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.

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Soil protistology rebooted: 30 fundamental questions to start with
Geisen, Stefan ; Mitchell, Edward A.D. ; Wilkinson, David M. ; Adl, Sina ; Bonkowski, Michael ; Brown, Matthew W. ; Fiore-Donno, Anna Maria ; Heger, Thierry J. ; Jassey, Vincent E.J. ; Krashevska, Valentyna ; Lahr, Daniel J.G. ; Marcisz, Katarzyna ; Mulot, Matthieu ; Payne, Richard ; Singer, David ; Anderson, O.R. ; Charman, Dan J. ; Ekelund, Flemming ; Griffiths, Bryan S. ; Rønn, Regin ; Smirnov, Alexey ; Bass, David ; Belbahri, Lassaâd ; Berney, Cédric ; Blandenier, Quentin ; Chatzinotas, Antonis ; Clarholm, Marianne ; Dunthorn, Micah ; Feest, Alan ; Fernández, Leonardo D. ; Foissner, Wilhelm ; Fournier, Bertrand ; Gentekaki, Eleni ; Hájek, Michal ; Helder, Hans ; Jousset, Alexandre ; Koller, Robert ; Kumar, Santosh ; Terza, Antonietta La; Lamentowicz, Mariusz ; Mazei, Yuri ; Santos, Susana S. ; Seppey, Christophe V.W. ; Spiegel, Frederick W. ; Walochnik, Julia ; Winding, Anne ; Lara, Enrique - \ 2017
Soil Biology and Biochemistry 111 (2017). - ISSN 0038-0717 - p. 94 - 103.
Protists are the most diverse eukaryotes. These microbes are keystone organisms of soil ecosystems and
regulate essential processes of soil fertility such as nutrient cycling and plant growth. Despite this,
protists have received little scientific attention, especially compared to bacteria, fungi and nematodes in
soil studies. Recent methodological advances, particularly in molecular biology techniques, have made
the study of soil protists more accessible, and have created a resurgence of interest in soil protistology.
This ongoing revolution now enables comprehensive investigations of the structure and functioning of
soil protist communities, paving the way to a new era in soil biology. Instead of providing an exhaustive
review, we provide a synthesis of research gaps that should be prioritized in future studies of soil
protistology to guide this rapidly developing research area. Based on a synthesis of expert opinion we
propose 30 key questions covering a broad range of topics including evolution, phylogenetics, functional
ecology, macroecology, paleoecology, and methodologies. These questions highlight a diversity of topics
that will establish soil protistology as a hub discipline connecting different fundamental and applied
fields such as ecology, biogeography, evolution, plant-microbe interactions, agronomy, and conservation
biology. We are convinced that soil protistology has the potential to be one of the most exciting frontiers
in biology.
Comment on "critical wind speed at which trees break"
Albrecht, Axel ; Badel, Eric ; Bonnesoeur, Vivien ; Brunet, Yves ; Constant, Thiéry ; Défossez, Pauline ; Langre, Emmanuel De; Dupont, Sylvain ; Fournier, Meriem ; Gardiner, Barry ; Schelhaas, Mart Jan - \ 2016
Physical Review. E, Statistical nonlinear, and soft matter physics 94 (2016)6. - ISSN 2470-0045

Virot et al. [E. Virot, Phys. Rev. E 93, 023001 (2016)10.1103/PhysRevE.93.023001] assert that the critical wind speed at which ≥50% of all trees in a population break is ≈42 m/s, regardless of tree characteristics. We show that empirical data do not support this assertion, and that the assumptions underlying the theory used by Virot et al. are inconsistent with the biomechanics of trees.

Remodeling of the infection chamber before infection thread formation reveals a two-step mechanism for rhizobial entry into the host legume root hair
Fournier, J. ; Teillet, A. ; Chabaud, M. ; Ivanov, S. ; Genre, A. ; Limpens, E.H.M. ; Carvalho-Niebel, F. de; Barker, D.G. - \ 2015
Plant Physiology 167 (2015)4. - ISSN 0032-0889 - p. 1233 - 1242.
In many legumes, root entry of symbiotic nitrogen-fixing rhizobia occurs via host-constructed tubular tip-growing structures known as infection threads (ITs). Here, we have used a confocal microscopy live-tissue imaging approach to investigate early stages of IT formation in Medicago truncatula root hairs (RHs) expressing fluorescent protein fusion reporters. This has revealed that ITs only initiate 10 to 20 h after the completion of RH curling, by which time major modifications have occurred within the so-called infection chamber, the site of bacterial entrapment. These include the accumulation of exocytosis (M. truncatula Vesicle-Associated Membrane Protein721e)- and cell wall (M. truncatula EARLY NODULIN11)-associated markers, concomitant with radial expansion of the chamber. Significantly, the infection-defective M. truncatula nodule inception-1 mutant is unable to create a functional infection chamber. This underlines the importance of the NIN-dependent phase of host cell wall remodeling that accompanies bacterial proliferation and precedes IT formation, and leads us to propose a two-step model for rhizobial infection initiation in legume RHs.
