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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Inferring causation from time series in Earth system sciences
Runge, Jakob ; Bathiany, Sebastian ; Bollt, Erik ; Camps-Valls, Gustau ; Coumou, Dim ; Deyle, Ethan ; Glymour, Clark ; Kretschmer, Marlene ; Mahecha, Miguel D. ; Muñoz-Marí, Jordi ; Nes, Egbert H. van; Peters, Jonas ; Quax, Rick ; Reichstein, Markus ; Scheffer, Marten ; Schölkopf, Bernhard ; Spirtes, Peter ; Sugihara, George ; Sun, Jie ; Zhang, Kun ; Zscheischler, Jakob - \ 2019
Nature Communications 10 (2019)1. - ISSN 2041-1723

The heart of the scientific enterprise is a rational effort to understand the causes behind the phenomena we observe. In large-scale complex dynamical systems such as the Earth system, real experiments are rarely feasible. However, a rapidly increasing amount of observational and simulated data opens up the use of novel data-driven causal methods beyond the commonly adopted correlation techniques. Here, we give an overview of causal inference frameworks and identify promising generic application cases common in Earth system sciences and beyond. We discuss challenges and initiate the benchmark platform causeme.net to close the gap between method users and developers.

Cascading use: a systematic approach to biomass beyond the energy sector
Keegan, D. ; Kretschmer, M. ; Elbersen, B.S. ; Panoutsou, C. - \ 2013
Biofuels Bioproducts and Biorefining 7 (2013)2. - ISSN 1932-104X - p. 193 - 206.
Growing demand for biomass for energy in Europe and beyond, alongside growing interest in the use of biomass to replace petroleum and other conventional materials in the production of industrial products and chemicals, necessitates consideration of how the limited supplies of biomass can be used most efficiently. This paper presents the concept of cascading the use of biomass (i.e. a mechanism for prioritizing its use for socially preferable products, notably materials over its use for energy). Such a mechanism would be an opportunity to maximize the efficiency of biomass use. Currently, barriers to the wider adoption of cascading persist in the form of underdeveloped supply chains to facilitate the reuse of biomass resources and a regulatory framework that focuses support on the energy use of biomass. This paper discusses policy mechanisms and instruments that could help lift these barriers, including measures under the EU Renewable Energy Directive to introduce more encompassing sustainability criteria and incentives for the use of end-of-life biomass. We further argue for more research to better understand the environmental and economic impacts of increased industrial biomass uses and to link any support for biomaterials closely to the outcome of such research.
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
Fungicide-driven evolution and molecular basis of multidrug resistance in field populations of the grey mould fungus Botrytis cinerea
Kretschmer, M. ; Leroch, M. ; Mosbach, A. ; Walker, A.S. ; Fillinger, S. ; Mernke, D. ; Schoonbeek, H.J. ; Pradier, J.M. ; Leroux, P. ; Waard, M.A. de; Hahn, M. - \ 2009
PLoS Pathogens 5 (2009)12. - ISSN 1553-7366 - 13 p.
abc transporter bcatrb - natural toxic compounds - botryotinia-fuckeliana - penicillium-digitatum - candida-albicans - functional-characterization - virulence factor - drug-resistance - gene - sensitivity
The grey mould fungus Botrytis cinerea causes losses of commercially important fruits, vegetables and ornamentals worldwide. Fungicide treatments are effective for disease control, but bear the risk of resistance development. The major resistance mechanism in fungi is target protein modification resulting in reduced drug binding. Multiple drug resistance (MDR) caused by increased efflux activity is common in human pathogenic microbes, but rarely described for plant pathogens. Annual monitoring for fungicide resistance in field isolates from fungicide-treated vineyards in France and Germany revealed a rapidly increasing appearance of B. cinerea field populations with three distinct MDR phenotypes. All MDR strains showed increased fungicide efflux activity and overexpression of efflux transporter genes. Similar to clinical MDR isolates of Candida yeasts that are due to transcription factor mutations, all MDR1 strains were shown to harbor activating mutations in a transcription factor (Mrr1) that controls the gene encoding ABC transporter AtrB. MDR2 strains had undergone a unique rearrangement in the promoter region of the major facilitator superfamily transporter gene mfsM2, induced by insertion of a retrotransposon-derived sequence. MDR2 strains carrying the same rearranged mfsM2 allele have probably migrated from French to German wine-growing regions. The roles of atrB, mrr1 and mfsM2 were proven by the phenotypes of knock-out and overexpression mutants. As confirmed by sexual crosses, combinations of mrr1 and mfsM2 mutations lead to MDR3 strains with higher broad-spectrum resistance. An MDR3 strain was shown in field experiments to be selected against sensitive strains by fungicide treatments. Our data document for the first time the rising prevalence, spread and molecular basis of MDR populations in a major plant pathogen in agricultural environments. These populations will increase the risk of grey mould rot and hamper the effectiveness of current strategies for fungicide resistance management.
Overexpression of efflux transporters leads to multidrug resistance in Botrytis cinerea field strains
Kretschmer, M. ; Walker, A.S. ; Leroch, M. ; Wiwiorra, M. ; Schoonbeek, H. ; Leroux, P. ; Fillinger, S. ; Waard, M. de; Hahn, M. - \ 2008
In: Book of Abstracts 9th International Congress of Plant Pathology, Torino, Italy, 24-29 August 2008. - - p. S2.140 - S2.140.
Drought tolerance of Aeschynomene, Macroptilium and Desmodium seedlings.
Boman, B.J. ; Kretschmer, A.E. ; Hoff, P. van 't - \ 1989
In: Soil and Crop Science Soc. Florida, Proceedings 47 - p. 178 - 183.
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