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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Genetic and molecular analysis of trichome development in Arabis alpina
Chopra, Divykriti ; Mapar, Mona ; Stephan, Lisa ; Albani, Maria C. ; Deneer, Anna ; Coupland, George ; Willing, Eva Maria ; Schellmann, Swen ; Schneeberger, Korbinian ; Fleck, Christian ; Schrader, Andrea ; Hülskamp, Martin - \ 2019
Proceedings of the National Academy of Sciences of the United States of America 116 (2019)24. - ISSN 0027-8424 - p. 12078 - 12083.
Arabis alpina - Genetic analysis - Trichomes

The genetic and molecular analysis of trichome development in Arabidopsis thaliana has generated a detailed knowledge about the underlying regulatory genes and networks. However, how rapidly these mechanisms diverge during evolution is unknown. To address this problem, we used an unbiased forward genetic approach to identify most genes involved in trichome development in the related crucifer species Arabis alpina. In general, we found most trichome mutant classes known in A. thaliana. We identified orthologous genes of the relevant A. thaliana genes by sequence similarity and synteny and sequenced candidate genes in the A. alpina mutants. While in most cases we found a highly similar gene-phenotype relationship as known from Arabidopsis, there were also striking differences in the regulation of trichome patterning, differentiation, and morphogenesis. Our analysis of trichome patterning suggests that the formation of two classes of trichomes is regulated differentially by the homeodomain transcription factor AaGL2. Moreover, we show that overexpression of the GL3 basic helix–loop–helix transcription factor in A. alpina leads to the opposite phenotype as described in A. thaliana. Mathematical modeling helps to explain how this nonintuitive behavior can be explained by different ratios of GL3 and GL1 in the two species.

Zoonotic chlamydia caviae presenting as community-acquired pneumonia
Ramakers, Bart P. ; Heijne, Marloes ; Lie, Natascha ; Le, Thuy Nga ; Vliet, Monique Van; Claessen, Vivian P.J. ; Tolsma, Paulien J.P. ; Rosa, Mauro De; Roest, Hendrik I.J. ; Vanrompay, Daisy ; Heddema, Edou R. ; Schneeberger, Peter ; Hermans, Mirjam H.A. - \ 2017
New England Journal of Medicine 377 (2017)10. - ISSN 0028-4793 - p. 992 - 993.
Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms
Zapata, Luis ; Ding, Jia ; Willing, Eva Maria ; Hartwig, Benjamin ; Bezdan, Daniela ; Jiao, Wen Biao ; Patel, Vipul ; James, Geo Velikkakam ; Koornneef, Maarten ; Ossowski, Stephan ; Schneeberger, Korbinian - \ 2016
Proceedings of the National Academy of Sciences of the United States of America 113 (2016)28. - ISSN 0027-8424 - p. E4052 - E4060.
Arabidopsis - De novo assembly - Gene absence/presence polymorphisms - Inversions - PacBio sequencing

Resequencing or reference-based assemblies reveal large parts of the small-scale sequence variation. However, they typically fail to separate such local variation into colinear and rearranged variation, because they usually do not recover the complement of large-scale rearrangements, including transpositions and inversions. Besides the availability of hundreds of genomes of diverse Arabidopsis thaliana accessions, there is so far only one full-length assembled genome: the reference sequence. We have assembled 117 Mb of the A. thaliana Landsberg erecta (Ler) genome into five chromosome-equivalent sequences using a combination of short Illumina reads, long PacBio reads, and linkage information. Whole-genome comparison against the reference sequence revealed 564 transpositions and 47 inversions comprising ∼3.6 Mb, in addition to 4.1 Mb of nonreference sequence, mostly originating from duplications. Although rearranged regions are not different in local divergence from colinear regions, they are drastically depleted for meiotic recombination in heterozygotes. Using a 1.2-Mb inversion as an example, we show that such rearrangement-mediated reduction of meiotic recombination can lead to genetically isolated haplotypes in the worldwide population of A. thaliana. Moreover, we found 105 single-copy genes, which were only present in the reference sequence or the Ler assembly, and 334 single-copy orthologs, which showed an additional copy in only one of the genomes. To our knowledge, this work gives first insights into the degree and type of variation, which will be revealed once complete assemblies will replace resequencing or other reference-dependent methods.

Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana
Fransz, Paul ; Linc, Gabriella ; Lee, Cheng Ruei ; Aflitos, Saulo Alves ; Lasky, Jesse R. ; Toomajian, Christopher ; Ali, Hoda ; Peters, Janny ; Dam, Peter van; Ji, Xianwen ; Kuzak, Mateusz ; Gerats, Tom ; Schubert, Ingo ; Schneeberger, Korbinian ; Colot, Vincent ; Martienssen, Rob ; Koornneef, Maarten ; Nordborg, Magnus ; Juenger, Thomas E. ; Jong, Hans de; Schranz, Eric - \ 2016
The Plant Journal 88 (2016)2. - ISSN 0960-7412 - p. 159 - 178.
Arabidopsis thaliana - Chromosome rearrangement - Haplotype pattern - Introgression - Phylogenetic relationship - Transposon

Chromosomal inversions can provide windows onto the cytogenetic, molecular, evolutionary and demographic histories of a species. Here we investigate a paracentric 1.17-Mb inversion on chromosome 4 of Arabidopsis thaliana with nucleotide precision of its borders. The inversion is created by Vandal transposon activity, splitting an F-box and relocating a pericentric heterochromatin segment in juxtaposition with euchromatin without affecting the epigenetic landscape. Examination of the RegMap panel and the 1001 Arabidopsis genomes revealed more than 170 inversion accessions in Europe and North America. The SNP patterns revealed historical recombinations from which we infer diverse haplotype patterns, ancient introgression events and phylogenetic relationships. We find a robust association between the inversion and fecundity under drought. We also find linkage disequilibrium between the inverted region and the early flowering Col-FRIGIDA allele. Finally, SNP analysis elucidates the origin of the inversion to South-Eastern Europe approximately 5000 years ago and the FRI-Col allele to North-West Europe, and reveals the spreading of a single haplotype to North America during the 17th to 19th century. The 'American haplotype' was identified from several European localities, potentially due to return migration.

Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
Willing, Eva Maria ; Rawat, Vimal ; Mandáková, Terezie ; Maumus, Florian ; James, Geo Velikkakam ; Nordström, Karl J.V. ; Becker, Claude ; Warthmann, Norman ; Chica, Claudia ; Szarzynska, Bogna ; Zytnicki, Matthias ; Albani, Maria C. ; Kiefer, Christiane ; Bergonzi, Sara ; Castaings, Loren ; Mateos, Julieta L. ; Berns, Markus C. ; Bujdoso, Nora ; Piofczyk, Thomas ; Lorenzo, Laura De; Barrero-Sicilia, Cristina ; Mateos, Isabel ; Piednoël, Mathieu ; Hagmann, Jörg ; Chen-Min-Tao, Romy ; Iglesias-Fernández, Raquel ; Schuster, Stephan C. ; Alonso-Blanco, Carlos ; Roudier, François ; Carbonero, Pilar ; Paz-Ares, Javier ; Davis, Seth J. ; Pecinka, Ales ; Quesneville, Hadi ; Colot, Vincent ; Lysak, Martin A. ; Weigel, Detlef ; Coupland, George ; Schneeberger, Korbinian - \ 2015
Nature Plants 1 (2015). - ISSN 2055-026X - 7 p.
Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 .Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.
T lymphocytes control microbial composition by regulating the abundance of Vibrio in the zebrafish gut
Brugman, S. ; Schneeberger, K. ; Witte, M. ; Klein, M.R. - \ 2014
Gut Microbes 5 (2014)6. - ISSN 1949-0976 - p. 737 - 747.
