Staff Publications

Staff Publications

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    '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.

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Non-destructive detection of flawed hazelnut kernels and lipid oxidation assessment using NIR spectroscopy
Pannico, A. ; Schouten, R.E. ; Basile, B. ; Woltering, E.J. ; Cirillo, C. - \ 2015
Journal of Food Engineering 160 (2015). - ISSN 0260-8774 - p. 42 - 48.
corylus-avellana l. - fatty-acid-composition - near-infrared spectroscopy - reflectance spectroscopy - vis/nir spectroscopy - chemical-composition - quality - storage - fungal - seeds
Microbial contamination, seed browning, bad taste and lipid oxidation are primary causes of quality deterioration in stored hazelnuts, affecting their marketability. The feasibility of NIR spectroscopy to detect flawed kernels and estimate lipid oxidation in in-shell and shelled hazelnuts was investigated. ‘Mortarella’ hazelnuts were measured twice by NIR spectroscopy, first in-shell, and then as kernels. Afterwards, the kernels were evaluated visually, externally and internally, and by sensory evaluation with a subsequent measurement of fat oxidation. A satisfactory PLS model was created for the detection of flawed kernels. For lipid oxidation estimation the best performance of PLS models was obtained by first removing the flawed kernels from the calibration set. The PLS model for the K232 extinction coefficient, that is indicative of lipid primary oxidation, was able to predict K232 for both in-shell (R2 = 0.79) and shelled (R2 = 0.85) hazelnuts. Our results suggest, for shelled hazelnuts, a two-step NIR procedure: a first PLS model to detect and separate flawed kernels and then a second PLS model to grade healthy kernels by lipid oxidation levels.
Soil biodiversity and DNA barcodes: opportunities and challenges
Orgiazzi, A. ; Bonnet Dunbar, M. ; Panagos, P. ; Groot, G.A. de; Lemanceau, P. - \ 2015
Soil Biology and Biochemistry 80 (2015)1. - ISSN 0038-0717 - p. 244 - 250.
molecular microbial ecology - bacterial communities - ecosystem services - diversity - fungal - patterns - identification - assemblages - resilience - extraction
Soils encompass a huge diversity of organisms which mostly remains to be characterized due to a number of methodological and logistical issues. Nonetheless, remarkable progress has been made in recent years toward developing strategies to characterize and describe soil biodiversity, especially thanks to the development of molecular approaches relying on direct DNA extraction from the soil matrix.Metabarcoding can be applied to DNA from any environment or organism, and is gaining increasing prominence in biodiversity studies. This approach is already commonly used to characterize soil microbial communities and its application is now being extended to other soil organisms, i.e. meso- and macro-fauna.These developments offer unprecedented scientific and operational opportunities in order to better understand soil biodiversity distribution and dynamics, and to propose tools and strategies for biodiversity diagnosis. However, these opportunities also come with challenges that the scientific community must face. Such challenges are related to i) clarification of terminology, (ii) standardisation of methods and further methodological development for additional taxonomic groups, (iii) development of a common database, and (iv) ways to avoid waste of information and data derived from metabarcoding. In order to facilitate common application of metabarcoding in soil biodiversity assessment, we discuss these opportunities and challenges and propose solutions towards a more homogeneous framework.
Unravelling the microbiome of eggs of the endangered sea turtle Eretmochelys imbricata identifies bacteria with activity against the emerging pathogen Fusarium falciforme
Sarmiento-Ramírez, J.M. ; Voort, M. van der; Raaijmakers, J.M. ; Diéguez-Uribeondo, J. - \ 2014
PLoS ONE 9 (2014)4. - ISSN 1932-6203 - 8 p.
