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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    Erratum to: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study
    Hellenkamp, Björn ; Schmid, Sonja ; Doroshenko, Olga ; Opanasyuk, Oleg ; Kühnemuth, Ralf ; Adariani, Soheila Rezaei ; Ambrose, Benjamin ; Aznauryan, Mikayel ; Barth, Anders ; Birkedal, Victoria ; Bowen, Mark E. ; Chen, Hongtao ; Cordes, Thorben ; Eilert, Tobias ; Fijen, Carel ; Gebhardt, Christian ; Götz, Markus ; Gouridis, Giorgos ; Gratton, Enrico ; Ha, Taekjip ; Hao, Pengyu ; Hanke, Christian A. ; Hartmann, Andreas ; Hendrix, Jelle ; Hildebrandt, Lasse L. ; Hirschfeld, Verena ; Hohlbein, Johannes ; Hua, Boyang ; Hübner, Christian G. ; Kallis, Eleni ; Kapanidis, Achillefs N. ; Kim, Jae Yeol ; Krainer, Georg ; Lamb, Don C. ; Lee, Nam Ki ; Lemke, Edward A. ; Levesque, Brié ; Levitus, Marcia ; McCann, James J. ; Naredi-Rainer, Nikolaus ; Nettels, Daniel ; Ngo, Thuy ; Qiu, Ruoyi ; Robb, Nicole C. ; Röcker, Carlheinz ; Sanabria, Hugo ; Schlierf, Michael ; Schröder, Tim ; Schuler, Benjamin ; Seidel, Henning - \ 2018
    Nature Methods : techniques for life scientists and chemists 15 (2018)11. - ISSN 1548-7091 - p. 984 - 984.
    Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study
    Hellenkamp, Björn ; Schmid, Sonja ; Doroshenko, Olga ; Opanasyuk, Oleg ; Kühnemuth, Ralf ; Rezaei Adariani, Soheila ; Ambrose, Benjamin ; Aznauryan, Mikayel ; Barth, Anders ; Birkedal, Victoria ; Bowen, Mark E. ; Chen, Hongtao ; Cordes, Thorben ; Eilert, Tobias ; Fijen, Carel ; Gebhardt, Christian ; Götz, Markus ; Gouridis, Giorgos ; Gratton, Enrico ; Ha, Taekjip ; Hao, Pengyu ; Hanke, Christian A. ; Hartmann, Andreas ; Hendrix, Jelle ; Hildebrandt, Lasse L. ; Hirschfeld, Verena ; Hohlbein, Johannes ; Hua, Boyang ; Hübner, Christian G. ; Kallis, Eleni ; Kapanidis, Achillefs N. ; Kim, Jae Yeol ; Krainer, Georg ; Lamb, Don C. ; Lee, Nam Ki ; Lemke, Edward A. ; Levesque, Brié ; Levitus, Marcia ; McCann, James J. ; Naredi-Rainer, Nikolaus ; Nettels, Daniel ; Ngo, Thuy ; Qiu, Ruoyi ; Robb, Nicole C. ; Röcker, Carlheinz ; Sanabria, Hugo ; Schlierf, Michael ; Schröder, Tim ; Schuler, Benjamin ; Seidel, Henning ; Streit, Lisa ; Thurn, Johann ; Tinnefeld, Philip ; Tyagi, Swati ; Vandenberk, Niels ; Vera, Andrés Manuel ; Weninger, Keith R. ; Wünsch, Bettina ; Yanez-Orozco, Inna S. ; Michaelis, Jens ; Seidel, Claus A.M. ; Craggs, Timothy D. ; Hugel, Thorsten - \ 2018
    Nature Methods : techniques for life scientists and chemists 15 (2018)9. - ISSN 1548-7091 - p. 669 - 676.

    Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods.

    Guiding principles for the development and application of solid-phase phosphorus adsorbents for freshwater ecosystems
    Douglas, G.B. ; Hamilton, D.P. ; Robb, M.S. ; Pan, G. ; Spears, B.M. ; Lurling, M. - \ 2016
    Aquatic Ecology 50 (2016)3. - ISSN 1386-2588 - p. 385 - 405.
