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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Volksdijk; de adaptieve dijk, studielocatie Grebbedijk : De adaptieve dijk; strategieën voor dijktransitie in de komende 100 jaar
Blokland, J. ; Ziegler, P. ; Aben, R. ; Vries, R. de; Broekhuizen, R.E. van; Agricola, H. ; Kuiper, E. - \ 2016
In: Volksdijk; de adaptieve dijk, studielocatie Grebbedijk BNA Onderzoek Amsterdam - p. 32 - 41.
dijken - veiligheid - hoogwaterbeheersing - waterbouwkunde - innovaties - ruimtelijke ordening - gebiedsontwikkeling - dykes - safety - flood control - hydraulic engineering - innovations - physical planning - area development
Hoe kan de dijk weer volwaardig onderdeel worden van de maatschappij, zonder daarbij de veiligheid aan te tasten? Kunnen we onze democratie –die een oorsprong heeft in de waterschappen- herijken en waarde geven? Hoe maken van de dijk als technisch kunstwerk ook een democratisch kunstwerk dat past bij 21ste eeuw? Hoe transformeren we de verkrampte en functioneel eenzijdige dijk in een adaptieve en veelzijdige dijk?
CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3
Westra, E.R. ; Erp, P.B.G. ; Künne, T. ; Wong, S.P. ; Staals, R.H.J. ; Seegers, C.L.C. ; Bollen, S. ; Jore, M.M. ; Semenova, E. ; Severinov, K. ; Vos, W.M. de; Dame, R.T. ; Vries, R. de; Brouns, S.J.J. ; Oost, J. van der - \ 2012
Molecular Cell 46 (2012)5. - ISSN 1097-2765 - p. 595 - 605.
rna-polymerase - complex - prokaryotes - mechanism - protein - bacteriophage - resistance - sequence - defense - system
The prokaryotic CRISPR/Cas immune system is based on genomic loci that contain incorporated sequence tags from viruses and plasmids. Using small guide RNA molecules, these sequences act as a memory to reject returning invaders. Both the Cascade ribonucleoprotein complex and the Cas3 nuclease/helicase are required for CRISPR interference in Escherichia coli, but it is unknown how natural target DNA molecules are recognized and neutralized by their combined action. Here we show that Cascade efficiently locates target sequences in negatively supercoiled DNA, but only if these are flanked by a protospacer-adjacent motif (PAM). PAM recognition by Cascade exclusively involves the crRNA-complementary DNA strand. After Cascade-mediated R loop formation, the Cse1 subunit recruits Cas3, which catalyzes nicking of target DNA through its HD-nuclease domain. The target is then progressively unwound and cleaved by the joint ATP-dependent helicase activity and Mg(2+)-dependent HD-nuclease activity of Cas3, leading to complete target DNA degradation and invader neutralization
Coronary microvascular dysfunction in a porcine model of early atherosclerosis and diabetes
Heuvel, M. van den; Sorop, O. ; Koopmans, S.J. ; Dekker, R.A. ; Vries, R. de; Beusekom, H.M.M. ; Eringa, E.C. ; Duncker, D.J. ; Danser, A.H.J. ; Giessen, W.J. - \ 2012
American Journal of Physiology : Heart and Circulatory Physiology 302 (2012)1. - ISSN 0363-6135 - p. H85 - H95.
prediabetic metabolic syndrome - arterial resistance vessels - endothelial dysfunction - insulin-resistance - contractile responses - glucose-tolerance - s-nitrosothiols - risk-factors - blood-flow - mellitus
Detailed evaluation of coronary function early in diabetes mellitus (DM)-associated coronary artery disease (CAD) development is difficult in patients. Therefore, we investigated coronary conduit and small artery function in a preatherosclerotic DM porcine model with type 2 characteristics. Streptozotocin-induced DM pigs on a saturated fat/cholesterol (SFC) diet (SFC + DM) were compared with control pigs on SFC and standard (control) diets. SFC + DM pigs showed DM-associated metabolic alterations and early atherosclerosis development in the aorta. Endothelium-dependent vasodilation to bradykinin (BK), with or without blockade of nitric oxide (NO) synthase, endothelium-independent vasodilation to an exogenous NO-donor (S-nitroso-N-acetylpenicillamine), and vasoconstriction to endothelin (ET)-1 with blockade of receptor subtypes, were assessed in vitro. Small coronary arteries, but not conduit vessels, showed functional alterations including impaired BK-induced vasodilatation due to loss of NO (P <0.01 vs. SFC and control) and reduced vasoconstriction to ET-1 (P <0.01 vs. SFC and control), due to a decreased ETA receptor dominance. Other vasomotor responses were unaltered. In conclusion, this model demonstrates specific coronary microvascular alterations with regard to NO and ET-1 systems in the process of early atherosclerosis in DM. In particular, the altered ET-1 system correlated with hyperglycemia in atherogenic conditions, emphasizing the importance of this system in DM-associated CAD development.
