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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    Tree seedling recruitment dynamics in forest-savanna transitions : Trait responses to vegetation controls mediate differential seedling establishment success of tree functional types
    Issifu, Hamza - \ 2020
    Wageningen University. Promotor(en): F. van Langevelde, co-promotor(en): E. Veenendaal; P. Vergeer. - Wageningen : Wageningen University - ISBN 9789463953887 - 211

    In the transition between tropical forests and savannas, forest may be lost to savanna-like vegetation or may occasionally encroach on savannas affecting climate and other benefits to humans. Vegetation in the forest savanna-transition of Ghana often appears stable, except in forests with significant human-induced deforestation where forests are being replaced by savanna-like vegetation. This phenomenon is still poorly understood, but may be explained by how changes in vegetation controls (e.g. fire and precipitation) affect recruitment of forest and savanna-transition tree seedlings differently. Savanna-transition species occur both in forest and humid savanna. I showed that high grass biomass in savanna both directly (via competition) and indirectly (via dry season fire) select for species which invest higher in belowground resource capture and carbohydrate storage. Lower precipitation decreases chances of tree seedling recovery from defoliation disturbance, but allocation trait differences between forest and savanna-transition tree species may explain relative stability of transition forests and the lack of success of true forest species in the forest-savanna transition.

    Variation in vegetation cover and seedling performance of tree species in a forest-savanna ecotone
    Issifu, Hamza ; Ametsitsi, George K.D. ; Vries, Lana J. De; Djagbletey, Gloria Djaney ; Adu-Bredu, Stephen ; Vergeer, Philippine ; Langevelde, Frank Van; Veenendaal, Elmar - \ 2019
    Journal of Tropical Ecology 35 (2019)2. - ISSN 0266-4674 - p. 74 - 82.
    Biomass allocation - canopy cover - drought survival - fuel load - root starch - seedling traits - soil properties - tropical trees

    Differential tree seedling recruitment across forest-savanna ecotones is poorly understood, but hypothesized to be influenced by vegetation cover and associated factors. In a 3-y-long field transplant experiment in the forest-savanna ecotone of Ghana, we assessed performance and root allocation of 864 seedlings for two forest (Khaya ivorensis and Terminalia superba) and two savanna (Khaya senegalensis and Terminalia macroptera) species in savanna woodland, closed-woodland and forest. Herbaceous vegetation biomass was significantly higher in savanna woodland (1.0 ± 0.4 kg m-2 vs 0.2 ± 0.1 kg m-2 in forest) and hence expected fire intensities, while some soil properties were improved in forest. Regardless, seedling survival declined significantly in the first-year dry-season for all species with huge declines for the forest species (50% vs 6% for Khaya and 16% vs 2% for Terminalia) by year 2. After 3 y, only savanna species survived in savanna woodland. However, best performance for savanna Khaya was in forest, but in savanna woodland for savanna Terminalia which also had the highest biomass fraction (0.8 ± 0.1 g g-1 vs 0.6 ± 0.1 g g-1 and 0.4 ± 0.1 g g-1) and starch concentration (27% ± 10% vs 15% ± 7% and 10% ± 4%) in roots relative to savanna and forest Khaya respectively. Our results demonstrate that tree cover variation has species-specific effects on tree seedling recruitment which is related to root storage functions.

    Corrigendum to "Proteome catalog of Zymoseptoria tritici captured during pathogenesis in wheat". [Fung. Genet. Biol. 79 (2015) 42-53]
    Mbarek, Sarrah Ben; Cordewener, J.H.G. ; Lee, T.A.J. Van der; America, A.H.P. ; Gohari, Amir Mirzadi ; Mehrabi, Rahim ; Hamza, Sonia ; Wit, P.J.G.M. de; Kema, Gert - \ 2015
    Fungal Genetics and Biology 82 (2015). - ISSN 1087-1845 - p. 291 - 291.