Dysbiosis of the intestinal microbial community is considered a risk factor for development of chronic intestinal inflammation as well as other diseases such as diabetes, obesity and even cancer. Study of the innate and adaptive immune pathways controlling bacterial colonization has however proven difficult in rodents, considering the extensive cross-talk between bacteria and innate and adaptive immunity. Here, we used the zebrafish to study innate and adaptive immune processes controlling the microbial community. Zebrafish lack a functional adaptive immune system in the first weeks of life, enabling study of the innate immune system in the absence of adaptive immunity. We show that in wild type zebrafish, the initial lack of adaptive immunity associates with overgrowth of Vibrio species (a group encompassing fish and human pathogens), which is overcome upon adaptive immune development. In Rag1-deficient zebrafish (lacking adaptive immunity) Vibrio abundance remains high, suggesting that adaptive immune processes indeed control Vibrio species. Using cell transfer experiments, we confirm that adoptive transfer of T lymphocytes, but not B lymphocytes into Rag1-deficient recipients suppresses outgrowth of Vibrio. In addition, ex vivo exposure of intestinal T lymphocytes to Rag1-deficient microbiota results in increased interferon-gamma expression by these T lymphocytes, compared to exposure to wild type microbiota. In conclusion, we show that T lymphocytes control microbial composition by effectively suppressing the outgrowth of Vibrio species in the zebrafish intestine.
Where do academic entrepreneurs locate their firms? How to access the development of entrepreneurship education at university level
Kolympiris, C. ; Kalaitzandonakes, N. ; Schneeberger, K. - \ 2014
In: Handbook on the Entrepreneurial University / Fayolle, A, Redford, D.T., Cheltenham, UK : Edward Elgar - ISBN 9781781007013 - p. 414 - 434.
The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana
Wijnker, T.G. ; Velikkakam James, G. ; Ding, J. ; Becker, F.F.M. ; Klasen, J.R. ; Rawat, V. ; Rowan, B.A. ; Jong, de, D.F. ; Snoo, de, C.B. ; Zapata, L. ; Jong, H. de; Ossowski, S. ; Weigel, D. ; Koornneef, M. ; Keurentjes, J.J.B. ; Schneeberger, K. - \ 2013
eLife 2 (2013). - ISSN 2050-084X
dna methylation - recombination landscape - saccharomyces-cerevisiae - short reads - yeast - meiosis - reveals - mouse - sex - populations
Knowledge of the exact distribution of meiotic crossovers (COs) and gene conversions (GCs) is essential for understanding many aspects of population genetics and evolution, from haplotype structure and long-distance genetic linkage to the generation of new allelic variants of genes. To this end, we resequenced the four products of 13 meiotic tetrads along with 10 doubled haploids derived from Arabidopsis thaliana hybrids. GC detection through short reads has previously been confounded by genomic rearrangements. Rigid filtering for misaligned reads allowed GC identification at high accuracy and revealed an ~80-kb transposition, which undergoes copy-number changes mediated by meiotic recombination. Non-crossover associated GCs were extremely rare most likely due to their short average length of ~25-50 bp, which is significantly shorter than the length of CO-associated GCs. Overall, recombination preferentially targeted non-methylated nucleosome-free regions at gene promoters, which showed significant enrichment of two sequence motifs.
Microcolony Imaging of Aspergillus fumigatus Treated with Echinocandins Reveals Both Fungistatic and Fungicidal Activities
Ingham, C.J. ; Schneeberger, P.M. - \ 2012
PLoS ONE 7 (2012)4. - ISSN 1932-6203
in-vitro - caspofungin - pharmacodynamics - microorganisms - antifungal - micafungin - culture - growth - chip
Background: The echinocandins are lipopeptides that can be employed as antifungal drugs that inhibit the synthesis of 1,3-beta-glucans within the fungal cell wall. Anidulafungin and caspofungin are echinocandins used in the treatment of Candida infections and have activity against other fungi including Aspergillus fumigatus. The echinocandins are generally considered fungistatic against Aspergillus species. Methods: Culture of A. fumigatus from conidia to microcolonies on a support of porous aluminium oxide (PAO), combined with fluorescence microscopy and scanning electron microscopy, was used to investigate the effects of anidulafungin and caspofungin. The PAO was an effective matrix for conidial germination and microcolony growth. Additionally, PAO supports could be moved between agar plates containing different concentrations of echinocandins to change dosage and to investigate the recovery of fungal microcolonies from these drugs. Culture on PAO combined with microscopy and image analysis permits quantitative studies on microcolony growth with the flexibility of adding or removing antifungal agents, dyes, fixatives or osmotic stresses during growth with minimal disturbance of fungal microcolonies. Significance: Anidulafungin and caspofungin reduced but did not halt growth at the microcony level; additionally both drugs killed individual cells, particularly at concentrations around the MIC. Intact but not lysed cells showed rapid recovery when the drugs were removed. The classification of these drugs as either fungistatic or fungicidal is simplistic. Microcolony analysis on PAO appears to be a valuable tool to investigate the action of antifungal agents.
