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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    Tracing the ancestry of modern bread wheats
    Pont, Caroline ; Leroy, Thibault ; Seidel, Michael ; Tondelli, Alessandro ; Duchemin, Wandrille ; Armisen, David ; Lang, Daniel ; Bustos-Korts, Daniela ; Goué, Nadia ; Balfourier, François ; Molnár-Láng, Márta ; Lage, Jacob ; Kilian, Benjamin ; Özkan, Hakan ; Waite, Darren ; Dyer, Sarah ; Letellier, Thomas ; Alaux, Michael ; Russell, Joanne ; Keller, Beat ; Eeuwijk, Fred van; Spannagl, Manuel ; Mayer, Klaus F.X. ; Waugh, Robbie ; Stein, Nils ; Cattivelli, Luigi ; Haberer, Georg ; Charmet, Gilles ; Salse, Jérôme - \ 2019
    Nature Genetics 51 (2019)5. - ISSN 1061-4036 - p. 905 - 911.

    For more than 10,000 years, the selection of plant and animal traits that are better tailored for human use has shaped the development of civilizations. During this period, bread wheat (Triticum aestivum) emerged as one of the world’s most important crops. We use exome sequencing of a worldwide panel of almost 500 genotypes selected from across the geographical range of the wheat species complex to explore how 10,000 years of hybridization, selection, adaptation and plant breeding has shaped the genetic makeup of modern bread wheats. We observe considerable genetic variation at the genic, chromosomal and subgenomic levels, and use this information to decipher the likely origins of modern day wheats, the consequences of range expansion and the allelic variants selected since its domestication. Our data support a reconciled model of wheat evolution and provide novel avenues for future breeding improvement.

    Effects of temperature and food source on reproduction and longevity of aphid hyperparasitoids of the genera Dendrocerus and Asaphes
    Boer, Jetske G. de; Salis, Lucia ; Tollenaar, Ward ; Heumen, Lisa J.M. van; Costaz, Thibault P.M. ; Harvey, Jeffrey A. ; Kos, Martine ; Vet, Louise E.M. - \ 2019
    BioControl 64 (2019)3. - ISSN 1386-6141 - p. 277 - 290.
    Aphidius colemani - Fourth trophic level - Hymenoptera - Megaspilidae - Myzus persicae - Pteromalidae

    Hyperparasitoids of aphid parasitoids commonly occur in (sweet pepper) greenhouses, and can pose a threat to effective biological control of aphids. Here, we studied life history characteristics of laboratory colonies of Dendrocerus spp. Ratzeburg (Hymenoptera: Megaspilidae) and Asaphes spp. Walker (Pteromalidae) that originated from a commercial sweet pepper greenhouse. We aimed to clarify how these two hyperparasitoid taxa can coexist inside greenhouses. Hyperparasitoids of both taxa have a long lifespan that was extended significantly by food sources that are naturally available in a greenhouse environment, including aphid honeydew and sweet pepper flowers. Differences in sensitivity to decreased or increased temperatures did not appear to explain seasonal patterns in abundance of Dendrocerus spp. and Asaphes spp. in sweet pepper greenhouses. Instead, Dendrocerus spp. may have an advantage early in the season because it thrives on aphid honeydew, while Asaphes spp. may do better later in the season because of its long lifespan and extensive reproductive period.

    Determination of total dissolved nitrogen in seawater by isotope dilution gas chromatography mass spectrometry following digestion with persulfate and derivatization with aqueous triethyloxonium
    Pagliano, Enea ; Campanella, Beatrice ; Shi, Lisa ; Thibault, Marie-Pier ; Onor, Massimo ; Crum, S.J.H. ; Melanson, Jeremy E. ; Mester, Zoltán - \ 2018
    Journal of Chromatography. A, Including electrophoresis and other separation methods 1569 (2018). - ISSN 0021-9673 - p. 193 - 199.