caretta-caretta - biological-control - gut microbiota - dna-sequences - costa-rica - streptomyces - diseases - community - fungal - health
Habitat bioaugmentation and introduction of protective microbiota have been proposed as potential conservation strategies to rescue endangered mammals and amphibians from emerging diseases. For both strategies, insight into the microbiomes of the endangered species and their habitats is essential. Here, we sampled nests of the endangered sea turtle species Eretmochelys imbricata that were infected with the fungal pathogen Fusarium falciforme. Metagenomic analysis of the bacterial communities associated with the shells of the sea turtle eggs revealed approximately 16,664 operational taxonomic units, with Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes as the most dominant phyla. Subsequent isolation of Actinobacteria from the eggshells led to the identification of several genera (Streptomyces, Amycolaptosis, Micromomospora Plantactinospora and Solwaraspora) that inhibit hyphal growth of the pathogen F. falciforme. These bacterial genera constitute a first set of microbial indicators to evaluate the potential role of microbiota in conservation of endangered sea turtle species.
Positive selection and intragenic recombination contribute to high allelic diversity in effector genes of Mycosphaerella fijiensis, causal agent of the black leaf streak disease of banana
Stergiopoulos, I. ; Cordovez da Cunha, V. ; Okmen, B. ; Beenen, H.G. ; Kema, G.H.J. ; Wit, P.J.G.M. de - \ 2014
Molecular Plant Pathology 15 (2014)5. - ISSN 1464-6722 - p. 447 - 460.
pathogen cladosporium-fulvum - phylogenetic analysis - musa-acuminata - cf-4-mediated resistance - population-genetics - maximum-likelihood - evolution - proteins - fungal - tomato
Previously, we have determined the nonhost-mediated recognition of the MfAvr4 and MfEcp2 effector proteins from the banana pathogen Mycosphaerella fijiensis in tomato, by the cognate Cf-4 and Cf-Ecp2 resistance proteins, respectively. These two resistance proteins could thus mediate resistance against M.¿fijiensis if genetically transformed into banana (Musa spp.). However, disease resistance controlled by single dominant genes can be overcome by mutated effector alleles, whose products are not recognized by the cognate resistance proteins. Here, we surveyed the allelic variation within the MfAvr4, MfEcp2, MfEcp2-2 and MfEcp2-3 effector genes of M.¿fijiensis in a global population of the pathogen, and assayed its impact on recognition by the tomato Cf-4 and Cf-Ecp2 resistance proteins, respectively. We identified a large number of polymorphisms that could reflect a co-evolutionary arms race between host and pathogen. The analysis of nucleotide substitution patterns suggests that both positive selection and intragenic recombination have shaped the evolution of M.¿fijiensis effectors. Clear differences in allelic diversity were observed between strains originating from South-East Asia relative to strains from other banana-producing continents, consistent with the hypothesis that M.¿fijiensis originated in the Asian-Pacific region. Furthermore, transient co-expression of the MfAvr4 effector alleles and the tomato Cf-4 resistance gene, as well as of MfEcp2, MfEcp2-2 and MfEcp2-3 and the putative Cf-Ecp2 resistance gene, indicated that effector alleles able to overcome these resistance genes are already present in natural populations of the pathogen, thus questioning the durability of resistance that can be provided by these genes in the field.
Effector diversification within compartments of the Leptosphaeria maculans genome affected by repeat induced point mutations
Rouxel, T. ; Grandaubert, J. ; Hane, J.K. ; Hoede, C. ; Wouw, A. ; Couloux, A. ; Dominguez, V. ; Anthouard, V. ; Bally, P. ; Bourras, S. ; Cozijnsen, A.J. ; Ciuffetti, L.M. ; Degrave, A. ; Dilmaghani, A. ; Duret, L. ; Fudal, L. ; Goodwin, S.B. ; Gout, L. ; Glaser, N. ; Linglin, J. ; Kema, G.H.J. ; Lapalu, N. ; Lawrence, C.B. ; May, K. ; Meyer, M. ; Ollivier, B. ; Poulain, J. ; Schoch, C.L. ; Simon, A. ; Spatafora, J.W. ; Stachowiak, A. ; Turgeon, B.G. ; Tyler, B.M. ; Vincent, D. ; Weissenbach, J. ; Amselem, J. ; Quesneville, H. ; Oliver, R.P. ; Wincker, P. ; Balesdent, M.H. ; Howlett, B.J. - \ 2011
Nature Communications 2 (2011). - ISSN 2041-1723 - p. 202 - 202.