Rapid Susceptibility Testing and Microcolony Analysis of Candida spp. Cultured and Imaged on Porous Aluminum Oxide
Ingham, C.J. ; Boonstra, S. ; Levels, S. ; Lange, H.J. ; Meis, J.F. ; Schneeberger, P.M. - \ 2012
PLoS ONE 7 (2012)3. - ISSN 1932-6203
antifungal drug-resistance - flow-cytometry - interpretive breakpoints - voriconazole - growth - fun-1 - microorganisms - fluconazole - albicans - support
Background: Acquired resistance to antifungal agents now supports the introduction of susceptibility testing for species-drug combinations for which this was previously thought unnecessary. For pathogenic yeasts, conventional phenotypic testing needs at least 24 h. Culture on a porous aluminum oxide (PAO) support combined with microscopy offers a route to more rapid results. Methods: Microcolonies of Candida species grown on PAO were stained with the fluorogenic dyes Fun-1 and Calcofluor White and then imaged by fluorescence microscopy. Images were captured by a charge-coupled device camera and processed by publicly available software. By this method, the growth of yeasts could be detected and quantified within 2 h. Microcolony imaging was then used to assess the susceptibility of the yeasts to amphotericin B, anidulafungin and caspofungin (3.5 h culture), and voriconazole and itraconazole (7 h culture). Significance: Overall, the results showed good agreement with EUCAST (86.5% agreement; n = 170) and E-test (85.9% agreement; n = 170). The closest agreement to standard tests was found when testing susceptibility to amphotericin B and echinocandins (88.2 to 91.2%) and the least good for the triazoles (79.4 to 82.4%). Furthermore, large datasets on population variation could be rapidly obtained. An analysis of microcolonies revealed subtle effects of antimycotics on resistant strains and below the MIC of sensitive strains, particularly an increase in population heterogeneity and cell density-dependent effects of triazoles. Additionally, the method could be adapted to strain identification via germ tube extension. We suggest PAO culture is a rapid and versatile method that may be usefully adapted to clinical mycology and has research applications.
Rapid antibiotic sensitivity testing and trimethoprim-mediated filamentation of clinical isolates of the Enterobacteriaceae assayed on a novel porous culture support
Ingham, C.J. ; Ende, M. van den; Wever, P.C. ; Schneeberger, P.M. - \ 2006
Journal of Medical Microbiology 55 (2006)11. - ISSN 0022-2615 - p. 1511 - 1519.
membrane filters - sos response - sulfadiazine - bacteria - anopore - growth - microorganisms - morphology - cloacae
A porous inorganic material (Anopore) was employed as a microbial culture and microcolony imaging support. Rapid Anopore-based antibiotic sensitivity testing (AST) methods were developed to assess the growth of clinical isolates, with the primary focus on testing the response of the Enterobacteriaceae to trimethoprim, but with the method supporting a wider applicability in terms of strains and antibiotics. It was possible to detect the growth of Enterobacter aerogenes after 25 min culture and to distinguish a trimethoprim-sensitive from a trimethoprim-resistant strain with 40 min incubation. MIC90 determinations were made on Anopore; these were in good agreement with the results from the Vitek 2 and E-test methods. The Anopore method correctly identified sensitive (40/40) and resistant (17/17) strains of the Enterobacteriaceae and other Gram-negative rods within only 2-3 h culture. Additionally, a trimethoprim-resistant subpopulation (10% of population) could be detected by microcolony formation within 2 h, and a smaller subpopulation (1%) after 3-5 h. These results suggest that this is a viable approach for the rapid AST of purified strains, and that it may be able to deal with mixed populations. The microscopic examination of microcolonies during AST is an advantage of this method which revealed additional information. Filamentation triggered by trimethoprim was discovered in many species of the Enterobacteriaceae for which this phenomenon has not previously been reported. Filamentation was characterized by heterogeneity in terms of cell length, and also uneven nucleic acid distribution and flattening of damaged cells. The development and application of Anopore-based AST within clinical diagnostics is discussed.