    Total dissolved nitrogen, Seawater, Isotope dilution, Gas chromatography mass spectrometry, Persulfate, Triethyloxonium derivatization
    In this study, we propose a novel approach for the determination of total dissolved nitrogen (TDN) in seawater combining high-precision isotope dilution GC–MS with persulfate digestion. A 2 mL sample aliquot was digested with an alkaline solution of persulfate to convert nitrogen containing compounds to nitrate. Digested samples were spiked with 15NO3−internal standard and treated with aqueous tri-ethyloxonium to convert the analyte into volatile EtONO2. This derivative was readily separated from the matrix under gaseous form and could be sampled from the headspace before GC–MS analysis. The resulting chromatograms showed a stable flat baseline with EtONO2 as the only eluting peak (retention time 2.75 min on a DB 5.625 column). Such an approach provides specificity and obviates the shortcomings of current detection methods employed to analyze seawater samples after digestion with persulfate. In negative chemical ionization mode, the method reached a detection limit of 0.5 µmol/kg TDN (7 ng/gN) and could be applied to quantify seawater samples with 1–25 µmol/kg TDN. On the upper end of the range, quantitation could be repeated within 1%, whereas on a 6 µmol/kg TDN sample repeatability was 2.3% on eight measurements. The method was employed in two proficiency testing exercises providing results in agreement with consensus values. We investigated the impact of reagent blank and we implemented a blank-matching optimal design to account for such contribution. Finally, we performed a study on the yield of persulfate oxidation for organic and inorganic nitrogen compounds typically present in seawater. Whilst nitrite and ammonium are fully converted to nitrate, more complex organic molecules showed recoveries varying from 70% to 100%.
    Biomonitoring of intermittent rivers and ephemeral streams in Europe : Current practice and priorities to enhance ecological status assessments
    Stubbington, Rachel ; Chadd, Richard ; Cid, Núria ; Csabai, Zoltán ; Miliša, Marko ; Morais, Manuela ; Munné, Antoni ; Pařil, Petr ; Pešić, Vladimir ; Tziortzis, Iakovos ; Verdonschot, Ralf C.M. ; Datry, Thibault - \ 2018
    Science of the Total Environment 618 (2018). - ISSN 0048-9697 - p. 1096 - 1113.
    Bioassessment - Bioindicators - River typology - Temporary rivers - Temporary streams - Water Framework Directive
    Intermittent rivers and ephemeral streams (IRES) are common across Europe and dominate some Mediterranean river networks. In all climate zones, IRES support high biodiversity and provide ecosystem services. As dynamic ecosystems that transition between flowing, pool, and dry states, IRES are typically poorly represented in biomonitoring programmes implemented to characterize EU Water Framework Directive ecological status. We report the results of a survey completed by representatives from 20 European countries to identify current challenges to IRES status assessment, examples of best practice, and priorities for future research. We identify five major barriers to effective ecological status classification in IRES: 1. the exclusion of IRES from Water Framework Directive biomonitoring based on their small catchment size; 2. the lack of river typologies that distinguish between contrasting IRES; 3. difficulties in defining the 'reference conditions' that represent unimpacted dynamic ecosystems; 4. classification of IRES ecological status based on lotic communities sampled using methods developed for perennial rivers; and 5. a reliance on taxonomic characterization of local communities. Despite these challenges, we recognize examples of innovative practice that can inform modification of current biomonitoring activity to promote effective IRES status classification. Priorities for future research include reconceptualization of the reference condition approach to accommodate spatiotemporal fluctuations in community composition, and modification of indices of ecosystem health to recognize both taxon-specific sensitivities to intermittence and dispersal abilities, within a landscape context.
    Cyanodermella asteris sp. nov. (Ostropales) from the inflorescence axis of Aster tataricus
    Jahn, Linda ; Schafhauser, Thomas ; Pan, Stefan ; Weber, Tilmann ; Wohlleben, Wolfgang ; Fewer, David P. ; Sivonen, Kaarina ; Flor, Liane ; Pée, Karl Heinz van; Caradec, Thibault ; Jacques, Philippe ; Huijbers, Mieke M.E. ; Berkel, Willem J.H. van; Ludwig-Müller, Jutta - \ 2017
    Mycotaxon 132 (2017)1. - ISSN 0093-4666 - p. 107 - 123.
    Ascomycota - Asteraceae - Lecanoromycetes - Pezizomycotina

    An endophytic fungus isolated from the inflorescence axis of Aster tataricus is proposed as a new species. Phylogenetic analyses based on sequences from the ribosomal DNA cluster (the ITS1+5.8S+ITS2, 18S, and 28S regions) and the RPB2 gene revealed a relationship between the unknown fungus and the Stictidaceae lineage of the Ostropales. The new species, Cyanodermella asteris, grows in standard fungal growth media as a fluffy, pink filamentous fungus. Asexual and sexual sporulation has not yet been observed on media or in the plant.