transposable elements - molecular evolution - pathogen effectors - brassica-napus - gene-transfer - oilseed rape - stem canker - avirulence - plant - fungal
Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification. In this study, we report the genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans and characterize its repertoire of protein effectors. The L. maculans genome has an unusual bipartite structure with alternating distinct guanine and cytosine-equilibrated and adenine and thymine (AT)-rich blocks of homogenous nucleotide composition. The AT-rich blocks comprise one-third of the genome and contain effector genes and families of transposable elements, both of which are affected by repeat-induced point mutation, a fungal-specific genome defence mechanism. This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints
InIdentification and characterization of pathotypes in Puccinia horiana, a rust pathogen of Chrysanthemum x morifolium
Backer, M. de; Alaei, H. ; Bockstaele, E. van; Roldan-Ruiz, I. ; Lee, T. van der; Maes, M. ; Heungens, K. - \ 2011
European Journal of Plant Pathology 130 (2011)3. - ISSN 0929-1873 - p. 325 - 338.
white rust - flax rust - resistance - disease - fungal - henn - cultivars - effectors - genetics - wales
Puccinia horiana is the causal agent of chrysanthemum white rust or Japanese rust. This microcyclic autoecious rust has a quarantine status and can cause major damage in the commercial production of Chrysanthemum x morifolium. Given the international and often trans-continental production of planting material and cut flowers of chrysanthemum and the decreasing availability of registered fungicides in specific regions, breeding for resistance against P. horiana will gain importance and will need to involve the appropriate resistance genes for the pathotypes that may be present. As pathotypes have not been well characterized in this system, the main objective was to build an international collection of isolates and screen these on a large collection of cultivars to identify different pathotypes. Using a robust and high throughput bioassay, we tested 36 selected cultivars with 22 individual single-pustule isolates of P. horiana. The isolates originated from three different continents over 4 different collection years and included some isolates from cultivars previously reported as resistant. In most cases the bioassays resulted in a clear scoring of interaction phenotypes as susceptible or resistant, while in several cases consistent intermediate phenotypes were found, often on specific cultivars. Twenty-four of the cultivars gave a differential interaction phenotype profile. All isolates produced a unique profile, infecting a minimum of 4 and a maximum of 19 differential cultivars. Based on the Person analysis of these profiles, this pathosystem contains at least seven resistance genes (and seven avirulence genes), demonstrating the highly complex race structure in this pathosystem
Effects of ß-glucan from Agaricus bisporus on ex vivo cytokine production by LPS and PHA-stimulated PBMCs; a placebo-controlled study in slightly hypercholesterolimic subjects
Volman, J.J. ; Mensink, R.P. ; Griensven, L.J.L.D. van; Plat, J. - \ 2010
European Journal of Clinical Nutrition 64 (2010). - ISSN 0954-3007 - p. 720 - 726.