Management and control applications in Agriculture domain via a Future Internet Business-to-Business platform
Barmpounakis, S. ; Kaloxylos, A. ; Groumas, A. ; Katsikas, L. ; Sarris, V. ; Dimtsa, K. ; Fournier, F. ; Antoniou, E. ; Alonistioti, N. ; Wolfert, J. - \ 2015
Information Processing in Agriculture 2 (2015)1. - ISSN 2214-3173 - p. 51 - 63.
The Agriculture business domain, as a vital part of the overall supply chain, is expected to highly evolve in the upcoming years via the developments, which are taking place on the side of the Future Internet. This paper presents a novel Business-to-Business collaboration platform from the agri-food sector perspective, which aims to facilitate the collaboration of numerous stakeholders belonging to associated business domains, in an effective and flexible manner. The contemporary B2B collaboration schemes already place the requirements for swift deployment of cloud applications, capable of both integrating diverse legacy systems, as well as developing in a rapid way new services and systems, which will be able to instantly communicate and provide complete, “farm-to-fork” solutions for farmers, agri-food and logistics service providers, ICT companies, end-product producers, etc. To this end, this conceptual paper describes how these requirements are addressed via the FIspace B2B platform, focusing on the Greenhouse Management & Control scenarios.
Resolving the polyphyletic nature of Pyricularia (Pyriculariaceae)
Klaubauf, S. ; Tharreau, D. ; Fournier, E. ; Groenewald, J.Z. ; Crous, P.W. ; Vries, R.P. de; Lebrun, M.H. - \ 2014
Studies in Mycology 79 (2014). - ISSN 0166-0616 - p. 85 - 120.
rice blast fungus - magnaporthe-oryzae - juncus-roemerianus - molecular-data - fresh-water - grisea - phylogeny - genera - specificity - resistance
Species of Pyricularia (magnaporthe-like sexual morphs) are responsible for major diseases on grasses. Pyricularia oryzae (sexual morph Magnaporthe oryzae) is responsible for the major disease of rice called rice blast disease, and foliar diseases of wheat and millet, while Pyricularia grisea (sexual morph Magnaporthe grisea) is responsible for foliar diseases of Digitaria. Magnaporthe salvinii, M. poae and M. rhizophila produce asexual spores that differ from those of Pyricularia sensu stricto that has pyriform, 2-septate conidia produced on conidiophores with sympodial proliferation. Magnaporthe salvinii was recently allocated to Nakataea, while M. poae and M. rhizophila were placed in Magnaporthiopsis. To clarify the taxonomic relationships among species that are magnaporthe- or pyricularia-like in morphology, we analysed phylogenetic relationships among isolates representing a wide range of host plants by using partial DNA sequences of multiple genes such as LSU, ITS, RPB1, actin and calmodulin. Species of Pyricularia s. str. belong to a monophyletic clade that includes all P. oryzae/P. grisea isolates tested, defining the Pyriculariaceae, which is sister to the Ophioceraceae, representing two novel families. These clades are clearly distinct from species belonging to the Gaeumannomyces pro parte/Magnaporthiopsis/Nakataea generic complex that are monophyletic and define the Magnaporthaceae. A few magnaporthe- and pyricularia-like species are unrelated to Magnaporthaceae and Pyriculariaceae. Pyricularia oryzae/P. grisea isolates cluster into two related clades. Host plants such as Eleusine, Oryza, Setaria or Triticum were exclusively infected by isolates from P. oryzae, while some host plant such as Cenchrus, Echinochloa, Lolium, Pennisetum or Zingiber were infected by different Pyricularia species. This demonstrates that host range cannot be used as taxonomic criterion without extensive pathotyping. Our results also show that the typical pyriform, 2-septate conidium morphology of P. grisea/P. oryzae is restricted to Pyricularia and Neopyricularia, while most other genera have obclavate to more ellipsoid 2-septate conidia. Some related genera (Deightoniella, Macgarvieomyces) have evolved 1-septate conidia. Therefore, conidium morphology cannot be used as taxonomic criterion at generic level without phylogenetic data. We also identified 10 novel genera, and seven novel species. A re-evaluation of generic and species concepts within Pyriculariaceae is presented, and novelties are proposed based on morphological and phylogenetic data.
