniam, V. - \ 2012
    The Journal of Physical Chemistry Part C: Nanomaterials and Interfaces 116 (2012)31. - ISSN 1932-7447 - p. 16687 - 16693.
    raman-scattering sers - field enhancement - optical antennas - hot-spots - surface - spectroscopy - molecule - nanoantennas - nanoshells - decay
    The enhanced local fields around plasmonic structures can lead to enhancement of the excitation and modification of the emission quantum yield of fluorophores. So far, high enhancement of fluorescence intensity from dye molecules was demonstrated using bow-tie gap antenna made by e-beam lithography. However, the high manufacturing cost and the fact that currently there are no effective ways to place fluorophores only at the gap prevent the use of these structures for enhancing fluorescence-based biochemical assays. We report on the simultaneous modification of fluorescence intensity and lifetime of dye-labeled DNA in the presence of aggregated silver nanoparticles. The nanoparticle aggregates act as efficient plasmonic antennas, leading to more than 2 orders of magnitude enhancement of the average fluorescence. This is comparable to the best-reported fluorescence enhancement for a single molecule but here applies to the average signal detected from all fluorophores in the system. This highlights the remarkable efficiency of this system for surface-enhanced fluorescence. Moreover, we show that the fluorescence intensity enhancement varies with the plasmon resonance position and measure a significant reduction (300×) of the fluorescence lifetime. Both observations are shown to be in agreement with the electromagnetic model of surface-enhanced fluorescence.
    Mical links semaphorins to F-actin disassembly
    Hung, R.J. ; Yazdani, U. ; Yoon, J. ; Wu, H. ; Yang, T. ; Gupta, N. ; Huang, Z. ; Berkel, W.J.H. van; Terman, J.R. - \ 2010
    Nature 463 (2010). - ISSN 0028-0836 - p. 823 - 827.
    growth cones - drosophila - collapse - molecule - protein - 3a - microtubules - organization - cytoskeleton - morphology
    How instructive cues present on the cell surface have their precise effects on the actin cytoskeleton is poorly understood. Semaphorins are one of the largest families of these instructive cues and are widely studied for their effects on cell movement, navigation, angiogenesis, immunology and cancer(1). Semaphorins/collapsins were characterized in part on the basis of their ability to drastically alter actin cytoskeletal dynamics in neuronal processes(2), but despite considerable progress in the identification of semaphorin receptors and their signalling pathways(3), the molecules linking them to the precise control of cytoskeletal elements remain unknown. Recently, highly unusual proteins of the Mical family of enzymes have been found to associate with the cytoplasmic portion of plexins, which are large cell-surface semaphorin receptors, and to mediate axon guidance, synaptogenesis, dendritic pruning and other cell morphological changes(4-7). Mical enzymes perform reduction-oxidation (redox) enzymatic reactions(4,5,8-10) and also contain domains found in proteins that regulate cell morphology(4,11). However, nothing is known of the role of Mical or its redox activity in mediating morphological changes. Here we report that Mical directly links semaphorins and their plexin receptors to the precise control of actin filament (F-actin) dynamics. We found that Mical is both necessary and sufficient for semaphorin-plexin-mediated F-actin reorganization in vivo. Likewise, we purified Mical protein and found that it directly binds F-actin and disassembles both individual and bundled actin filaments. We also found that Mical utilizes its redox activity to alter F-actin dynamics in vivo and in vitro, indicating a previously unknown role for specific redox signalling events in actin cytoskeletal regulation. Mical therefore is a novel F-actin-disassembly factor that provides a molecular conduit through which actin reorganization-a hallmark of cell morphological changes including axon navigation-can be precisely achieved spatiotemporally in response to semaphorins.
    A virus-based single-enzyme nanoreactor
    Comellas-Aragones, M. ; Engelkamp, H. ; Claessen, V.I. ; Sommerdijk, N.A.J.M. ; Rowan, A.E. ; Christianen, P.C.M. ; Maan, J.C. ; Verduin, B.J.M. ; Cornelissen, J.J.L.M. ; Nolte, R.J.M. - \ 2007
    Nature Nanotechnology 2 (2007)10. - ISSN 1748-3387 - p. 635 - 639.
    fluorescence correlation spectroscopy - tobacco-mosaic-virus - protein - molecule - cage - encapsulation - organization
    Most enzyme studies are carried out in bulk aqueous solution, at the so-called ensemble level, but more recently studies have appeared in which enzyme activity is measured at the level of a single molecule, revealing previously unseen properties1, 2, 3, 4. To this end, enzymes have been chemically or physically anchored to a surface, which is often disadvantageous because it may lead to denaturation. In a natural environment, enzymes are present in a confined reaction space, which inspired us to develop a generic method to carry out single-enzyme experiments in the restricted spatial environment of a virus capsid. We report here the incorporation of individual horseradish peroxidase enzymes in the inner cavity of a virus, and describe single-molecule studies on their enzymatic behaviour. These show that the virus capsid is permeable for substrate and product and that this permeability can be altered by changing pH.
    Depletion-induced instability in protein-DNA mixtures: Influence of protein charge and size
    Vries, R.J. de - \ 2006
    Journal of Chemical Physics 125 (2006). - ISSN 0021-9606 - p. 014905 - 1-014905-8.
    coil-globule transition - poly(ethylene glycol) - psi-condensation - polymer - particles - molecule - collapse - driven - chain
    While there is abundant experimental and theoretical work on polymer-induced DNA condensation, it is still unclear whether globular proteins can condense linear DNA or not. We develop a simple analytical approximation for the depletion attraction between rodlike segments of semiflexible polyelectrolytes such as DNA, induced by nonbinding globular proteins. Monte Carlo simulations show that the approximation works well up to protein volume fractions of at least 20%. From the expression for the depletion attraction we estimate instability thresholds by computing the effective virial coefficient of DNA segments in protein solutions. While globular proteins are found to be much poorer depletion agents than flexible polymers, it should be possible to condense linear DNA with small highly charged globular proteins, at relatively low ionic strengths
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