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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Characterisation of biofilms formed by Lactobacillus plantarum WCFS1 and food spoilage isolates
Fernández Ramírez, M.D. ; Smid, E.J. ; Abee, T. ; Nierop Groot, M.N. - \ 2015
International Journal of Food Microbiology 207 (2015). - ISSN 0168-1605 - p. 23 - 29.
lactic-acid bacteria - enterococcal surface protein - listeria-monocytogenes - pseudomonas-putida - bacillus-subtilis - starter cultures - genetic-analysis - rhamnosus gg - resistance - industry
Lactobacillus plantarum has been associated with food spoilage in a wide range of products and the biofilm growth mode has been implicated as a possible source of contamination. In this study we analysed the biofilm forming capacity of L. plantarum WCFS1 and six food spoilage isolates. Biofilm formation as quantified by crystal violet staining and colony forming units was largely affected by the medium composition, growth temperature and maturation time and by strain specific features. All strains showed highest biofilm formation in Brain Heart Infusion medium supplemented with manganese and glucose. For L. plantarum biofilms the crystal violet (CV) assay, that is routinely used to quantify total biofilm formation, correlates poorly with the number of culturable cells in the biofilm. This can in part be explained by cell death and lysis resulting in CV stainable material, conceivably extracellular DNA (eDNA), contributing to the extracellular matrix. The strain to strain variation may in part be explained by differences in levels of eDNA, likely as result of differences in lysis behaviour. In line with this, biofilms of all strains tested, except for one spoilage isolate, were sensitive to DNase treatment. In addition, biofilms were highly sensitive to treatment with Proteinase K suggesting a role for proteins and/or proteinaceous material in surface colonisation. This study shows the impact of a range of environmental factors and enzyme treatments on biofilm formation capacity for selected L. plantarum isolates associated with food spoilage, and may provide clues for disinfection strategies in food industry.
Quantitative trait locus mapping for bruising sensitivity and cap color of Agaricus bisporus (button mushrooms)
Gao, W. ; Weijn, A. ; Baars, J.J.P. ; Mes, J.J. ; Visser, R.G.F. ; Sonnenberg, A.S.M. - \ 2015
Fungal Genetics and Biology 77 (2015). - ISSN 1087-1845 - p. 69 - 81.
melanin biosynthesis pathway - latent isoform ppo4 - pseudomonas-tolaasii - genetic-analysis - tyrosinase - purification - behavior - strains - genome
White button mushrooms discolor after mechanical damage of the cap skin. This hampers the development of a mechanical harvest system for the fresh market. To unravel the genetic basis for bruising sensitivity, two haploid populations (single spore cultures) were generated derived from crosses between parental lines differing in discoloration after mechanical damage (bruising sensitivity). The haploids were crossed with different homokaryotic tester lines to generate mushrooms and allow assessment of the bruising sensitivity in different genetic backgrounds. Bruising sensitivity appears to be a polygenic highly heritable trait (H2: 0.88-0.96) and a significant interaction between genotypes and tester lines and genotypes and flushes was found. Using SNP markers evenly spread over all chromosomes, a very low recombination was found between markers allowing only assignment of QTL for bruising sensitivity to chromosomes and not to sub-regions of chromosomes. The cap color of the two parental lines of population 1 is white and brown respectively. A major QTL for bruising sensitivity was assigned to chromosome 8 in population 1 that also harbors the main determinant for cap color (brown versus white). Splitting offspring in white and non-white mushrooms made minor QTL for bruising sensitivity on other chromosomes (e.g. 3 and 10) more prominent. The one on chromosome 10 explained 31% phenotypic variation of bruising sensitivity in flush 2 in the subpopulations of population 1. The two parental lines of population 2 are both white. Major QTL of bruising sensitivity were detected on chromosome 1 and 2, contributing totally more than 44% variation of the bruising sensitivity in flush 1 and 54% variation of that in flush 2. A considerable consistency was found in QTL for bruising sensitivity in the different populations studied across tester lines and flushes indicating that this study will provide a base for breeding cultivars that are less sensitive for bruising allowing the use of mechanical harvest and automatic postharvest handling for produce for the fresh market. The low recombination between homologous chromosomes, however, underlines the need to introduce a normal recombination pattern found in a subspecies of the button mushroom.
Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling
Wodke, J.A. ; Puchalka, J. ; Lluch-Senar, M. ; Marcos, J. ; Yus, E. ; Godinho, M. ; Gutierrez-Gallego, R. ; Martins Dos Santos, V.A.P. ; Serrano, L. ; Klipp, E. ; Maier, T. - \ 2013
Molecular Systems Biology 9 (2013). - ISSN 1744-4292 - 19 p.
cobra toolbox extension - flux balance models - escherichia-coli - reduced bacterium - biochemical networks - invivo measurement - bacillus-subtilis - optimal selection - genetic-analysis - membrane-lipids
Mycoplasma pneumoniae, a threatening pathogen with a minimal genome, is a model organism for bacterial systems biology for which substantial experimental information is available. With the goal of understanding the complex interactions underlying its metabolism, we analyzed and characterized the metabolic network of M. pneumoniae in great detail, integrating data from different omics analyses under a range of conditions into a constraint-based model backbone. Iterating model predictions, hypothesis generation, experimental testing, and model refinement, we accurately curated the network and quantitatively explored the energy metabolism. In contrast to other bacteria, M. pneumoniae uses most of its energy for maintenance tasks instead of growth. We show that in highly linear networks the prediction of flux distributions for different growth times allows analysis of time-dependent changes, albeit using a static model. By performing an in silico knock-out study as well as analyzing flux distributions in single and double mutant phenotypes, we demonstrated that the model accurately represents the metabolism of M. pneumoniae. The experimentally validated model provides a solid basis for understanding its metabolic regulatory mechanisms
Mapping quantitative trait loci for tissue culture response in VCS3M-DH population of Brassica rapa
Seo, M.S. ; Jin, M. ; Lee, S.S. ; Kwon, S.J. ; Mun, J.H. ; Park, B.S. ; Visser, R.G.F. ; Bonnema, A.B. ; Sohn, S.H. - \ 2013
Plant Cell Reports 32 (2013)8. - ISSN 0721-7714 - p. 1251 - 1261.
hordeum-vulgare l - shoot regeneration - cotyledonary explants - plant-regeneration - genetic-analysis - auxin receptor - ssp pekinensis - qtls - identification - rice
Quantitative trait loci (QTL) controlling callus induction and plant regeneration were identified in the VCS3M-DH population of Brassica rapa. The VCS3M-DH population showed wide and continuous variation in callus induction and shoot regeneration. Significant coefficient correlations were detected between these two parameters. Broad-sense heritability (h2) for the two traits was around 0.7, indicating genetic regulation of regeneration ability in this population. In the composite interval mapping analysis, two QTLs for callus induction ability, qCi2 and qCi7, were mapped on chromosome A02 and A07, explaining 28.6 % of phenotypic variation. For plant regeneration, four QTLs, qPr6-1 qPr6-2, qPr7, and qPr9 were identified on chromosome A06, A07, and A09, which in total explained 50.1 % of phenotypic variation. Furthermore, 15 putative candidate genes were found on the interval of the six QTLs, which were related to various plant hormones, MADS-box genes, and serine/threonine related genes. These results provide important information to identify genes related to tissue culture ability in B. rapa
Identification of quantitative trait loci for ion homeostasis and salt tolerance in barley (Hordeum vulgare L.)
Nguyen Viet Long, L. ; Ribot, S.A. ; Dolstra, O. ; Niks, R.E. ; Visser, R.G.F. ; Linden, C.G. van der - \ 2013
Molecular Breeding 31 (2013)1. - ISSN 1380-3743 - p. 137 - 152.
salinity tolerance - physiological traits - na+ exclusion - durum-wheat - seedling stage - k+/na+ discrimination - sodium transporter - genetic-analysis - stressed barley - major genes
Ion homeostasis is considered to be one of the most important mechanisms underlying salt stress tolerance. We used the Steptoe × Morex barley doubled haploid population to screen for genetic variation in response to salinity stress at an early development stage in a hydroponics system, focusing on ion homeostasis. Salinity induced a strong adverse effect on growth of the parents and their derived population, with Steptoe as the more tolerant parent. Steptoe maintained higher concentrations of K+, Na+ and Cl- in the roots and a similar shoot/root ion ratio (
Exploiting expressed sequence tag databases for mapping markers associated with fruit development and fruit quality in apple
Cova, V. ; Perini, D. ; Soglio, V. ; Komjanc, M. ; Weg, W.E. van de; Gessler, C. ; Gianfranceschi, L. - \ 2012
Molecular Breeding 29 (2012)3. - ISSN 1380-3743 - p. 699 - 715.