Neotypification and phylogeny of Kalmusia
Zhang, Y. ; Zhang, J.Q. ; Wang, Z.D. ; Fournier, J. ; Crous, P.W. ; Zhang, X.D. ; Li, W.J. ; Ariyawansa, H.A. ; Hyde, K.D. - \ 2014
Phytotaxa 176 (2014)1. - ISSN 1179-3155 - p. 164 - 173.
pleosporales - likelihood
Kalmusia ebuli, the type species of Kalmusia, lacks type material and therefore its phylogenetic position remains unresolved. As a consequence the familial position of Kalmusia is based on morphology and molecular phylogeny of species other than the type. A fresh collection of K. ebuli, recently obtained from decorticated wood of Populus tremula in the foothills of the French Pyrenees is, therefore, designated as neotype to stabilize the application of the species and/or genus name. The holotype of K. ebuli f. sarothamni represents a synonym of K. ebuli. The genus Kalmusia is shown to be polyphyletic within the family Montagnulaceae, with K. ebuli being distant from K. brevispora and K. scabrispora, which appear to represent a different genus.
Fungal Planet description sheets: 214–280
Crous, P.W. ; Shivas, R.G. ; Quaedvlieg, W. ; Bank, M. van der; Zhang, Y. ; Summerell, B.A. ; Guarro, J. ; Wingfield, M.J. ; Wood, A.R. ; Alfenas, A.C. ; Braun, U. ; Cano-Lira, J.F. ; Garcia, D. ; Marin-Felix, Y. ; Alvarado, P. ; Andrade, J.P. ; Armengol, J. ; Assefa, A. ; Breeÿen, A. den; Camele, I. ; Cheewangkoon, R. ; Souza, J.T. De; Duong, T.A. ; Esteve-Raventós, F. ; Fournier, J. ; Frisullo, S. ; García-Jiménez, J. ; Gardiennet, A. ; Gené, J. ; Hernández-Restrepo, M. ; Hirooka, Y. ; Hospenthal, D.R. ; King, A. ; Lechat, C. ; Lombard, L. ; Mang, S.M. ; Marbach, P.A.S. ; Marincowitz, S. ; Montaño-Mata, N.J. ; Moreno, G. ; Perez, C.A. ; Pérez Sierra, A.M. ; Robertson, J.L. ; Roux, J. ; Rubio, E. ; Schumacher, R.K. ; Stchigel, A.M. ; Sutton, D.A. ; Tan, Y.P. ; Thompson, E.H. ; Vanderlinde, E. ; Walker, A.K. ; Walker, D.M. ; Wickes, B.L. ; Wong, P.T.W. ; Groenewald, J.Z. - \ 2014
Persoonia 32 (2014). - ISSN 0031-5850 - p. 184 - 306.
sp-nov - phylogeny reveals - eucalyptus-microfungi - host-associations - gene phylogeny - sequence data - diaporthales - morphology - gnomoniaceae - conioscypha
Novel species of microfungi described in the present study include the following from South Africa: Cercosporella dolichandrae from Dolichandra unguiscati, Seiridium podocarpi from Podocarpus latifolius, Pseudocercospora parapseudarthriae from Pseudarthria hookeri, Neodevriesia coryneliae from Corynelia uberata on leaves of Afrocarpus falcatus, Ramichloridium eucleae from Euclea undulata and Stachybotrys aloeticola from Aloe sp. (South Africa), as novel member of the Stachybotriaceae fam. nov. Several species were also described from Zambia, and these include Chaetomella zambiensis on unknown Fabaceae, Schizoparme pseudogranati from Terminalia stuhlmannii, Diaporthe isoberliniae from Isoberlinia angolensis, Peyronellaea combreti from Combretum mossambiciensis, Zasmidium rothmanniae and Phaeococcomyces rothmanniae from Rothmannia engleriana, Diaporthe vangueriae from Vangueria infausta and Diaporthe parapterocarpi from Pterocarpus brenanii. Novel species from the Netherlands include: Stagonospora trichophoricola, Keissleriella trichophoricola and Dinemasporium trichophoricola from Trichophorum cespitosum, Phaeosphaeria poae, Keissleriella poagena, Phaeosphaeria poagena, Parastagonospora poagena and Pyrenochaetopsis poae from Poa sp., Septoriella oudemansii from Phragmites australis and Dendryphion europaeum from Hedera helix (Germany) and Heracleum sphondylium (the Netherlands). Novel species from Australia include: Anungitea eucalyptorum from Eucalyptus leaf litter, Beltraniopsis neolitseae and Acrodontium neolitseae from Neolitsea australiensis, Beltraniella endiandrae from Endiandra introrsa, Phaeophleospora parsoniae from Parsonia straminea, Penicillifer martinii from Cynodon dactylon, Ochroconis macrozamiae from Macrozamia leaf litter, Triposporium cycadicola, Circinotrichum cycadis, Cladosporium cycadicola and Acrocalymma cycadis from Cycas spp. Furthermore, Vermiculariopsiella dichapetali