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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Data-Driven Modeling of Intracellular Auxin Fluxes Indicates a Dominant Role of the ER in Controlling Nuclear Auxin Uptake
Middleton, Alistair M. ; Bosco, Cristina Dal; Chlap, Phillip ; Bensch, Robert ; Harz, Hartmann ; Ren, Fugang ; Bergmann, Stefan ; Wend, Sabrina ; Weber, Wilfried ; Hayashi, Ken Ichiro ; Zurbriggen, Matias D. ; Uhl, Rainer ; Ronneberger, Olaf ; Palme, Klaus ; Fleck, Christian ; Dovzhenko, Alexander - \ 2018
Cell Reports 22 (2018)11. - ISSN 2211-1247 - p. 3044 - 3057.
auxin - auxin flux - auxin sensor - endoplasmic reticulum - fluorescent aux - mathematical modeling - microscopy - nucleus - protoplasts - single cells
In plants, the phytohormone auxin acts as a master regulator of developmental processes and environmental responses. The best characterized process in the auxin regulatory network occurs at the subcellular scale, wherein auxin mediates signal transduction into transcriptional programs by triggering the degradation of Aux/IAA transcriptional repressor proteins in the nucleus. However, whether and how auxin movement between the nucleus and the surrounding compartments is regulated remain elusive. Using a fluorescent auxin analog, we show that its diffusion into the nucleus is restricted. By combining mathematical modeling with time course assays on auxin-mediated nuclear signaling and quantitative phenotyping in single plant cell systems, we show that ER-to-nucleus auxin flux represents a major subcellular pathway to directly control nuclear auxin levels. Our findings propose that the homeostatically regulated auxin pool in the ER and ER-to-nucleus auxin fluxes underpin auxin-mediated downstream responses in plant cells. Middleton et al. study how the plant phytohormone auxin enters the nucleus by using quantitative phenotyping in single plant cell systems and bespoke mathematical models that relate controlled perturbations to experimentally measurable responses. Their findings show that auxin predominantly enters the nucleus via the endoplasmic reticulum.
A holistic sustainability assessment tool for bioenergy using the Global Bioenergy Partnership (GBEP) sustainability indicators
Hayashi, T. ; Ierland, E.C. van; Zhu, X. - \ 2014
Biomass and Bioenergy 66 (2014). - ISSN 0961-9534 - p. 70 - 80.
weak sustainability - food-prices - biofuels
In 2011 the Global Bioenergy Partnership (GBEP) released a set of indicators for sustainable bioenergy. However, two important issues still remain unresolved. One of them is the definition of “sustainability”, and the other is the lack of a holistic assessment tool for drawing conclusions from the indicators. The aim of this paper is to provide clarification on the concept of sustainability in the context of the GBEP indicators, and to develop a holistic assessment tool for assessing the sustainability of bioenergy programmes. The GBEP indicators are diverse in terms of “what to measure”, and some of them are not sufficiently directly related to the concept of sustainability. This makes the indicators ambiguous regarding to sustainability assessment. This study identifies whether the GBEP indicators are concerned with strong or weak sustainability, and develops a tool based on Multi Criteria Analysis (MCA) which can be used for assessing sustainability of bioenergy programmes using the GBEP indicators. The tool is demonstrated in an example for assessing the sustainability of biofuel production in a case study of Kyoto. We found that the biodiesel production in Kyoto performs well on the environmental pillar, but badly on the economic pillar, and based on the weights applied in this study the overall sustainability is better than diesel fuel. The holistic assessment tool provides practical information to policymakers on both ex-ante and ex-post policy evaluations.
Development of a cucumber leaf picing device for greenhouse production
Ota, T. ; Bontsema, J. ; Hayashi, S. ; Kubota, K. ; Henten, E.J. van; Os, E.A. van; Ajiki, K. - \ 2007
Biosystems Engineering 98 (2007)4. - ISSN 1537-5110 - p. 381 - 390.
autonomous robot
A leaf picking device for cucumbers was designed and evaluated. The picking device is manually operated but can be used as a picking tool for a robot. The device consisted of a picking rotor composed from knives and brushes, a motor and a vacuum cleaner. The performance of removal, cutting, torque and shredding was investigated in the laboratory experiments. In the greenhouse experiments, the performance of picking and cutting was investigated. The results were as follows: (1) the highest removal success rate was achieved at a rotation speed of 1000 min¿1, a rotor configuration of `two knives and two brushes¿ and an insertion speed of 50 mm s¿1; (2) in this mechanical setting, the percentage of the summation of the smooth cut surface of the leaf stalk and the smooth cut surface with small skin was 90%; (3) the required torque was 0.09¿0.96 N m and the average particle size of the shredded leaves was 7.3¿21.2 cm2; (4) the percentages of area of the dropped particles to the average area of leaves was 10¿16%; (5) the average execution time per leaf was 1.1¿2.3 s.