x-domestica borkh. - quantitative trait loci - malus-pumila mill. - tomato fruit - 1-aminocyclopropane-1-carboxylate synthase - ethylene production - molecular-biology - genetic-analysis - linkage maps - shelf-life
Apple (Malus x domestica Borkh.) is one of the most important fruit trees grown in Europe and around the world for human consumption, and therefore plant breeders aim at producing new apple varieties with high fruit quality. The availability of molecular markers suitable for marker-assisted selection could greatly increase the efficiency and power of breeding. The recent release of the cv. Golden Delicious genome sequence contributed to an exponential increase in the number of Malus sequences publicly available, while the successful achievement of two apple expressed sequence tag (EST) projects permitted the development of molecular markers from coding sequences. Here we present the setting up and mapping of new EST-based markers specific for fruit development and fruit quality traits. Since a large proportion of the ESTs used in our work were transcriptionally characterized and some of them co-localize within quantitative trait locus regions controlling fruit quality traits, the data reported will be effective in the identification of candidate genes. Due to the high level of polymorphism present in the Malus genome, 70% of the entire set of ESTs analyzed were polymorphic and 80% of them were successfully located using the conventional map-based approach. Fifty new EST-based markers were placed on the apple reference genetic map Fiesta x Discovery, thus enhancing the saturation of some regions, and 17 on Prima x Fiesta. Finally, another 17 markers were located on the Golden Delicious genome sequence using an in-silico approach.
Single-cell genomics: unravelling the genomes of unculturable microorganisms
Jager, V.C.L. de; Siezen, R.J. - \ 2011
Microbial Biotechnology 4 (2011)4. - ISSN 1751-7907 - p. 431 - 437.
genetic-analysis - marine sponges - flow-cytometry - amplification - heterogeneity - communities - polymerase
Tomato chlorotic mottle virus is a target of RNA silencing but the presence of specific short interfering RNAs does not guarantee resistance in transgenic plants
Ribeiro, S.G. ; Lohuis, H. ; Goldbach, R.W. ; Prins, M. - \ 2007
Journal of Virology 81 (2007)4. - ISSN 0022-538X - p. 1563 - 1573.
golden mosaic-virus - whitefly-transmitted geminiviruses - broad-spectrum resistance - curl-sardinia-virus - double-stranded-rna - dna virus - antisense rna - coat protein - genetic-analysis - replication
Tomato chlorotic mottle virus (ToCMoV) is a begomovirus found widespread in tomato fields in Brazil. ToCMoV isolate BA-Se1 (ToCMoV-[BA-Se1]) was shown to trigger the plant RNA silencing surveillance in different host plants and, coinciding with a decrease in viral DNA levels, small interfering RNAs (siRNAs) specific to ToCMoV-[BA-Se1] accumulated in infected plants. Although not homogeneously distributed, the siRNA population in both infected Nicotiana benthamiana and tomato plants represented the entire DNA-A and DNA-B genomes. We determined that in N. benthamiana, the primary targets corresponded to the 5' end of AC1 and the embedded AC4, the intergenic region and 5' end of AV1 and overlapping central part of AC5. Subsequently, transgenic N. benthamiana plants were generated that were preprogrammed to express double-stranded RNA corresponding to this most targeted portion of the virus genome by using an intron-hairpin construct. These plants were shown to indeed produce ToCMoV specific siRNAs. When challenge inoculated, most transgenic lines showed significant delays in symptom development, and two lines had immune plants. Interestingly, the levels of transgene- produced siRNAs were similar in resistant and susceptible siblings of the same line. This indicates that, in contrast to RNA viruses, the mere presence of transgene siRNAs corresponding to DNA virus sequences does not guarantee virus resistance and that other factors may play a role in determining RNA-mediated resistance to DNA viruses.
Quantitative assessment of phytopathogenic fungi in various substrates using a DNA macroarray
Lievens, B. ; Brouwer, M. ; Vanachter, A.C.R.C. ; Lévesque, C.A. ; Cammue, B.P.A. ; Thomma, B.P.H.J. - \ 2005
Environmental Microbiology 7 (2005)11. - ISSN 1462-2912 - p. 1698 - 1710.
dot-blot hybridization - real-time pcr - verticillium-dahliae - oligonucleotide array - genetic-analysis - rapid detection - amplified dna - identification - soil - pathogens
Detection, identification and quantification of plant pathogens are the cornerstones of preventive plant disease management. To detect multiple pathogens in a single assay, DNA array technology currently is the most suitable technique. However, for sensitive detection, polymerase chain reaction (PCR) amplification before array hybridization is required. To evaluate whether DNA array technology can be used to simultaneously detect and quantify multiple pathogens, a DNA macroarray was designed and optimized for accurate quantification over at least three orders of magnitude of the economically important vascular wilt pathogens Verticillium albo-atrum and Verticillium dahliae. A strong correlation was observed between hybridization signals and pathogen concentrations for standard DNA added to DNA from different origins and for infested samples. While accounting for specific criteria like amount of immobilized detector oligonucleotide and controls for PCR kinetics, accurate quantification of pathogens was achieved in concentration ranges typically encountered in horticultural practice. Subsequently, quantitative assessment of other tomato pathogens (Fusarium oxysporum, Fusarium solani, Pythium ultimum and Rhizoctonia solani) in environmental samples was performed using DNA array technology and correlated to measurements obtained using real-time PCR. As both methods of quantification showed a very high degree of correlation, the reliability and robustness of the DNA array technology is shown
Isolation of a fluffy mutant of Aspergillus niger from chemostat culture and its potential use as a morphologically stable host for protein production
Vondervoort, P.J.I. van de; Poulsen, B.R. ; Ruijter, G.J.G. ; Schuleit, T. ; Visser, J. ; Iversen, J.J.L. - \ 2004
Biotechnology and Bioengineering 86 (2004)3. - ISSN 0006-3592 - p. 301 - 307.