is described from Dichapetalum rhodesicum (Botswana), Marasmius vladimirii from leaf litter (India), Ophiognomonia acadiensis from Picea rubens (Canada), Setophoma vernoniae from Vernonia polyanthes and Penicillium restingae from soil (Brazil), Pseudolachnella guaviyunis from Myrcianthes pungens (Uruguay) and Pseudocercospora neriicola from Nerium oleander (Italy). Novelties from Spain include: Dendryphiella eucalyptorum from Eucalyptus globulus, Conioscypha minutispora from dead wood, Diplogelasinospora moalensis and Pseudoneurospora canariensis from soil and Inocybe lanatopurpurea from reforested woodland of Pinus spp. Novelties from France include: Kellermania triseptata from Agave angustifolia, Zetiasplozna acaciae from Acacia melanoxylon, Pyrenochaeta pinicola from Pinus sp. and Pseudonectria rusci from Ruscus aculeatus. New species from China include: Dematiocladium celtidicola from Celtis bungeana, Beltrania pseudorhombica, Chaetopsina beijingensis and Toxicocladosporium pini from Pinus spp. and Setophaeosphaeria badalingensis from Hemerocallis fulva. Novel genera of Ascomycetes include Alfaria from Cyperus esculentus (Spain), Rinaldiella from a contaminated human lesion (Georgia), Hyalocladosporiella from Tectona grandis (Brazil), Pseudoacremonium from Saccharum spontaneum and Melnikomyces from leaf litter (Vietnam), Annellosympodiella from Juniperus procera (Ethiopia), Neoceratosperma from Eucalyptus leaves (Thailand), Ramopenidiella from Cycas calcicola (Australia), Cephalotrichiella from air in the Netherlands, Neocamarosporium from Mesembryanthemum sp. and Acervuloseptoria from Ziziphus mucronata (South Africa) and Setophaeosphaeria from Hemerocallis fulva (China). Several novel combinations are also introduced, namely for Phaeosphaeria setosa as Setophaeosphaeria setosa, Phoma heteroderae as Peyronellaea heteroderae and Phyllosticta maydis as Peyronellaea maydis. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
Towards modelling the flexible timing of shoot development: simulation of maize organogenesis based on coordination within and between phytomers
Zhu, J. ; Andrieu, B. ; Vos, J. ; Werf, W. van der; Fournier, C. ; Evers, J.B. - \ 2014
Annals of Botany 114 (2014)4. - ISSN 0305-7364 - p. 753 - 762.
functional-structural model - zea-mays l. - perennial ryegrass - leaf development - sheath tube - grass leaf - elongation - growth - phyllochron - internodes
* Background and Aims: Experimental evidence challenges the approximation, central in crop models, that developmental events followa fixed thermal time schedule, and indicates that leaf emergence events play a role in the timing of development. The objective of this studywas to build a structural development model of maize (Zeamays) based on a set of coordination rules at organ level that regulate duration of elongation, and to show how the distribution of leaf sizes emerges from this. * Methods: A model of maize developmentwas constructed based on three coordination rules between leaf emergence events and the dynamics of organ extension. The model was parameterized with data frommaize grown at a low plant population density and tested using data from maize grown at high population density. * Key Results: The model gave a good account of the timing and duration of organ extension. By using initial conditions associated with high population density, the model reproduced well the increase in blade elongation duration and the delay in sheath extension in high-density populations compared with low-density populations. Predictions of the sizes of sheaths at high densitywere accurate, whereas predictions of the dynamics of blade length were accurate up to rank 9; moderate overestimation of blade length occurred at higher ranks. * Conclusions: A set of simple rules for coordinated growth of organs is sufficient to simulate the development of maize plant structure without taking into account any regulation by assimilates. In this model, whole-plant architecture is shaped through initial conditions that feed a cascade of coordination events.