From cell wall architecture to wall modelling: a systems biology approach 'avant la lettre'
Emons, A.M.C. - \ 2006
In: The Science and lore of the plant cell wall: biosynthesis, structure and function / Hayashi, Takahisa, Boca Raton2006 : Brown Walker Press - ISBN 1581124457 - p. 30 - 40.
Impact of fungal drug transporters on fungicide sensitivity, multidrug resistance and virulence
Waard, M.A. de; Andrade, A.C. ; Hayashi, K. ; Schoonbeek, H. ; Stergiopoulos, I. ; Zwiers, L.H. - \ 2006
Pest Management Science 62 (2006)3. - ISSN 1526-498X - p. 195 - 207.
atp-binding cassette - pathogen mycosphaerella-graminicola - azole antifungal agents - natural toxic compounds - yeast abc proteins - candida-albicans - botrytis-cinerea - aspergillus-nidulans - penicillium-digitatum - venturia-inaequalis
Drug transporters are membrane proteins that provide protection for organisms against natural toxic products and fungicides. In plant pathogens, drug transporters function in baseline sensitivity to fungicides, multidrug resistance (MDR) and virulence on host plants. This paper describes drug transporters of the filamentous fungi Aspergillus nidulans (Eidam) Winter, Botrytis cinerea Pers and Mycosphaerella graminicola (Fu¿ckel) Schroter that function in fungicide sensitivity and resistance. The fungi possess ATP-binding cassette (ABC) drug transporters that mediate MDR to fungicides in laboratory mutants. Similar mutants are not pronounced in field resistance to most classes of fungicide but may play a role in resistance to azoles. MDR may also explain historical cases of resistance to aromatic hydrocarbon fungicides and dodine. In clinical situations, MDR development in Candida albicans (Robin) Berkhout mediated by ABC transporters in patients suffering from candidiasis is common after prolonged treatment with azoles. Factors that can explain this striking difference between agricultural and clinical situations are discussed. Attention is also paid to the risk of MDR development in plant pathogens in the future. Finally, the paper describes the impact of fungal drug transporters on drug discovery
Development of a Leaf Picking Device for Cucumber Greenhouse Production
Ota, T. ; Bontsema, J. ; Hayashi, S. ; Kubota, K. ; Henten, E.J. van; Os, E.A. van; Ajiki, K. - \ 2006
In: Proceedings Mechatronics 2006, 4th IFAC-Symposium on Mechatronics Systems. - Heidelberg : IFAC - p. 1012 - 1017.
Development of a cucumber leaf picking mechanism for greenhouse production (In Japanese)
Ota, T. ; Hayashi, S. ; Kubota, K. ; Ajiki, K. ; Bontsema, J. ; Henten, E.J. van; Os, E.A. van - \ 2006
In: The 42th annual report of Kanto branch of the Japanese Society of Agricultural Machinery, Kanto, Japan, 10 July 2006. - Kanto, Japan : Japanese Society of Agricultural Machinery - p. 14 - 15.
Genetic linkage maps of Japanese and European pears aligned to the apple consensus map
Yamamoto, T. ; Kimura, T. ; Saito, T. ; Kotobuki, K. ; Matsuta, N. ; Liebhard, R. ; Gessler, C. ; Weg, W.E. van de; Hayashi, T. - \ 2004
Acta Horticulturae 663 (2004). - ISSN 0567-7572 - p. 51 - 56.
Genetic linkage maps of the Japanese pear (Pyrus pyrifolia Nakai) cultivar `Housui¿ and the European pear (Pyrus communis L.) cultivar `Bartlett¿ were constructed based on Amplified Fragment Length Polymorphism markers (AFLPs), Simple Sequence Repeat markers (SSRs) (from pear, apple and Prunus), isozymes, and phenotypic traits by using their F1 progenies. The map of the female parent `Bartlett¿ consisted of 256 loci including 178 AFLPs, 76 SSRs (32 pear, 39 apple, 5 Prunus SSRs), 1 isozyme and a self-incompatibility locus on 19 linkage groups over a total length of 1020 cM. The map of `Housui¿ contained 180 loci including 110 AFLPs, 64 SSRs (29 pear, 29 apple, 6 Prunus SSRs), 2 phenotypic traits and 4 other markers on 20 linkage groups encompassing a genetic distance of 995 cM. These 2 pear maps were aligned using 37 co-dominant markers that showed segregating alleles in both parents. Out of 80 tested SSR markers developed from apple, more than four-fifth could produce discrete amplified fragments in pear. Thirty-eight apple SSR markers showed 39 segregating loci in the linkage map of `Bartlett¿, while 27 markers produced 29 loci in `Housui¿. All pear linkage groups could be successfully aligned to the apple consensus map by at least 1 apple SSRs, suggesting that positions and linkages of SSR loci were well conserved between pear and apple. The self-incompatibility locus (S locus) was mapped to linkage group 17 in Japanese and European pears as well as apple. Our results are the first major effort in comparative mapping of pear and apple
Drug transporter proteins from Botrytis cinerea function in protection against fungitoxic compounds and biotic interactions
Waard, M.A. de; Hayashi, K. ; Raaijmakers, J.M. ; Schoonbeek, H. - \ 2004
In: Book of Abstracts XIII International Botrytis Symposium, Antalya, Turkey, 25-31 October 2004 - p. 113 - 113.
