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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    Mapping European canker spatial pattern and disease progression in apples using GIS, Tasman, New Zealand
    Iorio, Diletta Di ; Walter, Monika ; Lantinga, Egbert ; Kerckhoffs, Huub ; Campbell, Rebecca E. - \ 2019
    New Zealand Plant Protection 72 (2019). - ISSN 1175-9003 - p. 176 - 184.
    Apple - Disease progression - European canker - Geographical Information Systems - GIS - Hot-spots - Neonectria ditissima - Spatial - Temporal

    European canker (EC), caused by Neonectria ditissima, is an important disease in apple-producing regions in New Zealand. In order to improve plant protection, Geographic Information Systems (GIS) can be used to map plant disease location and severity in agricultural settings. Data were compiled from apple growers in Tasman, New Zealand, to investigate EC distribution over 4 years, for the period 2015–2018. ArcGIS software, including the Spatial Analyst, Interpolation and Geospatial statistics toolboxes, was used to map EC incidence at the spatial scale of orchard blocks, which allowed the identification of disease hot-spots. A clustered spatial pattern of disease was detected every year and areas with higher risk of EC were identified within the region. The spatial patterns detected were related to disease pressure over time for different apple cultivars. The use of GIS provides a platform for analysing and visually communicating disease patterns over time. Investigating disease spatial pattern allows the inference of spatial processes and further hypothesis generation to understand the pathogen.

    Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model
    Abbeele, P. van den; Belzer, C. ; Goossens, M. ; Kleerebezem, M. ; Vos, W.M. de; Thas, O. ; Weirdt, R. de; Kerckhoffs, D.M.F.J. ; Wiele, T. van der - \ 2013
    ISME Journal 7 (2013). - ISSN 1751-7362 - p. 949 - 961.
    inflammatory-bowel-disease - phylogenetic microarray analysis - gel-electrophoresis analysis - mucosa-associated microbiota - human large-intestine - 16s ribosomal-rna - fecal microbiota - sp-nov. - gastrointestinal-tract - spatial-organization
    The human gut is colonized by a complex microbiota with multiple benefits. Although the surface-attached, mucosal microbiota has a unique composition and potential to influence human health, it remains difficult to study in vivo. Therefore, we performed an in-depth microbial characterization (human intestinal tract chip (HITChip)) of a recently developed dynamic in vitro gut model, which simulates both luminal and mucosal gut microbes (mucosal-simulator of human intestinal microbial ecosystem (M-SHIME)). Inter-individual differences among human subjects were confirmed and microbial patterns unique for each individual were preserved in vitro. Furthermore, in correspondence with in vivo studies, Bacteroidetes and Proteobacteria were enriched in the luminal content while Firmicutes rather colonized the mucin layer, with Clostridium cluster XIVa accounting for almost 60% of the mucin-adhered microbiota. Of the many acetate and/or lactate-converting butyrate producers within this cluster, Roseburia intestinalis and Eubacterium rectale most specifically colonized mucins. These 16S rRNA gene-based results were confirmed at a functional level as butyryl-CoA:acetate-CoA transferase gene sequences belonged to different species in the luminal as opposed to the mucin-adhered microbiota, with Roseburia species governing the mucosal butyrate production. Correspondingly, the simulated mucosal environment induced a shift from acetate towards butyrate. As not only inter-individual differences were preserved but also because compared with conventional models, washout of relevant mucin-adhered microbes was avoided, simulating the mucosal gut microbiota represents a breakthrough in modeling and mechanistically studying the human intestinal microbiome in health and disease. Finally, as mucosal butyrate producers produce butyrate close to the epithelium, they may enhance butyrate bioavailability, which could be useful in treating diseases, such as inflammatory bowel disease
    Application of four pollination techniques and of hormone treatment for bypassing interspecific crossing barriers in Lilium L
    Creij, M.G.M. van; Kerckhoffs, D.M.F.J. ; Tuyl, J.M. van - \ 2000
    In: Cadic, A. (Ed.). Proceedings of the 19. international symposium on improvement of ornamental plants: breeding ornamentals in the future: goals, genes, tools, Angers, France, 27-30 Jul 1998. Leuven (Belgium). International Society for Horticultural Science. 2000. 356 p
    The effect of medium composition on ovary-slice culture and ovule culture in intraspecific Tulipa gesneriana crosses
    Creij, M.G.M. van; Kerckhoffs, D.M.F.J. ; Bruijn, S.M. de; Tuyl, J.M. van; Vreugdenhil, D. - \ 2000
    Plant Cell, Tissue and Organ Culture: an international journal on in vitro culture of higher plants 60 (2000). - ISSN 0167-6857 - p. 61 - 67.