    The cyclochlorotine mycotoxin is produced by the nonribosomal peptide synthetase CctN in Talaromyces islandicus ('Penicillium islandicum')
    Schafhauser, Thomas ; Kirchner, Norbert ; Kulik, Andreas ; Huijbers, Mieke M.E. ; Flor, Liane ; Caradec, Thibault ; Fewer, David P. ; Gross, Harald ; Jacques, Philippe ; Jahn, Linda ; Jokela, Jouni ; Leclère, Valérie ; Ludwig-Müller, Jutta ; Sivonen, Kaarina ; Berkel, Willem J.H. van; Weber, Tilmann ; Wohlleben, Wolfgang ; Pée, Karl Heinz van - \ 2016
    Environmental Microbiology 18 (2016)11. - ISSN 1462-2912 - p. 3728 - 3741.

    Talaromyces islandicus ('Penicillium islandicum') is a widespread foodborne mold that produces numerous secondary metabolites, among them potent mycotoxins belonging to different chemical classes. A notable metabolite is the hepatotoxic and carcinogenic pentapeptide cyclochlorotine that contains the unusual amino acids β-phenylalanine, 2-aminobutyrate and 3,4-dichloroproline. Although the chemical structure has been known for over five decades, nothing is known about the biosynthetic pathway of cyclochlorotine. Bioinformatic analysis of the recently sequenced genome of T. islandicus identified a wealth of gene clusters potentially coding for the synthesis of secondary metabolites. Here, we show by RNA interference-mediated gene silencing that a nonribosomal peptide synthetase, CctN, is responsible for the synthesis of cyclochlorotine. Moreover, we identified novel cyclochlorotine chemical variants, whose production also depended on cctN expression. Surprisingly, the halogenase required for cyclochlorotine biosynthesis is not encoded in the cct cluster. Nonetheless, our findings enabled us to propose a detailed model for cyclochlorotine biosynthesis. In addition, comparative genomics revealed that cct-like clusters are present in all of the sequenced Talaromyces strains indicating a high prevalence of cyclochlorotine production ability.

    Speciation analysis of aqueous nanoparticulate diclofenac complexes by solid-phase microextraction
    Zielinska, K. ; Leeuwen, H.P. van; Thibault, S. ; Town, R.M. - \ 2012
    Langmuir 28 (2012)41. - ISSN 0743-7463 - p. 14672 - 14680.
    bovine serum-albumin - walled carbon nanotubes - drug binding-sites - capillary-electrophoresis - aquatic environment - antiinflammatory drugs - mass-spectrometry - metal-complexes - water samples - nd-spme
    The dynamic sorption of an organic compound by nanoparticles (NPs) is analyzed by solid-phase microextraction (SPME) for the example case of the pharmaceutical diclofenac in dispersions of impermeable (silica, SiO(2)) and permeable (bovine serum albumin, BSA) NPs. It is shown that only the protonated neutral form of diclofenac is accumulated in the solid phase, and hence this species governs the eventual partition equilibrium. On the other hand, the rate of the solid/water partition equilibration is enhanced in the presence of the sorbing nanoparticles of SiO(2) and BSA. This feature demonstrates that the NPs themselves do not enter the solid phase to any appreciable extent. The enhanced rate of attainment of equilibrium is due to a shuttle-type of contribution from the NP-species to the diffusive supply of diclofenac to the water/solid interface. For both types of nanoparticulate complexes, the rate constant for desorption (k(des)) of bound diclofenac was derived from the measured thermodynamic affinity constant and a diffusion-limited rate of adsorption. The computed k(des) values were found to be sufficiently high to render the NP-bound species labile on the effective time scale of SPME. In agreement with theoretical prediction, the experimental results are quantitatively described by fully labile behavior of the diclofenac/nanoparticle system and an ensuing accumulation rate controlled by the coupled diffusion of neutral, deprotonated, and NP-bound diclofenac species.