ABC and MFS transporters from Botrytis cinerea involved in sensitivity to fungicides and natural toxic compounds
Hayashi, K. - \ 2003
University. Promotor(en): Pierre de Wit, co-promotor(en): M.A. de Waard. - [S.l.] : S.n. - ISBN 9058088979 - 143 p.
botrytis cinerea - plantenziekteverwekkende schimmels - plantenziekteverwekkers - fungiciden - fungicidentolerantie - meervoudige resistentie tegen geneesmiddelen - resistentie tegen pesticiden - atp - plant pathogenic fungi - plant pathogens - fungicides - fungicide tolerance - multiple drug resistance - pesticide resistance
Modulators of membrane drug transporters potentiate the activity of the DMI fungicide oxpoconazole against Botrytis cinerea
Hayashi, K. ; Schoonbeek, H. ; Waard, M.A. de - \ 2003
Pest Management Science 59 (2003)3. - ISSN 1526-498X - p. 294 - 302.
sterol demethylation inhibitors - natural toxic compounds - multidrug-resistance - efflux pump - wild-type - botryotinia-fuckeliana - penicillium-italicum - candida-albicans - accumulation - fenarimol
Modulators known to reduce multidrug resistance in tumour cells were tested for their potency to synergize the fungitoxic activity of the fungicide oxpoconazole, a sterol demethylation inhibitor (DMI), against Botrytis cinerea Pers. Chlorpromazine, a phenothiazine compound known as a calmodulin antagonist, appeared the most potent compound. Tacrolimus, a macrolide compound with immunosuppressive activity, was also active. The synergism of chlorpromazine negatively correlated with the sensitivity of the parent strain and mutants of B cinerea. The synergism was highest in a mutant that overexpressed the ATP-binding cassette transporter BcatrD, known to transport DMI fungicides such as oxpoconazole. The synergism of chlorpromazine positively correlated with its potency to enhance the accumulation of oxpoconazole in BcatrD mutants. These results indicate that chlorpromazine is a modulator of BcatrD activity in B cinerea and suggest that mixtures of DMI fungicides with modulators may represent a perspective for the development of new resistance management strategies.
Expression of the ABC transporter BcatrD from Botrytis cinerea reduces sensitivity to sterol demethylation inhibitor fungicides
Hayashi, K. ; Schoonbeek, H. ; Waard, M.A. De - \ 2002
Pesticide Biochemistry and Physiology 73 (2002). - ISSN 0048-3575 - p. 110 - 121.
The ATP-binding cassette (ABC) transporter gene BcatrD from Botrytis cinerea was cloned and characterized. The open reading frame of BcatrD contains seven introns and encodes a putative protein of 1502 amino acids. The function of BcatrD was analyzed by phenotypic characterization of gene-replacement and overexpression mutants. Replacement mutants of BcatrD displayed a higher sensitivity to sterol demethylation inhibitor (DMI) fungicides as compared to the parental isolate. Gene replacement mutants also showed a relatively high accumulation of the DMI fungicide oxpoconazole. Overexpression mutants showed increased levels of basal and oxpoconazole-induced expression of BcatrD. Mutants with the highest expression level displayed the highest decrease in sensitivity to oxpoconazole and a relatively low accumulation of the compound. These results indicate a relation between oxpoconazole sensitivity, expression of BcatrD, and accumulation of oxpoconazole and demonstrate that the ABC transporter BcatrD is a determinant of the sensitivity of B. cinerea to DMI fungicides.
Effect of high-pressure processing on the quality of green beans
Krebbers, B. ; Koets, M. ; Wall, F. van den; Matser, A.M. ; Moezelaar, R. ; Hoogerwerf, S.M. - \ 2002
In: Trends in high pressure bioscience and biotechnology : proceedings first international conference on high pressure bioscience and biotechnology (HPBB-2000), 26-30 November 2000, Kyoto, Japan - p. 389 - 396.
Bcmfs1, a novel major facilitator superfamily transporter from Botrytis cinerea, provides tolerance towards the natural toxic compounds camptothecin and cercosporin and towards fungicides
Hayashi, K. ; Schoonbeek, H. ; Waard, M.A. De - \ 2002
Applied and Environmental Microbiology 68 (2002)10. - ISSN 0099-2240 - p. 4996 - 5004.