    FPLC and liquid-chromatography mass spectrometry identify candidate necrosis-inducing proteins from culture filtrates of the fungal wheat pathogen Zymoseptoria tritici
    M'Barek, S. Ben; Cordewener, J.H.G. ; Tabib Ghaffary, M.S. ; Lee, T.A.J. van der; Liu, Z. ; Mirzadi Gohari, A. ; Mehrabi, R. ; America, A.H.P. ; Friesen, T.L. ; Hamza, S. ; Stergiopoulos, I. ; Wit, P.J.G.M. de; Kema, G.H.J. - \ 2015
    Fungal Genetics and Biology 79 (2015). - ISSN 1087-1845 - p. 54 - 62.
    host-selective toxins - mycosphaerella-graminicola - stagonospora-nodorum - septoria-tritici - rhynchosporium-secalis - cladosporium-fulvum - ptr toxa - hydrogen-peroxide - barley pathogen - tan spot
    Culture filtrates (CFs) of the fungal wheat pathogen Zymoseptoria tritici were assayed for necrosis-inducing activity after infiltration in leaves of various wheat cultivars. Active fractions were partially purified and characterized. The necrosis-inducing factors in CFs are proteinaceous, heat stable and their necrosis-inducing activity is temperature and light dependent. The in planta activity of CFs was tested by a time series of proteinase K (PK) co-infiltrations, which was unable to affect activity 30min after CF infiltrations. This suggests that the necrosis inducing proteins (NIPs) are either absent from the apoplast and likely actively transported into mesophyll cells or protected from the protease by association with a receptor. Alternatively, plant cell death signaling pathways might be fully engaged during the first 30min and cannot be reversed even after PK treatment. Further fractionation of the CFs with the highest necrosis-inducing activity involved fast performance liquid chromatography, SDS-PAGE and mass spectrometry. This revealed that most of the proteins present in the fractions have not been described before. The two most prominent ZtNIP encoding candidates were heterologously expressed in Pichia pastoris and subsequent infiltration assays showed their differential activity in a range of wheat cultivars.
    Proteome catalog of Zymoseptoria tritici captured during pathogenesis in wheat
    M'Barek, S. Ben; Cordewener, J.H.G. ; Lee, T.A.J. van der; America, A.H.P. ; Mirzadi Gohari, A. ; Mehrabi, R. ; Hamza, S. ; Wit, P.J.G.M. de; Kema, G.H.J. - \ 2015
    Fungal Genetics and Biology 79 (2015)June. - ISSN 1087-1845 - p. 42 - 53.
    wall-degrading enzymes - fungus mycosphaerella-graminicola - programmed cell-death - cladosporium-fulvum - septoria-tritici - plant-pathogen - magnaporthe-grisea - disease resistance - hydrogen-peroxide - blotch pathogen
    Zymoseptoria tritici is an economically important pathogen of wheat. However, the molecular basis of pathogenicity on wheat is still poorly understood. Here, we present a global survey of the proteins secreted by this fungus in the apoplast of resistant (cv. Shafir) and susceptible (cv. Obelisk) wheat cultivars after inoculation with reference Z. tritici strain IPO323. The fungal proteins present in apoplastic fluids were analyzed by gel electrophoresis and by data-independent acquisition liquid chromatography/mass spectrometry (LC/MS(E)) combined with data-dependent acquisition LC-MS/MS. Subsequent mapping mass spectrometry-derived peptide sequence data against the genome sequence of strain IPO323 identified 665 peptides in the MS(E) and 93 in the LC-MS/MS mode that matched to 85 proteins. The identified fungal proteins, including cell-wall degrading enzymes and proteases, might function in pathogenicity, but the functions of many remain unknown. Most fungal proteins accumulated in cv. Obelisk at the onset of necrotrophy. This inventory provides an excellent basis for future detailed studies on the role of these genes and their encoded proteins during pathogenesis in wheat
    A combined amplified fragment length polymorphism and randomly amplified polymorphism DNA genetic linkage map of Mycosphaerella graminicola, the Septoria tritici leaf blotch pathogen of wheat
    Kema, G.H.J. ; Goodwin, S.B. ; Hamza, S. ; Verstappen, E.C.P. ; Cavaletto, J.R. ; Lee, T.A.J. van der; Weerdt, M. de; Bonants, P.J.M. ; Waalwijk, C. - \ 2002
    Genetics 161 (2002)4. - ISSN 0016-6731 - p. 1497 - 1505.