recombinant glucoamylase production - fusarium-graminearum a3/5 - penicillium-chrysogenum - genetic-analysis - argb gene - nidulans - transformation - growth - ph - fungus
Chemostat cultivation of Aspergillus niger and other filamentous fungi is often hindered by the spontaneous appearance of morphologic mutants. Using the Variomixing bioreactor and applying different chemostat conditions we tried to optimize morphologic stability in both ammonium- and glucose-limited cultures. In most cultivations mutants with fluffy (aconidial) morphology became dominant. From an ammonium-limited culture, a fluffy mutant was isolated and genetically characterized using the parasexual cycle. The mutant contained a single morphological mutation, causing an increased colony radial growth rate. The fluffy mutant was subjected to transformation and finally conidiospores from a forced heterokaryon were shown to be a proper inoculum for fluffy strain cultivation. (C) 2004 Wiley Periodicals, Inc.
Design and development of a DNA array for rapid detection and identification of tomato vascular wilt pathogens
Lievens, B. ; Brouwer, M. ; Vanachter, A.C.R.C. ; Lévesque, C.A. ; Cammue, B.P.A. ; Thomma, B.P.H.J. - \ 2003
FEMS Microbiology Letters 223 (2003)1. - ISSN 0378-1097 - p. 113 - 122.
verticillium-albo-atrum - dot-blot hybridization - f-sp lycopersici - nonpathogenic fusarium-oxysporum - biological-control - genetic-analysis - dahliae - microsclerotia - combination - resistance
Fusarium wilt, caused by Fusarium oxysporum f. sp. lycopersici, and Verticillium wilt, caused by either Verticillium albo-atrum or Verticillium dahliae, are devastating diseases of tomato (Lycopersicon esculentum) found worldwide. Monitoring is the cornerstone of integrated pest management of any disease. The lack of rapid, accurate, and reliable means by which plant pathogens can be detected and identified is one of the main limitations in integrated disease management. In this paper, we describe the development of a molecular detection system, based on DNA array technology, for rapid and efficient detection of these vascular wilt pathogens. We show the utility of this array for the sensitive detection of these pathogens from complex substrates like soil, plant tissues and irrigation water, and samples that are collected by tomato growers in their greenhouses.
Identification of epistatic interaction affecting glycoalkalid content in tubers of tetraploid potato (Solanum tuberosum L.)
Dam, J. van; Levin, I. ; Struik, P.C. ; Levy, D. - \ 2003
Euphytica 134 (2003)3. - ISSN 0014-2336 - p. 353 - 360.
marker-assisted selection - quantitative resistance - molecular markers - steroidal glycoalkaloids - nematode resistance - genetic-analysis - diploid potato - late blight - tomato - genome
Glycoalkaloids are secondary metabolites characterised by an undesirable taste, and known to be toxic when consumed in large quantities. Their content in potato tubers should therefore be selected against and DNA markers can significantly facilitate such a process. This study was designed to describe the genetic control of the total content of glycoalkaloids (TGA) in the potato tuber and to enhance the development of DNA markers. A segregating population was constructed from tetraploid potato clones, which were characterised by divergent TGA-content. The population had a high-TGA parent, LT7, and a low-TGA parent, NT8. We used 342 Inter-Simple Sequence Repeat (ISSR) single primers or two such primer combinations and 36 Cleaved Amplified Polymorphic Sequence (CAPS) primer pairs, digested with various restriction enzymes, to amplify random PCR products. Parental clones of both populations were used to identify polymorphic PCR products for further linkage analyses with TGA-content. In these analyses, one single ISSR marker was found to be significantly associated with TGA-content. A multiple regression analysis was also carried out using a 'stepwise' procedure. In this regression analysis TGA-content was the dependent variable whereas the polymorphic PCR products and all possible two-way interactions among them were the independent variables. The resulting best model consisted of an interaction between two loci in addition to a single locus effect. This interaction suggests that the expression of TGA-content is partially modulated by two interacting loci.
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