Bcmfs1, a novel major facilitator superfamily gene from Botrytis cinerea, was cloned, and replacement and overexpression mutants were constructed to study its function. Replacement mutants showed increased sensitivity to the natural toxic compounds camptothecin and cercosporin, produced by the plant Camptotheca acuminata and the plant pathogenic fungus Cercospora kikuchii, respectively. Overexpression mutants displayed decreased sensitivity to these compounds and to structurally unrelated fungicides, such as sterol demethylation inhibitors (DMIs). A double-replacement mutant of Bcmfs1 and the ATP-binding cassette (ABC) transporter gene BcatrD was more sensitive to DMI fungicides than a single-replacement mutant of BcatrD, known to encode an important ABC transporter of DMIs. The sensitivity of the wild-type strain and mutants to DMI fungicides correlated with Bcmfs1 expression levels and with the initial accumulation of oxpoconazole by germlings of these isolates. The results indicate that Bcmfs1 is a major facilitator superfamily multidrug transporter involved in protection against natural toxins and fungicides and has a substrate specificity that overlaps with the ABC transporter BcatrD. Bcmfs1 may be involved in protection of B. cinerea against plant defense compounds during the pathogenic phase of growth on host plants and against fungitoxic antimicrobial metabolites during its saprophytic phase of growth
Advanced algorithms for estimation of surface physical parameters
Wen, J. ; Gamo, M. ; Hayashi, M. ; Su, Z. - \ 2001
In: ENVISAT - land surface processes / Su, Z., Roerink, G.J., Delft : BCRS (USP-2 Rep 01-07) - p. 31 - 54.
remote sensing - aardoppervlak - atmosfeer - klimaat - meteorologie - vegetatie - Azië - Mongolië
ATP-binding cassette (ABC) transporters from Botrytis cinerea
Waard, M.A. De; Hayashi, K. ; Schoonbeek, H. ; Vermeulen, T. - \ 2001
In: Book of Abstracts XXI Fungal Genetics Conference, Asilomar, USA, 13-18 March 2001 Asilomar, USA : - p. 97 - 97.
Multidrug resistance in Botrytis cinerea associated with decreased accumulation of the azole fungicide oxpoconazole and increased transcription of the ABC transporter gene BcatrD
Hayashi, K. ; Schoonbeek, H. ; Sugiura, H. ; Waard, M.A. De - \ 2001
Pesticide Biochemistry and Physiology 70 (2001). - ISSN 0048-3575 - p. 168 - 179.
Azole-resistant mutants of Botrytis cinerea have a multidrug resistance phenotype since they exhibit cross-resistance to unrelated chemicals. These mutants also display resistance to the new azole fungicide oxpoconazole. Resistance to oxpoconazole is associated with decreased accumulation of the fungicide, which is the result of energy-dependent efflux mediated by fungicide transporters. The ATP-binding cassette (ABC) transporter BcatrB (B. cinerea ABC transporter B), involved in efflux of phenylpyrrole fungicides, has no major role in efflux of oxpoconazole since accumulation of the fungicide by a replacement mutant of BcatrB showed a transient accumulation pattern similar to that of the wild-type isolate. The putative role of 10 additional ABC and 3 Major facilitator superfamily transporters in efflux of oxpoconazole was investigated by expression analysis of the corresponding genes. The basal transcription level of BcatrD in germlings of B. cinerea was correlated with the resistance level of two azole-resistant mutants. A short treatment of germlings with the azole fungicides oxpoconazole, prochloraz, and tebuconazole enhanced transcript levels of BcatrD in a wild-type isolate. Transcript levels induced by these fungicides in azole-resistant mutants also correlated with resistance levels. We propose that BcatrD is the ABC transporter that plays a role in azole sensitivity and azole resistance of B. cinerea. Expression of BcatrD is also induced by treatment of germlings with the dicarboximide fungicide iprodione, the benzimidazole fungicide carbendazim, and the antibiotic cycloheximide, suggesting that this gene indeed plays a role in multidrug resistance to fungicides.
ABC transporters involved insensitivity and resistance of Botrytis cinerea to azole fungicides and other botryticides
Hayashi, K. ; Waard, M.A. de - \ 2000
Ube, Japan : Ube Industries - 3 p.
ABC transporters involved insensitivity and resistance of Botrytis cinerea to azole fungicides and other botryticides
Hayashi, K. ; Waard, M.A. de - \ 2000
Unknown Publisher - 7 p.
ABC transporters involved insensitivity and resistance of Botrytis cinerea to azole fungicides and other botryticides
Hayashi, K. ; Waard, M.A. de - \ 2000
Unknown Publisher - 12 p.
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