Growth and multiplexed analysis of microorganisms on a subdivided, highly porous, inorganic chip manufactured from anopore
Ingham, C.J. ; Ende, M. van den; Pijnenburg, D. ; Wever, P.C. ; Schneeberger, P.M. - \ 2005
Applied and Environmental Microbiology 71 (2005)12. - ISSN 0099-2240 - p. 8978 - 8981.
membrane filters - bacteria
A highly porous inorganic material (Anopore) was shown to be an effective support for culturing and imaging a wide range of microorganisms. An inert barrier grid was printed on the rigid surface of Anopore to create a "living chip" of 336 miniaturized compartments (200/cm2) with broad applications in microbial culture.
Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome.
Fouchier, R.A.M. ; Schneeberger, P.M. ; Rozendaal, F.W. ; Broekman, J.M. ; Kemink, S.A.G. ; Munnster, V. ; Kuiken, T. ; Rimmelzwaan, G.F. ; Schutten, M. ; Doornum, G.J.J. van; Koch, G. ; Bosman, A. ; Koopmans, M. ; Osterhaus, A.D.M.E. - \ 2004
Proceedings of the National Academy of Sciences of the United States of America 101 (2004)5. - ISSN 0027-8424 - p. 1356 - 1361.
h5n1 virus - hong-kong - hemagglutinin - infection - amplification - replication - diagnosis - emergence - sequence - assay
Highly pathogenic avian influenza A viruses of subtypes H5 and H7 are the causative agents of fowl plague in poultry. Influenza A viruses of subtype H5N1 also caused severe respiratory disease in humans in Hong Kong in 1997 and 2003, including at least seven fatal cases, posing a serious human pandemic threat. Between the end of February and the end of May 2003, a fowl plague outbreak occurred in The Netherlands. A highly pathogenic avian influenza A virus of subtype H7N7, closely related to low pathogenic virus isolates obtained from wild ducks, was isolated from chickens. The same virus was detected subsequently in 86 humans who handled affected poultry and in three of their family members. Of these 89 patients, 78 presented with conjunctivitis, 5 presented with conjunctivitis and influenza-like illness, 2 presented with influenza-like illness, and 4 did not fit the case definitions. Influenza-like illnesses were generally mild, but a fatal case of pneumonia in combination with acute respiratory distress syndrome occurred also. Most virus isolates obtained from humans, including probable secondary cases, had not accumulated significant mutations. However, the virus isolated from the fatal case displayed 14 amino acid substitutions, some of which may be associated with enhanced disease in this case. Because H7N7 viruses have caused disease in mammals, including horses, seals, and humans, on several occasions in the past, they may be unusual in their zoonotic potential and, thus, form a pandemic threat to humans
Sugar beet pulp silage as dietary fermentable carbohydrate source for group-housed sows : effects on physical activity and energy metabolism
Rijnen, M.M.J.A. ; Schrama, J.W. ; Heetkamp, M.J.W. ; Verstegen, M.W.A. ; Haaksma, J. - \ 1999
In: Book of abstracts of the 50th Annual Meeting of European Association for Animal Production / ed. J.A.M. van Arendonk, A. Hofer, Y. van der Honing, F. Madec, M. Bonneau,D. Pullar, M. Schneeberger, J. Fernandez and E.W. Bruns. - Wageningen : Wageningen Press, 1999 - p. 371 - 371.
Individual feed intake and performance of group-housed weanling pigs
Bruininx, E.M.A.M. ; Peet-Schwering, C.M.C. van der; Schrama, J.W. ; Hartog, L.A. den - \ 1999
In: Book of abstracts of the 50th Annual Meeting of the European Association for Animal Production (ed. J.A.M. van Arendonk, A. Hofer, Y. van der Honing, F. Madec, M. Bonneau, D. Pullar, M. Schneeberger, J. Fernandez and E.W. Bruns - p. 326 - 326.
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