    The effect of several media components on the germination percentage of ovules in intraspecific T. gesneriana L. crosses was studied by using two embryo rescue techniques, viz. ovary-slice culture followed by ovule culture and direct ovule culture. The addition of 9% sucrose to medium for ovary-slice culture, started at 3 or at 5 weeks after pollination (WAP), significantly improved the germination percentage as compared to 5% sucrose. The germination percentage did not differ between both sucrose concentrations (3% and 5%) used in ovule culture started 4 weeks later with ovules excised from the ovary-slices (at 9 WAP). Similar germination percentages were obtained with media containing the full or half of the concentrations of micronutrients and macronutrients of the MS-medium during ovary-slice culture and ovule culture. For direct ovule culture, started at 4, at 6, and at 8 WAP, the germination percentages did not differ between ovules cultured on media with 3%, 6% or 9% sucrose. The addition of the cytokinin BAP (0.01 or 0.1 mg l-1) had no effect on the germination percentage. The use of liquid-shaken culture resulted in germination percentages which were similar to those on agar-solidified media. Analysis of the carbohydrate concentration of the media revealed that, in both media for ovary-slice culture and for ovule culture, ultimately all sucrose is converted into glucose and fructose. The total concentration of carbohydrates decreased with 19%–48% in the media for ovary-slice culture, whereas the total concentration of carbohydrates did not decrease remarkably in media for ovule culture.
    Characterization of the gene encoding the apoprotein of tomato phytochrome B2, and identification of molecular lesions in two mutant alleles
    Kerckhoffs, L.H.J. ; Kelmenson, P.M. ; Schreuder, M.E.L. ; Kendrick, R.E. ; Hanhart, C.J. ; Koornneef, M. ; Pratt, L.H. ; Cordonnier-Pratt, M.M. - \ 1999
    Molecular and General Genetics 261 (1999). - ISSN 0026-8925 - p. 901 - 907.
    Molecular analysis of PHYA in wild-type and phytochrome A-deficient mutants of tomato.
    Lazarova, G.I. ; Kerckhoffs, L.H.J. ; Brandstadter, J. ; Matsui, N. ; Kendrick, R.E. ; Cordonnier-Pratt, M. ; Pratt, L.H. - \ 1998
    The Plant Journal 14 (1998). - ISSN 0960-7412 - p. 653 - 662.
    Interspecific crosses in the genus Tulipa L.: Identification of pre-fertilization barriers
    Creij, M.G.M. van; Kerckhoffs, D.M.F.J. ; Tuyl, J.M. van - \ 1997
    Sexual Plant Reproduction 10 (1997). - ISSN 0934-0882 - p. 116 - 123.
    Application of three pollination techniques and of hormone treatments for overcoming interspecific crossing barriers in Tulipa
    Creij, M.G.M. van; Kerckhoffs, D.M.F.J. ; Tuyl, J.M. van - \ 1997
    Acta Horticulturae 430 (1997). - ISSN 0567-7572 - p. 547 - 557.