    Application - Guidelines - Nutrients - Phosphorus adsorptive materials

    Whilst a diverse array of phosphorus (P)-adsorbent materials is currently available for application to freshwater aquatic systems, selection of the most appropriate P-adsorbents remains problematic. In particular, there has to be a close correspondence between attributes of the P-adsorbent, its field performance and the management goals for treatment. These management goals may vary from a rapid reduction in dissolved P to address seasonal enrichments from internal loading, targeting external fluxes due to anthropogenic sources, or long-term inactivation of internal P inventories contained within bottom sediments. It also remains a challenge to develop new methods and materials that are ecologically benign and cost-effective. We draw on evidence in the literature and the authors’ personal experiences in the field, to summarise the attributes of a range of P-adsorbent materials. We offer ‘guiding principles’ to support practical use of existing materials and outline key development needs for new materials.

    Bolinductie en bolgroei bij weefselkweek van lelie
    Klerk, G.J.M. de - \ 2013
    Wageningen : Plant Breeding Wageningen UR - 32
    bloembollen - lilium - weefselkweek - cultuurmethoden - groei - bollen - besmetting - landbouwkundig onderzoek - ornamental bulbs - lilium - tissue culture - cultural methods - growth - bulbs - contamination - agricultural research
    Lelie is een van de twee bolgewassen die op grote schaal in weefselkweek worden vermeerderd. De technieken zijn grotendeels hetzelfde als gebruikt door Robb bij haar proefschrift over weefselkweek van lelie in 1954. Het belangrijkste verschil is dat de technieken die Robb toepaste bij veldbollen sinds ongeveer 1980 ook bij weefselkweekbolletjes worden toegepast. Het doel van het huidige onderzoek is weefselkweek van lelie te verbeteren, vooral wat betreft bolgroei. De resultaten kunnen bij andere bolgewassen toegepast worden.
    Genetic dissection of Verticillium wilt resistance mediated by tomato Ve1
    Fradin, E.F. ; Zhang, Z. ; Juarez Ayala, J.C. ; Castroverde, C.C.M. ; Nazar, R.N. ; Robb, J. ; Liu, Chun-Ming ; Thomma, B.P.H.J. - \ 2009
    Plant Physiology 150 (2009). - ISSN 0032-0889 - p. 320 - 332.
    receptor-like proteins - plant-disease resistance - leucine-rich repeats - cladosporium-fulvum - hypersensitive response - fungal pathogen - functional-analysis - scab resistance - cell-death - defense
    Vascular wilt diseases caused by soil-borne pathogens are among the most devastating plant diseases worldwide. The Verticillium genus includes vascular wilt pathogens with a wide host range. Although V. longisporum infects various hosts belonging to the Cruciferaceae, V. dahliae and V. albo-atrum cause vascular wilt diseases in over 200 dicotyledonous species, including economically important crops. A locus responsible for resistance against race 1 strains of V. dahliae and V. albo-atrum has been cloned from tomato (Solanum lycopersicum) only. This locus, known as Ve, comprises two closely linked inversely oriented genes, Ve1 and Ve2, that encode cell surface receptor proteins of the extracellular leucine-rich repeat receptor-like protein class of disease resistance proteins. Here, we show that Ve1, but not Ve2, provides resistance in tomato against race 1 strains of V. dahliae and V. albo-atrum and not against race 2 strains. Using virus-induced gene silencing in tomato, the signaling cascade downstream of Ve1 is shown to require both EDS1 and NDR1. In addition, NRC1, ACIF, MEK2, and SERK3/BAK1 also act as positive regulators of Ve1 in tomato. In conclusion, Ve1-mediated resistance signaling only partially overlaps with signaling mediated by Cf proteins, type members of the receptor-like protein class of resistance proteins.
    Is humane slaughter of fish possible for industry?
    Vis, J.W. van de; Kestin, S. ; Robb, D. ; Oehlenschlaeger, J. ; Lambooij, E. ; Kuhlmann, H. ; Kloosterboer, K. - \ 2003
    Aquaculture Research 34 (2003)3. - ISSN 1355-557X - p. 211 - 220.