Wheat 2003 outdoor
Evers, J.B. ; Vos, J. ; Fournier, C. ; Andrieu, B. ; Struik, P.C. - \ 2013
environment - L-system - phytomer - plant architecture - wheat (Triticum aestivum)
This dataset containts the underlying data for the study: Evers JB, Vos J, Fournier C, Andrieu B, Chelle M, Struik PC. 2005. Towards a generic architectural model of tillering in Gramineae, as exemplified by spring wheat (Triticum aestivum). New Phytologist, 166: 801-812, • This paper presents an architectural model of wheat (Triticum aestivum), designed to explain effects of light conditions at the individual leaf level on tillering kinetics. Various model variables, including blade length and curvature, were parameterized for spring wheat, and compared with winter wheat and other Gramineae species. • The architectural model enables simulation of plant properties at the level of individual organs. Parameterization was based on data derived from an outdoor experiment with spring wheat cv. Minaret. • Final organ dimensions of tillers could be modelled using the concept of relative phytomer numbers. Various variables in spring wheat showed marked similarities to winter wheat and other species, suggesting possibilities for a general Gramineae architectural model. • Our descriptive model is suitable for our objective: investigating light effects on tiller behaviour. However, we plan to replace the descriptive modelling solutions by physiological, mechanistic solutions, starting with the localized production and partitioning of assimilates as affected by abiotic growth factors.
Simulating maize plasticity in leaf appearance and size using regulation rules
Zhu, J. ; Andrieu, B. ; Vos, J. ; Werf, W. van der; Fournier, C. ; Evers, J.B. - \ 2013
In: Proceedings of the 7th International Conference on Functional-Structural Plant Models, 9-14 June, Saariselkä, Finland. - - p. 273 - 275.
Plants regulate their architecture in response to the growth environment, which challenges us to design models capable of performing well in different conditions. By using self-regulating rules, we reproduced blade and collar emergence time, and organ size distribution along phytomer rank in maize under varying growing conditions. The role of emergence events, e.g. blade tip emergence, collar emergence, in controlling growth phase and elongation duration of different components of one phytomer (blade, sheath and internode) are confirmed.
Paths to selection on life history loci in different natural environments across the native range of Arabidopsis thaliana
Fournier-Level, A. ; Wilczek, A.M. ; Cooper, M.D. ; Roe, J.L. ; Anderson, J. ; Eaton, D. ; Moyers, B.T. ; Petipas, R.H. ; Schaeffer, R.N. ; Pieper, B. ; Reymond, M. ; Koornneef, M. ; Welch, S.M. ; Remington, D.L. ; Schmitt, J. - \ 2013
Molecular Ecology 22 (2013)13. - ISSN 0962-1083 - p. 3552 - 3566.
quantitative trait loci - inbred line population - genome-wide association - flowering-time - landsberg erecta - allelic variation - genetic architecture - impatiens-capensis - floral repressors - growth
Selection on quantitative trait loci (QTL) may vary among natural environments due to differences in the genetic architecture of traits, environment-specific allelic effects or changes in the direction and magnitude of selection on specific traits. To dissect the environmental differences in selection on life history QTL across climatic regions, we grew a panel of interconnected recombinant inbred lines (RILs) of Arabidopsis thaliana in four field sites across its native European range. For each environment, we mapped QTL for growth, reproductive timing and development. Several QTL were pleiotropic across environments, three colocalizing with known functional polymorphisms in flowering time genes (CRY2, FRI and MAF2-5), but major QTL differed across field sites, showing conditional neutrality. We used structural equation models to trace selection paths from QTL to lifetime fitness in each environment. Only three QTL directly affected fruit number, measuring fitness. Most QTL had an indirect effect on fitness through their effect on bolting time or leaf length. Influence of life history traits on fitness differed dramatically across sites, resulting in different patterns of selection on reproductive timing and underlying QTL. In two oceanic field sites with high prereproductive mortality, QTL alleles contributing to early reproduction resulted in greater fruit production, conferring selective advantage, whereas alleles contributing to later reproduction resulted in larger size and higher fitness in a continental site. This demonstrates how environmental variation leads to change in both QTL effect sizes and direction of selection on traits, justifying the persistence of allelic polymorphism at life history QTL across the species range
Arabidopsis wat1 (walls are thin1)-mediated resistance to the bacterial vascular pathogen, Ralstonia solanacearum, is accompanied by cross-regulation of salicylic acid and tryptophan metabolism
Denancé, N. ; Ranocha, P. ; Oria, N. ; Barlet, X. ; Rivière, M.P. ; Yadeta, K.A. ; Hoffmann, L. ; Perreau, F. ; Clément, G. ; Maia-Grondard, A. ; Berg, G.C.M. van den; Savelli, B. ; Fournier, S. ; Aubert, Y. ; Pelletier, S. ; Thomma, B.P.H.J. ; Molina, A. ; Jouanin, L. ; Marco, Y. ; Goffner, D. - \ 2013
The Plant Journal 73 (2013)2. - ISSN 0960-7412 - p. 225 - 239.