    In tulip, interspecific crossing is restricted by both pre-fertilization and post-fertilization barriers. In order to introduce traits from wild species into the cultivar assortment these barriers must be bypassed. By application of embryo rescue techniques, unique hybrids have been obtained of several interspecific tulip crosses. Recently, four techniques have been tested on their capacity to overcome interspecific crossing barriers in tulip, namely hormone treatments of ovaries, cut-style method, grafted-ovary method and placental pollination. After treating ovaries with 0.1 percent BAP at 12 days after pollination, seeds were obtained on the plant from the cross T. gesneriana x T. agenensis. This cross has never been given seeds in vivo before. Treating ovaries with 1 percent BAP seemed to have a negative effect on seedset in compatible crosses, 1 percent NAA did not give any effect. After the application of the cut-style method, the percentage pollen tube penetration did not increase in crosses between T. gesneriana and 5 other Tulipa species. Apparently, crossing barriers were not overcome by using the cut-style method, nor after using the grafted-ovary method. After placental pollination, pollen tube penetration percentages were not increased compared to stigmatic pollination, however, most of the penetrated ovules with pollen tube penetration showedd embryo germination.
    Physiological characterization of exaggerated photoresponse mutants of tomato.
    Kerckhoffs, L.H.J. ; Groot, N.A.M.A. de; Tuinen, A. van; Schreuder, M.E.L. ; Nagatani, A. ; Koornneef, M. ; Kendrick, R.E. - \ 1997
    Journal of Plant Physiology 150 (1997). - ISSN 0176-1617 - p. 578 - 587.
    Phytochrome control of anthocyanin biosynthesis in tomato seedlings: analysis using photomorphogenic mutants.
    Kerckhoffs, L.H.J. ; Schreuder, M.E.L. ; Tuinen, A. van; Koornneef, M. ; Kendrick, R.E. - \ 1997
    Photochemistry and Photobiology 65 (1997). - ISSN 0031-8655 - p. 374 - 381.
    Photomorphogenic mutants of tomato.
    Kendrick, R.E. ; Kerckhoffs, L.H.J. ; Tuinen, A. van; Koornneef, M. - \ 1997
    Plant, Cell & Environment 20 (1997). - ISSN 0140-7791 - p. 746 - 751.
    Photocontrol of anthocyanin biosynthesis in tomato.
    Kerckhoffs, L.H.J. ; Kendrick, R.E. - \ 1997
    Journal of Plant Research 110 (1997). - ISSN 0918-9440 - p. 141 - 149.
    Growth analysis of wildtype and photomorphogenic-mutant tomato plants.
    Kerckhoffs, L.H.J. ; Sengers, M.M.T. ; Kendrick, R.E. - \ 1997
    Physiologia Plantarum 99 (1997). - ISSN 0031-9317 - p. 309 - 315.
    The progamic phase, embryo and endosperm development in an intraspecific Tulipa gesneria L. cross and in the incongruent interspecific cross T. gesneriana x T. agenensis DC.
    Creij, M.G.M. van; Went, J.L. van; Kerckhoffs, D.M.F.J. - \ 1997
    Sexual Plant Reproduction 10 (1997). - ISSN 0934-0882 - p. 241 - 249.
    A high resolution plant growth-measuring apparatus to study stem growth kinetics.
    Kerckhoffs, L.H.J. ; Adamse, P. ; Tonk, W. ; Ginkel, R. van; Kreel, J. van; Veenendaal, A. ; Ruyter, T.P.L. ; Buurmeijer, W.F. ; Bouma, R.M. ; Kendrick, R.E. - \ 1996
    Scientia Horticulturae 69 (1996). - ISSN 0304-4238 - p. 275 - 286.
    Molecular analysis of the tri-mutant alleles in tomato indicates the Tri locus is the gene encoding the apoprotein of phytochrome B1.
    Kerckhoffs, L.H.J. ; Tuinen, A. van; Hauser, B.A. ; Cordonnier-Pratt, M.M. ; Nagatani, A. ; Koornneef, M. ; Pratt, L.H. ; Kendrick, R.E. - \ 1996
    Planta 199 (1996). - ISSN 0032-0935 - p. 152 - 157.
    Analysis of phytochrome deficient yellow-green 2 and aurea mutants of tomato.
    Tuinen, A. van; Hanhart, C.J. ; Kerckhoffs, L.H.J. ; Nagatani, A. ; Boylan, M.T. ; Quail, P.H. ; Kendrick, R.E. ; Koornneef, M. - \ 1996
    The Plant Journal 9 (1996). - ISSN 0960-7412 - p. 173 - 182.