    salmon salmo-salar - meat quality - stress - brain
    The objective was to evaluate industrial and research slaughter methods for Atlantic salmon (Salmo salar), gilt-head seabream (Sparus auratus) and eel (Anguilla anguilla) with respect to welfare and quality. As a general term of reference, an optimal slaughter method should render fish unconscious until death without avoidable excitement, pain or suffering prior to killing. For Atlantic salmon, commercial slaughter methods (carbon dioxide stunning followed by gill cutting, and gill cutting alone) are not in conformity with the general term of reference, as the fish are not rendered unconscious immediately and possibly experience stress. Evaluation of automated percussive stunning remained unconclusive. More research should enable us to ascertain whether loss of consciousness is instantaneous. Electrical stunning can be humane if applied properly. However, because flesh of electrostunned fish was characterized by occasional bloodspots, optimization of the electrical parameters is required. Prototypes for percussive and electrical stunning of salmon have been recently developed. This implies that humane slaughter of salmon is feasible for industry. For gilt-head seabream, neither aphyxia in air nor transfer of the fish to an ice slurry were considered to be humane: the methods did not induce immediate brain dysfunction and vigorous attempts to escape occurred. Percussive and electrical stunning can be in conformity with the general term of reference. However, conditions for stunning whole batches of seabream have not been established. Quality of the fish slaughtered by percussive stunning was similar to that obtained by the industrial method, i.e. immersion in an ice slurry. Further work is required to establish optimal stunning conditions and to develop prototypes. For eel, desliming in a salt-bath followed by evisceration, electrical stunning performed under the conditions prescribed by the German legislation, and live chilling and freezing were not considered to be humane. In contrast, it was established that a 10-20 kg batch of eels in fresh water could be rendered unconscious immediately and until death by applying electricity in combination with nitrogen gas. The conditions used were 0.64 A dm2 for 1 s, followed by 0.17 A dm2 combined with nitrogen flushing for 5 min. A preliminary assessment of flesh quality suggests that it may be improved by application of the latter method, compared with the salt bath. The results clearly indicated that humane slaughter of eels is possible in practice.
    Protocol for assessing brain function in fish and the effectiveness of methods used to stun and kill them
    Kestin, S.C. ; Vis, J.W. van de; Robb, D.H.F. - \ 2002
    Veterinary Record 150 (2002)10. - ISSN 0042-4900 - p. 302 - 307.
    A method for the evaluation of brain function in fish has been developed which is based on assessments of self-initiated behaviours, responses to stimulation, and reflexes. These assessments were validated in several freshwater and marine species and applied to evaluate the brain function of fish while they were anaesthetised and while they were being killed by a variety of methods. The results of these investigations were compared with published neurophysiological observations and it is concluded that some of the tests can be used to identify, with reasonable confidence, the state of awareness, and thus the capacity to experience suffering of several species of fish.
    Preslaughter electrical stunning of eels
    Robb, D.H.F. ; Wotton, S.B. ; Vis, J.W. van de - \ 2002
    Aquaculture Research 33 (2002). - ISSN 1355-557X - p. 37 - 42.
    The current procedures for slaughtering European eels (Anguilla anguilla) for food are very slow and cause suffering. Although there is little legislation for protecting the welfare of fish at slaughter, the legislation covering farmed mammals and birds at slaughter is well defined, requiring that these animals be rendered insensible immediately or without fear or pain prior to being killed. For many mammals and birds this can be achieved using an electrical stun, which is then followed by a procedure that actually kills them, such as exsanguination. This paper reports the investigation of the possibility of using electricity to stun eels, rendering them insensible to pain. Using 1 s duration alternating currents at 50 Hz applied directly across the head of the fish, it was shown that it was possible to stun the fish with currents of 0.1 A and above. Increasing the applied current increased the length of the period of the stun. When the duration of the application of the current was increased to 30 s it was found that the fish could be killed using currents between 0.50 A and 0.95 A. These results show that it is possible to use electricity to instantly stun eels and also to kill them by using longer duration currents. The use of preslaughter electrical stunning at slaughter could allow the welfare of these fish at slaughter to be improved greatly.
    Method and device for stunning and killing aquatic animals
    Vis, J.W. van de; Robb, D.F.T. ; Kestin, S.C. ; Huidobro-Perez-Villamil, A. ; Kuhlman, H. ; Nesvada, P. ; Kloosterboer, R.J. - \ 2001
    Octrooinummer: WO0195732, gepubliceerd: 2001-12-20.
    The invention relates to a method for stunning and killing an aquatic animal, comprising of having the animal accommodated in water, connecting a source of electric current to the water such that during a first period an electric current with a first current intensity is generated in the animal such that it is stunned, and conditioning the water such that, substantially immediately thereafter, the animal remains stunned during a second period.