    Occurrence of Mycobacterium avium subspecies paratuberculosis across host species and European countries with evidence for transmission between wildlife and domestic ruminants
    Stevenson, K. ; Alvarez, J. ; Bakker, D. ; Biet, F. ; Juan, L. de; Denham, S. ; Dimareli, Z. ; Dohmann, K. ; Gerlach, G.F. ; Heron, I. ; Kopecna, M. ; May, L. ; Pavlik, I. ; Sharp, J.M. ; Thibault, V.C. ; Willemsen, P. ; Zadoks, R.N. ; Greig, A. - \ 2009
    BMC Microbiology 9 (2009). - ISSN 1471-2180 - 13 p.
    fragment-length-polymorphism - genetic diversity - s-strain - molecular characterization - sequence polymorphisms - culture-media - infection - cattle - is900 - rabbits
    Background: Mycobacterium avium subspecies paratuberculosis (Map) causes an infectious chronic enteritis (paratuberculosis or Johne's disease) principally of ruminants. The epidemiology of Map is poorly understood, particularly with respect to the role of wildlife reservoirs and the controversial issue of zoonotic potential (Crohn's disease). Genotypic discrimination of Map isolates is pivotal to descriptive epidemiology and resolving these issues. This study was undertaken to determine the genetic diversity of Map, enhance our understanding of the host range and distribution and assess the potential for interspecies transmission. Results: 164 Map isolates from seven European countries representing 19 different host species were genotyped by standardized IS900 - restriction fragment length polymorphism (IS900-RFLP), pulsed-field gel electrophoresis (PFGE), amplified fragment length polymorphisms (AFLP) and mycobacterial interspersed repeat unit-variable number tandem repeat (MIRU-VNTR) analyses. Six PstI and 17 BstEII IS900-RFLP, 31 multiplex [SnaBI-SpeI] PFGE profiles and 23 MIRU-VNTR profiles were detected. AFLP gave insufficient discrimination of isolates for meaningful genetic analysis. Point estimates for Simpson's index of diversity calculated for the individual typing techniques were in the range of 0.636 to 0.664 but a combination of all three methods increased the discriminating power to 0.879, sufficient for investigating transmission dynamics. Two predominant strain types were detected across Europe with all three typing techniques. Evidence for interspecies transmission between wildlife and domestic ruminants on the same property was demonstrated in four cases, between wildlife species on the same property in two cases and between different species of domestic livestock on one property. Conclusion: The results of this study showed that it is necessary to use multiple genotyping techniques targeting different sources of genetic variation to obtain the level of discrimination necessary to investigate transmission dynamics and trace the source of Map infections. Furthermore, the combination of genotyping techniques may depend on the geographical location of the population to be tested. Identical genotypes were obtained from Map isolated from different host species co-habiting on the same property strongly suggesting that interspecies transmission occurs. Interspecies transmission of Map between wildlife species and domestic livestock on the same property provides further evidence to support a role for wildlife reservoirs of infection
    A xylogalacturonan epitope is specifically associated with plant cell detachment.
    Willats, W.G.T. ; McCartney, L. ; Steele-King, C.G. ; Marcus, S.E. ; Mort, A.J. ; Huisman, M.M.H. ; Alebeek, G.J.W.M. van; Schols, H.A. ; Voragen, A.G.J. ; Goff, A. le; Bonnin, E. ; Thibault, J.F. ; Knox, J.P. - \ 2004
    Planta 218 (2004)4. - ISSN 0032-0935 - p. 673 - 681.
    pectic polysaccharides - spatial regulation - hairy regions - pea hulls - walls - homogalacturonan - tomato - cotyledons - separation - pericarp
    A monoclonal antibody (LM8) was generated with specificity for xyloglacturonan (XGA) isolated from pea (Pisum sativum L.) testae. Characterization of the LM8 epitope indicates that it is a region of XGA that is highly substituted with xylose. Immunocytochemical analysis indicates that this epitope is restricted to loosely attached inner parenchyma cells at the inner face of the pea testa and does not occur in other cells of the testa. Elsewhere in the pea seedling, the LM8 epitope was found only in association with root cap cell development at the root apex. Furthermore, the LM8 epitope is specifically associated with root cap cells in a range of angiosperm species. In embryogenic carrot suspension cell cultures the epitope is abundant at the surface of cell walls of loosely attached cells in both induced and non-induced cultures. The LM8 epitope is the first cell wall epitope to be identified that is specifically associated with a plant cell separation process that results in complete cell detachment.
    Mode of action of Fusarium moniliforme endopolygalacturonase towards acetylated pectin.