    Susceptibility of cultivated and wild barley (Hordeum vulgare sensu lato) to the leaf rust fungi of wheat and wall barley.
    Niks, R.E. ; Kerckhoffs, B.M.F.J. ; Rosa, R. de la - \ 1996
    Cereal Rusts and Powdery Mildews Bulletin 24 (1996). - p. 1 - 8.
    Physiological functions of phytochromes in tomato : a study using photomorphogenic mutants = [Fysiologische functies van fytochromen in tomaat : een studie gebruikmakend van fotomorfogenetische mutanten]
    Kerckhoffs, L.H.J. - \ 1996
    Agricultural University. Promotor(en): W.J. Vredenberg; R.E. Kendrick. - S.l. : Kerkchoffs - ISBN 9789054856276 - 195
    fytochroom - plantenpigmenten - fotosynthese - solanum lycopersicum - tomaten - genetische variatie - mutaties - phytochrome - plant pigments - photosynthesis - solanum lycopersicum - tomatoes - genetic variation - mutations

    Plant morphogenesis is influenced greatly by the irradiance, quality, direction and periodicity of the ambient light. At least three different photomorphogenic photoreceptors have been distinguished: (i) the red light (R)- and far-red light (FR)- absorbing phytochromes; (ii) the UV-A and blue light (B)-absorbing cryptochromes; and (iii) the UV-B photoreceptor. The phytochromes, which are the best characterized photosensory photoreceptors, are encoded by a small multigene family. In tomato (Lycopersicon esculentum Mill.) five phytochrome genes have been cloned: PHYA, PHYB1, PHYB2, PHYE and PHYF. In this thesis a genetic approach is used to assign functions to the different phytochrome types in tomato. Two classes of phytochrome mutants in tomato were analyzed both molecularly and physiologically: (i) phytochrome photoreceptor mutants: f ar- r ed light- i nsensitive (fri) mutants, deficient in phytochrome A (phyA); t emporarily r ed light- i nsensitive (tri) mutants, deficient in phytochrome B1 (phyB1) and a phytochrome chromophore biosynthesis mutant aurea (au); (ii) signal transduction chain mutants: h igh- p igment- 1(hp-1),h igh- p igment- 2(hp-2), a tro v iolacea (atv) and I ntensive p igmentation ( Ip ). In adult plant stages fri mutants are hardly phenotypically distinguishable from wild type (WT) in white light (WL). The phyB1 -deficient tri mutants are only insensitive during the first two days upon transition from darkness to R. The tri mutants are slightly taller than the WT when grown in WL. The kinetics of stem elongation rate of these mutants were determined very precisely using a custom-built plant growth-measuring apparatus as well as their response to vegetational shade light. The immature fruits of hp-1 and hp-2 mutants have higher chlorophyll levels and are darker-green in colour than WT. The signal transduction chain mutants all exhibit exaggerated phytochrome responses, i.e. high anthocyanin synthesis and short hypocotyl length compared to WT. Anthocyanin biosynthesis that accumulated during a 24-h period of different monochromatic irradiations was determined. At 660 nm the fluence rate-response relationships for induction of anthocyanin in WT are complex, showing a low fluence rate response (LFRR) and a fluence rate dependent high irradiance response (HIR), which have been attributed to phyA and phyB 1, respectively. The hp-1 mutant exhibits a strong amplification of both the LFRR and HIR. The atv mutant shows strongest amplification of the HIR component. The Ip mutant exhibits an exaggerated anthocyanin response in B. The results are discussed in relationship to the published work on photomorphogenesis.
    Parallel combined continuous and discrete simulation based on Time Warp.
    Kettenis, D.L. - \ 1996
    In: Proc. European Simulation Symp., San Diego: Simulation in Industry ESS96, Vol. 2, A.G. Bruzzone, E.J.H. Kerckhoffs (eds.). SCS Int., San Diego, USA - p. 369 - 373.
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