Influence of mobile DNA-protein-DNA bridges on DNA configurations: Coarse-grained Monte-Carlo simulations
Vries, R. de - \ 2011
Journal of Chemical Physics 135 (2011). - ISSN 0021-9606 - 10 p.
h-ns - statistical-mechanics - wormlike chains - organization - binding - flexibility - bacteria
A large literature exists on modeling the influence of sequence-specific DNA-binding proteins on the shape of the DNA double helix in terms of one or a few fixed constraints. This approach is inadequate for the many proteins that bind DNA sequence independently, and that are present in very large quantities rather than as a few copies, such as the nucleoid proteins in bacterial cells. The influence of such proteins on DNA configurations is better modeled in terms of a great number of mobile constraints on the DNA. Types of constraints that mimic the influence of various known non-specifically DNA binding proteins include DNA bending, wrapping, and bridging. Using Monte-Carlo simulations, we here investigate the influence of (non-interacting) mobile DNA-protein-DNA bridges on the configurations of a 1000 bp piece of linear DNA, for both homogeneous DNA and DNA with an intrinsic planar bend. Results are compared to experimental data on the bacterial nucleoid protein H-NS that forms DNA-protein-DNA bridges. In agreement with data on H-NS, we find very strong positioning of DNA-protein-DNA bridges in the vicinity of planar bends. H-NS binds to DNA very cooperatively, but for non-interacting bridges we only find a moderate DNA-induced clustering. Finally, it has been suggested that H-NS is an important contributor to the extreme condensation of bacterial DNA into a nucleoid structure, but we find only a moderate compaction of DNA coils with increasing numbers of non-interacting bridges. Our results illustrate the importance of quantifying the various effects on DNA configurations that have been proposed for proteins that bind DNA sequence independently.
Specific coronary drug-eluting stents interfere with distal microvascular function after single stent implantation in pigs.
Heuvel, M. van den; Sorop, O. ; Batenburg, W.W. ; Bakker, C.L. ; Vries, R. de; Koopmans, S.J. ; Beusekom, H.M.M. ; Duncker, D.J. ; Danser, A.H.J. ; Giessen, W.J. - \ 2010
JACC: cardiovascular interventions 3 (2010)7. - ISSN 1936-8798 - p. 723 - 730.
arteries in-vivo - endothelial dysfunction - hyperpolarizing factors - hydrogen-peroxide - s-nitrosothiols - sirolimus - paclitaxel - bradykinin - inhibition - dilation
Objectives The aim of this study was to compare the effects of single drug-eluting stents (DES) on porcine coronary function distal to the stent in vivo and in vitro. Background The mechanism of endothelial dysfunction occurring in human coronary conduit arteries up to 9 months after DES implantation is unknown. Methods A sirolimus-eluting stent (SES), paclitaxel-eluting stent (PES), and a bare-metal stent (BMS) were implanted in the 3 coronary arteries of 11 pigs. After 5 weeks, in vivo responses in distal coronary flow to different doses of bradykinin (BK) and nitrates were measured. In vitro, vasodilation to BK and nitrates, as well as vasoconstriction to endothelin (ET)-1 were assessed in both distal coronary conduit and small arteries. In addition, contributions of nitric oxide (NO) and endothelium-derived hyperpolarizing factors (EDHFs) and cyclic guanosine monophosphate (cGMP) responses to BK-stimulation were determined in vitro. Results Both DES did not alter in vivo distal vasomotion. In vitro distal conduit and small arterial responses to BK were also unaltered; DES did not alter the BK-induced increase in cGMP. However, after NO synthase blockade, PES showed a reduced BK-response in distal small arteries as compared with BMS and SES (p <0.05). The ET-1–induced vasoconstriction and vascular smooth muscle cell function were unaltered. Conclusions In this study of single stenting in healthy porcine coronaries for 5 weeks, SES did not affect distal coronary vascular function, whereas PES altered distal endothelial function of small arteries under conditions of reduced NO bioavailability. Therefore, specifically the EDH-component of microvascular function seems affected by PES.
Onkruid vergaat niet...zomaar, onderzoek naar het gebruik van gewasbeschermingsmiddelen en alternatieve methoden voor milieuvriendelijke bestrijding van ziekten, plagen en onkruiden op sportvelden en golfbanen.