    Bonnin, E. ; Alebeek, G.J.W.M. van; Voragen, A.G.J. ; Thibault, J.F. - \ 2003
    Carbohydrate Polymers 52 (2003). - ISSN 0144-8617 - p. 381 - 388.
    aspergillus-niger - endo-polygalacturonase - methylation - acid - degradation - hydrolysis
    Endopolygalacturonase from Fusarium moniliforme was used to degrade acetylated homogalacturonan previously prepared from sugar beet pulp. The initial velocity and the final percentage of hydrolysis decreased-very rapidly with increasing degree of acetylation, showing that acetyl substitution markedly affected the enzymatic activity. MALDI-TOF mass spectrometry was used to analyse the reaction products and to show acetyl groups on the oligogalacturonates. The results demonstrated that the enzyme was able to accommodate acetyl groups in its active site cleft. The influence of acetyl groups on the mode of action of the enzyme was discussed and compared to the influence of methyl groups. (C) 2003 Elsevier Science Ltd. All rights reserved.
    Isolation and structural characterisation of rhamnogalacturonan oligomers generated by controlled acid hydrolysis of sugar-beet pulp.
    Renard, C.M.G.C. ; Lahaye, M. ; Mutter, M. ; Voragen, A.G.J. ; Thibault, J.F. - \ 1998
    Carbohydrate Research : an international journal 305 (1998). - ISSN 0008-6215 - p. 271 - 280.
    Some preliminary results on the action of rhamnogalacturonase on rhamnogalacturonan oligosaccharides from beet pulp.
    Renard, C.M.G.C. ; Thibault, J.F. ; Mutter, M. ; Schols, H.A. ; Voragen, A.G.J. - \ 1995
    International Journal of Biological Macromolecules 17 (1995). - ISSN 0141-8130 - p. 333 - 336.
    10 Pectins.
    Voragen, A.G.J. ; Pilnik, W. ; Thibault, J.F. ; Axelos, M.A.V. ; Renard, C.M.G.C. - \ 1995
    In: Food polysaccharides and their applications / Stephen, A.M., - p. 287 - 339.
    Studies on apple protopectin 6: extraction of pectins from apple cell walls with rhamno-galacturonase.
    Renard, C.M.G.C. ; Thibault, J.F. ; Voragen, A.G.J. ; Broek, L.A.M. van den; Pilnik, W. - \ 1993
    Carbohydrate Polymers 22 (1993). - ISSN 0144-8617 - p. 203 - 210.
    Chapter 7. Gelation of sugar beet pectin by oxidative coupling.
    Thibault, J.F. ; Guillon, F. ; Rombouts, F.M. - \ 1991
    In: The chemistry and technology of pectin / Walter, R.H., San Diego : Academic Press Inc. - p. 119 - 133.
    Studies on apple protopectin. 5. Structural studies on enzymatically extracted pectins.
    Renard, C.M.G.C. ; Voragen, A.G.J. ; Thibault, J.F. ; Pilnik, W. - \ 1991
    Carbohydrate Polymers 16 (1991). - ISSN 0144-8617 - p. 137 - 154.
    Studies on apple protopectin. 4. Apple xyloglucans and influence of pectin extraction treatments on their solubility.
    Renard, C.M.G.C. ; Voragen, A.G.J. ; Thibault, J.F. ; Pilnik, W. - \ 1991
    Carbohydrate Polymers 15 (1991). - ISSN 0144-8617 - p. 387 - 403.
    Studies on apple protopectin. 3. Characterization of the material extracted by pure polysaccharidases from apple cell walls.
    Renard, C.M.G.C. ; Schols, H.A. ; Voragen, A.G.J. ; Thibault, J.F. ; Pilnik, W. - \ 1991
    Carbohydrate Polymers 15 (1991). - ISSN 0144-8617 - p. 13 - 32.
    Comparison between enzymatically and chemically extracted pectins from apple cell walls.
    Renard, C.M.G.C. ; Voragen, A.G.J. ; Thibault, J.F. ; Pilnik, W. - \ 1991
    Animal Feed Science and Technology 32 (1991). - ISSN 0377-8401 - p. 69 - 75.
    Studies on apple protopectin. 2. Apple cell wall degradation by pure polysaccharides and their combinations.
    Renard, C.M.G.C. ; Searle-van Leeuwen, M.J.F. ; Voragen, A.G.J. ; Thibault, J.F. ; Pilnik, W. - \ 1991
    Carbohydrate Polymers 14 (1991). - ISSN 0144-8617 - p. 295 - 314.
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