medicinal mushroom extracts - dendritic cells - monoclonal-antibodies - in-vitro - mice - antitumor - fungal - interferon - blazei - gamma
Introduction: Mushrooms are known for their immune modulating effect for which the polysaccharide fraction, mainly glucans, seem to be responsible. Fungal ß-glucans have been studied extensively, whereas little is known about mushroom a-glucans. We have earlier shown that the polysaccharide fraction from the mushroom A. bisporus, consisting 90% of a-glucans, induced in vitro tumor necrosis factor (TNF)a and nitric oxide production. The purpose of this study was to evaluate the effects of consuming. Method: A. bisporus a-glucan on ex vivo cytokine production by human peripheral mononuclear blood cells (PBMCs). A double-blind randomized trial was designed in which 56 mildly hypercholesterolemic subjects consumed a control fruit juice with no added a-glucans (200¿ml/day) for a 2-week run-in period. For the next 5 weeks, the control group (N=30) continued consumption of the control fruit juice, whereas the intervention group (N=26) consumed the same fruit juice enriched with a-glucans from A. bisporus (5¿g glucans/day). Changes in interleukin (IL)-1ß, IL-6 and TNFa cytokine production by lipopolysaccharide (LPS)-stimulated PBMCs were evaluated, as well as changes in T-helper (Th)1/Th2 cytokines by phytohemaggutinin (PHA)-stimulated PBMCs. Results: Consumption of A. bisporus a-glucans lower LPS-induced TNFa production by 69% (P=0.017) as compared with the control group, whereas no effect on IL-1ß and IL-6 was observed. No obvious Th1–Th2 skewing by PHA-stimulated PBMCs was observed. However, we observed a trend towards a decreased production of IL-12 and IL-10. Conclusion: Our current finding suggests that in vivo, a-glucans have lost their efficacy to stimulate the immune response as observed in our in vitro mouse model.
Effects of mushroom-derived ß-glucan rich polysaccharide extracts on nitric oxide production by bone marrow-derived macrophages and nuclear factor-kB transactivation in Caco-2 reporter cells: Can effects be explained by structure?
Volman, J.J. ; Helsper, J.P.F.G. ; Wei, S. ; Baars, J.J.P. ; Griensven, L.J.L.D. van; Sonnenberg, A.S.M. ; Mensink, R.P. ; Plat, J. - \ 2010
Molecular Nutrition & Food Research 54 (2010)2. - ISSN 1613-4125 - p. 268 - 276.
tumor-necrosis-factor - agaricus-blazei murill - in-vitro - liquid culture - fungal - cytokines - antitumor - immunity - dectin-1 - alpha
Mushrooms are known for their immune-modulating and anti-tumour properties. The polysaccharide fraction, mainly -glucans, is responsible for the immune-modulating effects. Fungal -glucans have been shown to activate leukocytes, which depend on structural characteristics of -glucans. As edible mushrooms come in contact with the intestinal immune system, effects on enterocytes are also interesting. Our aim was to evaluate the effect of mushroom polysaccharide extracts varying in -glucan structure on nitric oxide production by bone marrow-derived macrophages (BMMs) from mice and on nuclear factor-B transactivation in human intestinal Caco-2 cells. We demonstrated that extracts from Agaricus bisporus stimulated nitric oxide production by BMM, whereas extracts from Coprinus comatus and spores of Ganoderma lucidum had only minor effects. Furthermore, extracts of A. blazei Murill and Phellinus linteus had no effect at all. Almost all mushroom extracts lowered nuclear factor-B transactivation in Caco-2 cells. Structural analysis of A. bisporus compared with A. blazei Murill suggests that branching of the -glucan chain is essential for immune-stimulating activity. In conclusion, extracts from A. bisporus activate BMM, without activating enterocytes. These characteristics make A. bisporus an attractive candidate as a nutritional compound to stimulate the immune response in depressed states of immunity
Isolate specificity of quantitative trait loci for partial resistance of barley to Puccinia hordei confirmed in mapping populations and near-isogenic lines
Marcel, T.C. ; Gorguet, B.J.M. ; Truong Ta, M. ; Kohutova, Z. ; Vels, S.A. ; Niks, R.E. - \ 2008
New Phytologist 177 (2008)3. - ISSN 0028-646X - p. 743 - 755.