plant-cell wall - systemic acquired-resistance - fusarium-oxysporum - disease-resistance - wilt disease - plectosphaerella-cucumerina - medicago-truncatula - confers resistance - thaliana - mutant
Inactivation of Arabidopsis WAT1 (Walls Are Thin1), a gene required for secondary cell-wall deposition, conferred broad-spectrum resistance to vascular pathogens, including the bacteria Ralstonia solanacearum and Xanthomonas campestris pv. campestris, and the fungi Verticillium dahliae and Verticillium albo-atrum. Introduction of NahG, the bacterial salicylic acid (SA)-degrading salicylate hydroxylase gene, into the wat1 mutant restored full susceptibility to both R. solanacearum and X. campestris pv. campestris. Moreover, SA content was constitutively higher in wat1 roots, further supporting a role for SA in wat1-mediated resistance to vascular pathogens. By combining transcriptomic and metabolomic data, we demonstrated a general repression of indole metabolism in wat1-1 roots as shown by constitutive down-regulation of several genes encoding proteins of the indole glucosinolate biosynthetic pathway and reduced amounts of tryptophan (Trp), indole-3-acetic acid and neoglucobrassicin, the major form of indole glucosinolate in roots. Furthermore, the susceptibility of the wat1 mutant to R. solanacearum was partially restored when crossed with either the trp5 mutant, an over-accumulator of Trp, or Pro35S:AFB1-myc, in which indole-3-acetic acid signaling is constitutively activated. Our original hypothesis placed cell-wall modifications at the heart of the wat1 resistance phenotype. However, the results presented here suggest a mechanism involving root-localized metabolic channeling away from indole metabolites to SA as a central feature of wat1 resistance to R. solanacearum.
Harmonization of risk assessment methods of soil erosion by water in the European Union
Rectalá, L. ; Año, C. ; Verzandvoort, S.J.E. ; Ritsema, C.J. - \ 2011
In: Soil erosion causes, processes and effects / Fournier, A.J., New York, USA : Nova Science Publishers - ISBN 9781617611865 - p. 161 - 176.
Genome analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea
Amselem, J. ; Cuomo, C.A. ; Kan, J.A.L. van; Viaud, M. ; Benito, E.P. ; Couloux, A. ; Coutinho, P.M. ; Vries, R.P. de; Dyer, P.S. ; Fillinger, S. ; Fournier, E. ; Gout, L. ; Hahn, M. ; Kohn, L. ; Lapalu, N. ; Plummer, K.M. ; Pradier, J.M. ; Quévillon, E. ; Sharon, A. ; Simon, A. ; Have, A. ten; Tudzynski, B. ; Tudzynski, P. ; Wincker, P. ; Andrew, M. ; Anthouard, V. ; Beever, R.E. ; Beffa, R. ; Benoit, I. ; Bouzid, O. ; Brault, B. ; Chen, Z. ; Choquer, M. ; Collemare, J. ; Cotton, P. ; Danchin, E.G. ; Silva, C. Da; Gautier, A. ; Giraud, C. ; Giraud, T. ; Gonzalez, C. ; Grossetete, S. ; Güldener, U. ; Henrissat, B. ; Howlett, B.J. ; Kodira, C. ; Kretschmer, M. ; Lappartient, A. ; Leroch, M. ; Levis, C. ; Mauceli, E. ; Neuvéglise, C. ; Oeser, B. ; Pearson, M. ; Poulain, J. ; Poussereau, N. ; Quesneville, H. ; Rascle, C. ; Schumacher, J. ; Ségurens, B. ; Sexton, A. ; Silva, E. ; Sirven, C. ; Soanes, D.M. ; Talbot, N.J. ; Templeton, M. ; Yandava, C. ; Yarden, O. ; Zeng, Q. ; Rollins, J.A. ; Lebrun, M.H. ; Dickman, M. - \ 2011
Plos Genetics 7 (2011)8. - ISSN 1553-7404 - 27 p.
rice blast fungus - development-specific protein - expressed sequence tags - programmed cell-death - mating-type loci - oxalic-acid - neurospora-crassa - arabidopsis-thaliana - secondary metabolism - molecular phylogeny
Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to
Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation
Zhang, Y. ; Schoch, C.L. ; Fournier, J. ; Crous, P.W. ; Gruyter, J. de; Woudenberg, J.H.C. ; Hirayama, K. ; Tanaka, K. ; Pointing, S.B. ; Spatafora, J.W. ; Hyde, K.D. - \ 2009
Studies in Mycology 64 (2009)1. - ISSN 0166-0616 - p. 85 - 102.