Smidt, R.A. ; Spijker, J.H. ; Schepel, E. ; Dol, R. ; Vries, R. de - \ 2010
Rijen : Branchevereniging Sport en Cultuurtechniek - ISBN 9789087850074 - 45
golfbanen - sportveldgronden - sportterreinen - onkruidbestrijding - grasmatverbetering - duurzaamheid (sustainability) - golf courses - sports turf soils - sports grounds - weed control - sward renovation - sustainability
Onderhoud van grassportvelden en golfbanen zonder gewasbeschermingsmiddelen. Wat betekent het voor u? Nederland telt in totaal ruim 20.000 buitensportvelden en tientallen golfbanen. Het beheer van de buitensportvelden gebeurt voor het grootste deel door gemeenten. De regelgeving over het gebruik van gewasbeschermingsmiddelen op sportvelden en golfbanen verandert op termijn door Europese regelgeving. De Branchevereniging Sport- en Cultuurtechniek (BSNC) heeft laten uitzoeken wat de gevolgen zijn als chemische gewasbeschermingsmiddelen niet meer zijn toegestaan bij het onderhoud
Biosynthetic and biomimetic block copoymers that encapsulate single nucleic acid molecules
Hernandez Garcia, A. ; Werten, M.W.T. ; Wolf, F.A. de; Vries, R. de - \ 2010
The Influence of Ligand Valency on Aggregation Mechanisms for Inhibiting Bacterial Toxins
Sisu, C. ; Baron, A.J. ; Branderhorst, H.M. ; Connell, S.D. ; Weijers, C.A.G.M. ; Vries, R. de; Hayes, E.D. ; Pukin, A.V. ; Gilbert, M. ; Pieters, R.J. ; Zuilhof, H. ; Visser, G.M. ; Turnbull, W.B. - \ 2009
ChemBioChem 10 (2009)2. - ISSN 1439-4227 - p. 329 - 337.
heat-labile enterotoxin - isothermal titration calorimetry - size-distribution analysis - cholera-toxin - escherichia-coli - receptor-binding - analytical ultracentrifugation - carbohydrate interactions - vibrio-cholerae - gm1 mimics
Divalent and tetravalent analogues of ganglioside GM1 are potent inhibitors of cholera toxin and Escherichia coli heat-labile toxin. However, they show little increase in inherent affinity when compared to the corresponding monovalent carbohydrate ligand. Analytical ultracentrifugation and dynamic light scattering have been used to demonstrate that the multivalent inhibitors induce protein aggregation and the formation of space-filling networks. This aggregation process appears to arise when using ligands that do not match the valency of the protein receptor. While it is generally accepted that multivalency is an effective strategy for increasing the activity of inhibitors, here we show that the valency of the inhibitor also has a dramatic effect on the kinetics of aggregation and the stability of intermediate protein complexes. Structural studies employing atomic force microscopy have revealed that a divalent inhibitor induces head-to-head dimerization of the protein toxin en route to higher aggregates
Valse meeldauw: een probleem in de zomerbloementeelt
Hal, J.A. van; Vries, R. de; Meijer, D.A. ; Bos, F. ; Helm, F.P.M. van der; Wurff, A.W.G. van der - \ 2008
Gewasbescherming 39 (2008)1. - ISSN 0166-6495 - p. 1 - 2.
bloementeelt - snijbloemen - peronospora farinosa - onderzoek - infectieziekten - ziektepreventie - rotaties - hygiëne - vragenlijsten - gewasbescherming - zomerteelt - wetenschappelijk onderzoek - zomerbloemen - floriculture - cut flowers - research - infectious diseases - disease prevention - rotations - hygiene - questionnaires - plant protection - summer cultivation - scientific research - summer flowers
Valse meeldauw is een toenemend probleem in de zomerbloementeelt. Onderzoek naar de biologie van valse meeldauw is op dit moment noodzakelijk om effectieve aangrijpingspunten voor bestrijding te vinden. WUR Glastuinbouw verricht onderzoek naar bestrijdingsmaatregelen van valse meeldauw in zomerbloemgewassen. PPO bollenteelt, boomkwekerij en fruit (PPO-BBF) doet onderzoek naar de biologie van en beheersmaatregelen tegen valse meeldauw in zonnebloemen
Moleculair genetische benadering van het fenomeen "knobbels" (vierde fase van het project 'genetisch-fysiologisch model voor de omgevingsgevoeligheid van varkens')
Visscher, A.H. ; Vries, R. de; Setten, M.C. van; Hoving, A.H. ; Gerritsen, C.L.M. ; Pas, M.F.W. te; Smits, M.A. ; Janss, L.L.G. ; Ducro-Steverink, D.W.B. ; Harlizius, B. ; Erp, T. van; Wesel, A.A.M. van - \ 2003
Lelystad : Animal Sciences Group (Rapport / Animal Sciences Group 03/0021811) - 29 p.
In vitro conversion of normal prion protein into pathologic isoforms
Bossers, A. ; Rigter, A. ; Vries, R. de; Smits, M.A. - \ 2003
Clinics in Laboratory Medicine 23 (2003)1. - ISSN 0272-2712 - p. 227 - 247.
creutzfeldt-jakob-disease - mouse neuroblastoma-cells - transmissible mink encephalopathy - scrapie-associated form - natural scrapie - resistant state - cultured-cells - synthetic peptides - incubation period - species barriers
This article describes the various available in vitro systems used to study transmissible spongiform encephalopathy (TSE) replication and the processes involved in prion protein (PrP) conversion. Advantages and disadvantages of these in vitro systems and the underlying molecular mechanisms of PrP conversion are discussed. Several applications of these systems are outlined more extensively, including their species specificity, polymorphism specificity, strain specificity, and the potential that these systems have in screening and discovering TSE therapeutics.
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