    Effect of the commercial and experimental slaughter of eels (Aguilla anguilla L.) on quality and welfare
    Vis, J.W. van de; Oehlenschlaeger, J. ; Kuhlmann, H. ; Muenkner, W. ; Robb, D.H.F. ; Schelvis-Smit, A.A.M. - \ 2001
    In: Farmed fish quality / Kestin, Steve C., Warriss, Paul D., Oxford : Fishing News Books - ISBN 9780852382608 - p. 234 - 248.
    Novel structure and redox chemistry of the prosthetic groups of the iron-sulfur flavoprotein sulfide dehydrogenase from Pyrococcus furiosus; evidence for a [2Fe-2S] cluster with Asp(Cys) (3) ligands
    Hagen, W.R. ; Silva, P.J. da; Amorim, M.A. ; Hagedoorn, P.L. ; Wassink, J.H. ; Haaker, H. ; Robb, F.T. - \ 2000
    Journal of Biological Inorganic Chemistry 5 (2000). - ISSN 0949-8257 - p. 527 - 534.
    Enzymes of hydrogen metabolism in Pyrococcus furiosus
    Silva, P.A. da; Ban, E.C.D. van den; Wassink, J.H. ; Haaker, H. ; Castro, B. de; Robb, F.T. ; Hagen, W.R. - \ 2000
    European Journal of Biochemistry 267 (2000). - ISSN 0014-2956 - p. 6541 - 6551.
    The genome of Pyrococcus furiosus contains the putative mbhABCDEFGHIJKLMN operon for a 14-subunit transmembrane complex associated with a Ni-Fe hydrogenase. Ten ORFs (mbhA-I and mbhM) encode hydrophobic, membrane-spanning subunits. Four ORFs (mbhJKL and mbhN) encode putative soluble proteins. Two of these correspond to the canonical small and large subunit of Ni-Fe hydrogenase, however, the small subunit can coordinate only a single iron-sulfur cluster, corresponding to the proximal [4Fe-4S] cubane. The structural genes for the small and the large subunits, mbhJ and mbhL, are separated in the genome by a third ORF, mbhK, encoding a protein of unknown function without Fe/S binding. The fourth ORF, mbhN, encodes a 2[4Fe-4S] protein. With P. furiosus soluble [4Fe-4S] ferredoxin as the electron donor the membranes produce H2, and this activity is retained in an extracted core complex of the mbh operon when solubilized and partially purified under mild conditions. The properties of this membrane-bound hydrogenase are unique. It is rather resistant to inhibition by carbon monoxide. It also exhibits an extremely high ratio of H2 evolution to H2 uptake activity compared with other hydrogenases. The activity is sensitive to inhibition by dicyclohexylcarbodiimide, an inhibitor of NADH dehydrogenase (complex I). EPR of the reduced core complex is characteristic for interacting iron-sulfur clusters with Em 0.33 V. The genome contains a second putative operon, mbxABCDFGHH'MJKLN, for a multisubunit transmembrane complex with strong homology to the mbh operon, however, with a highly unusual putative binding motif for the Ni-Fe-cluster in the large hydrogenase subunit. Kinetic studies of membrane-bound hydrogenase, soluble hydrogenase and sulfide dehydrogenase activities allow the formulation of a comprehensive working hypothesis of H2 metabolism in P. furiosus in terms of three pools of reducing equivalents (ferredoxin, NADPH, H2) connected by devices for transduction, transfer, recovery and safety-valving of energy
    Insights into the molecular basis of thermal stability from the analysis of ion-pair networks in the glutamate dehydrogenase family.
    Yip, K.S.P. ; Britton, L. ; Stillman, T.J. ; Lebbink, J. ; Vos, W.M. de; Robb, F.T. ; Vetriani, C. ; Maeder, D. ; Rice, D.W. - \ 1998
    European Journal of Biochemistry 255 (1998). - ISSN 0014-2956 - p. 336 - 346.
    Guar, but not psyllium, increases breath methane and serum acetate concentrations in human subjects.
    Wolever, Th.M.S. ; Wal, P. ter; Spadafora, P. ; Robb, P. - \ 1992
    American Journal of Clinical Nutrition 55 (1992). - ISSN 0002-9165 - p. 719 - 722.
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