ribosomal dna-sequences - stagonospora-nodorum - molecular phylogeny - leptosphaeria-maculans - phaeosphaeria-nodorum - multigene phylogeny - multiple alignment - endophytic fungi - sp-nov - ascomycota
Five loci, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, are used for analysing 129 pleosporalean taxa representing 59 genera and 15 families in the current classification of Pleosporales. The suborder Pleosporineae is emended to include four families, viz. Didymellaceae, Leptosphaeriaceae, Phaeosphaeriaceae and Pleosporaceae. In addition, two new families are introduced, i.e. Amniculicolaceae and Lentitheciaceae. Pleomassariaceae is treated as a synonym of Melanommataceae, and new circumscriptions of Lophiostomataceae s. str, Massarinaceae and Lophiotrema are proposed. Familial positions of Entodesmium and Setomelanomma in Phaeosphaeriaceae, Neophaeosphaeria in Leptosphaeriaceae, Leptosphaerulina, Macroventuria and Platychora in Didymellaceae, Pleomassaria in Melanommataceae and Bimuria, Didymocrea, Karstenula and Paraphaeosphaeria in Montagnulaceae are clarified. Both ecological and morphological characters show varying degrees of phylogenetic significance. Pleosporales is most likely derived from a saprobic ancestor with fissitunicate asci containing conspicuous ocular chambers and apical rings. Nutritional shifts in Pleosporales likely occured from saprotrophic to hemibiotrophic or biotrophic.
Towards a phylogenetic clarification of Lophiostoma / Massarina and morphologically similar genera in the Pleosporales
Zhang, Y. ; Wang, H.K. ; Fournier, J. ; Crous, P.W. ; Jeewon, R. ; Pointing, S.B. ; Hyde, K.D. - \ 2009
Fungal Diversity 38 (2009). - ISSN 1560-2745 - p. 225 - 251.
submerged wood - ribosomal dna - fresh-water - hong-kong - fungi - ascomycota - revision - epitypification - teleomorph - sequences
Lophiostoma, Lophiotrema and Massarina are similar genera that are difficult to distinguish morphologically. In order to obtain a better understanding of these genera, lectotype material of the generic types, Lophiostoma macrostomun, Lophiotrema nucula and Massarina eburnea were examined and are re-described. The phylogeny of these genera is investigated based oil the analysis of 26 Lophiostoma- and Massarina-like taxa and three genes - 18S, 28S rDNA and RPB2. These taxa formed five well-supported sub-clades in Pleosporales. This Study confirms that both Lophiostoma and Massarina are polyphyletic. Massarina-like taxa can presently be differentiated into two groups - the Lentithecium group and the Massarina group. Of these, the type species M. eburnea together with the Massarina group represents Massarina sensu stricto. Lophiostoma taxa Clustered in two groups - one group, including the type species L. macrostomum, is characterized by fusiform, hyaline one-septate ascospores which are pigmented and 3-septate when senescent, clavate asci, and apical structures which are highly variable, being crest-like in L. macrostomum, all umbilicate pore surrounded by 4-6 radial ridges in L. rugulosum, or papillate in L. glabrotunicatum. The second group comprises Lophiostoma species with heavily pigmented multi-septate ascospores and compressed crests. Lophiotrema species including the type species L. nucula form a monophyletic group. One new genus - Lentithecium with five new species - Lentithecium aquaticum, Lophiostoma glabrotunicatum, L. rugulosum, Lophiotrema brunneosporum and L. lignicola and three new combinations - Lentithecium arundinaceum, L. fluviatile and L. lineare are introduced in this paper.
Phylogenetic and morphological assessment of two new species of Amniculicola and their allies (Pleosporales)
Zhang, Y. ; Fournier, J. ; Crous, P.W. ; Pointing, S.B. ; Hyde, K.D. - \ 2009
Persoonia 23 (2009). - ISSN 0031-5850 - p. 48 - 54.
fresh-water - molecular characterization - gene-sequences - ribosomal dna - xylariaceae - fungi - china
Two new species of Amniculicola, A. immersa sp. nov. and A. parva sp. nov. from submerged wood in a freshwater environment in Denmark and France are respectively described and illustrated. In addition, partial 28S rDNA sequence data is analysed to investigate their phylogenetic relationships with other pleosporalean taxa. All presently known Amniculicola species, A. immersa, A. lignicola and A. parva, form a robust clade together with the anamorphic species Anguillospora longissima, Spirosphaera cupreorufescens and Repetophragma ontariense. These six species, which are all from freshwater and mostly from Europe, constitute a well-supported group containing Pleospora rubicunda and Massariosphaeria typhicola. This putative monophyletic assemblage may represent an aquatic group in the Pleosporales. It is also pertinent that all five ascomycete taxa in this group stain their host substrates purple
Activation of human T cells by a tumor vaccine infected with recombinant Newcastle disease virus producing IL-2
Janke, M. ; Peeters, B. ; Zhao, H. ; Leeuw, O. ; Moormann, R.J.M. ; Arnold, A. ; Ziouta, Y. ; Fournier, P. ; Schirrmacher, V. - \ 2008
International Journal of Oncology 33 (2008)4. - ISSN 1019-6439 - p. 823 - 832.