leaf rust resistance - polygenic resistance - disease resistance - gene rph7 - qtls - identification - fungal - plants - cultivars - pathogens
¿ Partial resistance is considered race-nonspecific and durable, consistent with the concept of `horizontal¿ resistance. However, detailed observations of partial resistance to leaf rust (Puccinia hordei) in barley (Hordeum vulgare) revealed small cultivar × isolate interactions, suggesting a minor-gene-for-minor-gene interaction model, similar to so-called `vertical¿ resistance. ¿ Three consistent quantitative trait loci (QTLs), labelled Rphq2, Rphq3 and Rphq4, that were detected in the cross susceptible L94 × partially resistant Vada have been incorporated into the L94 background to obtain near-isogenic lines (NILs). Three isolates were used to map QTLs on seedlings of the L94 × Vada population and to evaluate the effect of each QTL on adult plants of the respective NILs under field conditions. ¿ Rphq2 had a strong effect in seedlings but almost no effect in adult plants, while Rphq3 was effective in seedlings and in adult plants against all three isolates. However, Rphq4 was effective in seedlings and in adult plants against two isolates but ineffective in both development stages against the third, demonstrating a clear and reproducible isolate-specific effect. The resistance governed by the three QTLs was not associated with a hypersensitive reaction. ¿ Those results confirm the minor-gene-for-minor-gene model suggesting specific interactions between QTLs for partial resistance and P. hordei isolates.
Fusarium ear rot and how to screen for resistance in open pollinated maize in the Andean regions
Silva, E. ; Mora, E.A. ; Medina, A. ; Vasquez, J. ; Valdez, D. ; Danial, D.L. ; Parlevliet, J.E. - \ 2007
Euphytica 153 (2007)3. - ISSN 0014-2336 - p. 329 - 337.
graminearum infection - corn - moniliforme - genotype - colonization - fumonisins - mycotoxins - hybrids - fungal
Ears infected with ear rot were collected from five provinces in Ecuador. Of the 44 samples analysed 26 carried Fusarium verticillioides, 11 F. subglutinans, two F. graminearum and five carried fungi different from Fusarium. The pathogenicity of ten isolates, seven of F. verticillioides and three of F. subglutinans, were tested. Per isolate 30 ears of the susceptible cultivar Mishca were inoculated by pricking a steel pin, dipped into a spore suspension, through the husks in the central part of the ear 14 days after mid-silk. Ears inoculated with sterile water and ears without any treatment, natural infection, served as controls. The disease severity (DS) of the ears ranged from 14 to 58% ear rot, the range being similar for both species. The DS of the water control, 19%, was much higher than that of the natural control of 2%. Five strains gave a DS of over 40%, significantly higher than the water control. The DS of the others were similar to the water control. In a series of experiments the effect of various methods of applying Fusarium spores through the husks into young ears were compared. All tested methods resulted in DSs significantly higher than those of the two controls. Inoculation with tooth picks and steel pins dipped in a spore suspension gave similar ear rot percentages. Inoculations at 7 to 14 days after mid-silk produced the highest DS¿s. There was no significant effect of spore concentration on the DS. Cultivars differed considerably, the range being from around 20% to over 50%. Surprisingly, only wounding the husks, the sterile water control, resulted in a fairly high DS, much higher than that of the natural control. As the ranking order of the cultivars after wounding only and after inoculation did not seem to be different from the ranking order of the natural control it is suggested to use in areas with high inoculum pressures like the Andes only wounding by means of a steel pin for screening for resistance to maize ear rot.
Three QTLs for Botrytis cinerea resistance in tomato
Finkers, H.J. ; Berg, P.M.M.M. van den; Berloo, R. van; Have, A. ten; Heusden, A.W. van; Kan, J.A.L. van; Lindhout, P. - \ 2007
Theoretical and Applied Genetics 114 (2007)4. - ISSN 0040-5752 - p. 585 - 593.