    electrophoretic karyotype - aflp markers - resistance - rflp - construction - pathosystem - populations - avirulence - cultivars - virulence
    An F-1 mapping population of the septoria tritici blotch pathogen of wheat, Mycosphaerella graminicola, was generated by crossing the two Dutch field isolates IPO323 and IPO94269. AFLP and RAPD marker data sets were combined to produce a high-density genetic linkage map. The final map contained 223 AFLP and 57 RAPD markers, plus the biological traits mating type and avirulence, in 23 linkage groups spanning 1216 cM. Many AFLPs and some RAPD markers were clustered. When markers were reduced to 1 per cluster, 229 unique positions were mapped, with an average distance of 5.3 cM between markers. Because M. graminicola probably has 17 or 18 chromosomes, at least 5 of the 23 linkage groups probably will need to be combined with others once additional markers are added to the map. This was confirmed by pulsed-field gel analysis; probes derived from 2 of the smallest linkage groups hybridized to two of the largest chromosome-sized bands, revealing a discrepancy between physical and genetic distance. The utility of the map was demonstrated by identifying molecular markers tightly linked to two genes of biological interest, mating type and avirulence. Bulked segregant analysis was used to identify additional molecular markers closely linked to these traits. This is the first genetic linkage map for any species in the genus Mycosphaerella or the family Mycosphaerellaceae.
    Parameter control strategy in differential evolution algorithm for optimal control
    Lopez Cruz, I.L. ; Willigenburg, L.G. van; Straten, G. van - \ 2001
    In: Proceedings of the IASTED International Conference "Artificial Intelligence and Soft Computing", Cancun, Mexico, May 21-24, 2001 / Hamza, M.H., - p. 211 - 216.
    Evolutionary Algorithms for optimal control of chemical processes
    Lopez Cruz, I.L. ; Willigenburg, L.G. van; Straten, G. van - \ 2000
    In: Proceedings of the IASTED International Conference Control and Applications , Mexico, Cancun, 24-27 May 2000 / Hamza, M.H., - p. 155 - 161.
    Mapping the Mycosphaerella graminicola genome
    Kema, G.H.J. ; Goodwin, S.B. ; Hamza, S. ; Verstappen, E.C.P. ; Cavaletto, J.R. ; Lee, T.A.J. van der; Hagenaar-deWeerdt, M. ; Bonants, P.J.M. ; Waalwijk, C. - \ 1999
    Fungal Genetics Newsletter 46 (1999)supplement. - ISSN 0895-1942 - p. 133 - 133.
    Genetics of biological and molecular markers in Mycosphaerella graminicola, the cause of Septoria tritici leaf blotch of wheat
    Kema, G.H.J. ; Verstappen, E.C.P. ; Waalwijk, C. ; Bonants, P.J.M. ; Koning, J.R.A. de; Hagenaar-de Weerdt, M. ; Hamza, S. ; Koeken, J.G.P. ; Lee, T.A.J. van der - \ 1999
    In: Septoria on cereals / Lucas, J.A., Bowyer, P., Anderson, H.M., - p. 161 - 180.
    The first linkage map of Mycosphaerella graminicola (anamorph Septoria tritici), Europe's major fungal wheat pathogen.
    Kema, G.H.J. ; Hamza, S. ; Bonants, P.J.M. ; Waalwijk, C. ; Hagenaar-de Weerdt, M. ; Verstappen, E.C.P. ; Lee, T.A.J. van der - \ 1998
    In: 6th International Mycological Congress, Jerusalem, Israel - p. 81 - 81.
    Een koppelingskaart van het Mycosphaerella graminicola [anamorph Septoria tritici] genoom.
    Kema, G.H.J. ; Hamza, S. ; Bonants, P.J.M. ; Waalwijk, C. ; Hagenaar-de Weerdt, M. ; Verstappen, E.C.P. ; Lee, T.A.J. van der - \ 1998
    Gewasbescherming 29 (1998). - ISSN 0166-6495 - p. 55 - 56.
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