antitumor vaccination - fusion protein - bone-marrow - therapy - cancer - memory - immunotherapy - parameters - carcinoma
A new recombinant (rec) Newcastle disease virus (NDV) with incorporated human interleukin 2 (IL-2) as foreign therapeutic gene [rec(IL-2)] will be described. The foreign gene in rec(IL-2) did not affect the main features of NDV replication nor its tumor selectivity. Biologically active IL-2 was produced in high amounts by tumor cells infected with rec(IL-2). Tumor vaccine cells infected by rec(IL-2) stimulated human T cells to exert anti-tumor activity in vitro in a tumor neutralization assay. These effects were significantly increased when compared to vaccine infected by rec(-) virus without IL-2 gene. After incubation with rec(IL-2) infected tumor cells, T cells showed increased expression of the activation marker CD69 and produced increased amounts of IFN gamma when compared to T cells co-incubated with rec(-) infected tumor cells. CD8 T cells incubated with rec(IL-2) infected tumor cells showed upregulation of perform, cell surface exposure of the degranulation marker CD107a and increased anti-tumor cytotoxic activity. Purified T cells from lymph nodes of head and neck squamous cell carcinoma (HNSCC) patients could be stimulated to secrete IFN gamma in an ELISPOT assay upon 40 h of stimulation with rec(IL-2) infected autologous tumor cells [ATV-rec(IL-2)] but not upon stimulation with rec(IL-2) infected allogeneic U937 tumor cells. This suggests direct activation of patient derived tumor antigen-specific memory T cells by ATV-rec(IL-2). In conclusion, the already inherent immunostimulatory properties of NDV could be further augmented by the introduction of the therapeutic gene IL-2. Active specific immunization of patients with ATV-rec(IL-2) should provide the microenvironment at the vaccination site with IL-2 and avoid side effects as seen after systemic IL-2 application.
Simulating the red:far-red ratio of individual plant organs, a key issue for phytochrome-driven processes
Chelle, M. ; Evers, J.B. ; Fournier, C. ; Combes, D. ; Vos, J. ; Andrieu, B. - \ 2007
In: Proceedings of the 5th International Workshop on Functional-Structural Plant Models, Napier, New Zealand, 4¿9 November 2007. - Hawke's Bay : Print Solutions - p. 55.1 - 55.3.
Recombinant Newcastle disease virus (NDV) with inserted gene coding for GM-CSF as a new vector for cancer immunogene therapy
Janke, M. ; Peeters, B.P.H. ; Leeuw, O.S. de; Moormann, R.J.M. ; Arnold, A. ; Fournier, P. ; Schirrmacher, V. - \ 2007
Gene Therapy 14 (2007). - ISSN 0969-7128 - p. 1639 - 1649.
colony-stimulating factor - tumor-cell vaccine - apoptosis-inducing ligand - antitumor vaccination - postoperative immunotherapy - metastatic melanoma - adaptive immunity - clinical-trials - i interferon - infection
This is the first report describing recombinant (rec) Newcastle disease virus (NDV) as vector for gene therapy of cancer. The gene encoding granulocyte/macrophage colony-stimulating factor (GM-CSF) was inserted as an additional transcription unit at two different positions into the NDV genome. The rec virus with the strongest production of the gene product (rec(GM-CSF)) was selected for our study. The insertion of the new foreign gene did neither affect the main features of NDV replication nor its tumor selectivity. The gene product was biologically active and stable. Tumor vaccine cells infected by rec(GM-CSF) stimulated human peripheral blood mononuclear cells (PBMC) to exert antitumor bystander effects in vitro in a tumor neutralization assay. These effects were significantly increased when compared to vaccine infected by rec(-) virus. Furthermore, rec(GM-CSF) led to a much higher interferon- (IFN-) production than rec(-) when added as virus or as virus-modified vaccine to PBMC. Two distinct cell types, monocytes and plasmacytoid dendritic cells were shown to contribute to the augmented IFN- response of PBMC. In conclusion, the already inherent anti-neoplastic and immunostimulatory properties of NDV could be further augmented by the introduction of a therapeutic gene whose product initiates a broad cascade of immunological effects in the microenvironment of the vaccine.
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