recombinant inbred lines - lycopersicon-esculentum - linkage maps - backcross - hirsutum - phytoalexins - fungal - plants - aflp - populations
Tomato (Solanum lycopersicum) is susceptible to grey mold (Botrytis cinerea). Partial resistance to this fungus was identified in accessions of wild relatives of tomato such as S. habrochaites LYC4. In order to identify loci involved in quantitative resistance (QTLs) to B. cinerea, a population of 174 F2 plants was made originating from a cross between S. lycopersicum cv. Moneymaker and S. habrochaites LYC4. The population was genotyped and tested for susceptibility to grey mold using a stem bioassay. Rbcq1, a QTL reducing lesion growth (LG) and Rbcq2, a QTL reducing disease incidence (DI) were identified. Rbcq1 is located on Chromosome 1 and explained 12% of the total phenotypic variation while Rbcq2 is located on Chromosome 2 and explained 15% of the total phenotypic variation. Both QTL effects were confirmed by assessing disease resistance in two BC2S1 progenies segregating for either of the two QTLs. One additional QTL, Rbcq4 on Chromosome 4 reducing DI, was identified in one of the BC2S1 progenies. F2 individuals, homozygous for the Rbcq2 and Rbcq4 alleles of S. habrochaites showed a reduction of DI by 48%. QTLs from S. habrochaites LYC4 offer good perspectives for breeding B. cinerea resistant tomato cultivars.
Necrotizing activity of five Botrytis cinerea endopolygalacturonases produced in Pichia pastoris
Kars, I. ; Krooshof, G.H. ; Wagemakers, L. ; Joosten, R. ; Benen, J.A.E. ; Kan, J.A.L. van - \ 2005
The Plant Journal 43 (2005)2. - ISSN 0960-7412 - p. 213 - 225.
polygalacturonase-inhibiting proteins - site-directed mutagenesis - aspergillus-niger - cell-wall - sclerotinia-sclerotiorum - gene-expression - plant-pathogens - cutinase-a - fungal - tomato
Five Botrytis cinerea endopolygalacturonase enzymes (BcPGs) were individually expressed in Pichia pastoris, purified to homogeneity and biochemically characterized. While the pH optima of the five enzymes were similar (approximately pH 4.5) the maximum activity of individual enzymes differed significantly. For hydrolysis of polygalacturonic acid (PGA), the Vmax,app ranged from 10 to 900 U mg1, while the Km,app ranged from 0.16 to 0.6 mg ml1. Although all BcPGs are true endopolygalacturonases, they apparently have different modes of action. PGA hydrolysis by BcPG1, BcPG2 and BcPG4 leads to the transient accumulation of oligomers with DP <7, whereas PGA hydrolysis by BcPG3 and BcPG6 leads to the immediate accumulation of monomers and dimers. The necrotizing activity (NA) of all BcPGs was tested separately in tomato, broad bean and Arabidopsis thaliana. They showed different NAs on these plants. BcPG1 and BcPG2 possessed the strongest NA as tissue collapse was observed within 10 min after infiltration of broad bean leaves. The amino acid (aa) D192A substitution in the active site of BcPG2 not only abolished enzyme activity but also the NA, indicating that the NA is dependent on enzyme activity. Furthermore, deletion of the Bcpg2 gene in B. cinerea resulted in a strong reduction in virulence on tomato and broad bean. Primary lesion formation was delayed by approximately 24 h and the lesion expansion rate was reduced by 50¿85%. These data indicate that BcPG2 is an important virulence factor for B. cinerea
NSP1 of the GRAS protein family is essential for Rhizobial Nod factor-induced transcription
Smit, P. ; Raedts, J.G.J. ; Portyanko, V. ; Debellé, F. ; Gough, C. ; Bisseling, T. ; Geurts, R. - \ 2005
Science 308 (2005)5729. - ISSN 0036-8075 - p. 1789 - 1791.
receptor kinase gene - medicago-truncatula - bacterial - fungal - identification - transduction - symbiosis - mutants - calcium
Rhizobial Nod factors induce in their legume hosts the expression of many genes and set in motion developmental processes leading to root nodule formation. Here we report the identification of the Medicago GRAS-type protein Nodulation signaling pathway 1 (NSP1), which is essential for all known Nod factor–induced changes in gene expression. NSP1 is constitutively expressed, and so it acts as a primary transcriptional regulator mediating all known Nod factor–induced transcriptional responses, and therefore, we named it a Nod factor response factor.
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