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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    Biotechnological strategies for the recovery of valuable and critical raw materials from waste electrical and electronic equipment (WEEE) – A review
    Işıldar, Arda ; Hullebusch, Eric D. van; Lenz, Markus ; Laing, Gijs Du; Marra, Alessandra ; Cesaro, Alessandra ; Panda, Sandeep ; Akcil, Ata ; Kucuker, Mehmet Ali ; Kuchta, Kerstin - \ 2019
    Journal of Hazardous Materials 362 (2019). - ISSN 0304-3894 - p. 467 - 481.
    Bioleaching - Bioprecipitation - Biosorption - Biotechnologies - Critical metals - Electronic waste

    Critical raw materials (CRMs) are essential in the development of novel high-tech applications. They are essential in sustainable materials and green technologies, including renewable energy, emissionfree electric vehicles and energy-efficient lighting. However, the sustainable supply of CRMs is a major concern. Recycling end-of-life devices is an integral element of the CRMs supply policy of many countries. Waste electrical and electronic equipment (WEEE) is an important secondary source of CRMs. Currently, pyrometallurgical processes are used to recycle metals from WEEE. These processes are deemed imperfect, energy-intensive and non-selective towards CRMs. Biotechnologies are a promising alternative to the current industrial best available technologies (BAT). In this review, we present the current frontiers in CRMs recovery from WEEE using biotechnology, the biochemical fundamentals of these bio-based technologies and discuss recent research and development (R&D) activities. These technologies encompass biologically induced leaching (bioleaching) from various matrices,biomass-induced sorption (biosorption), and bioelectrochemical systems (BES).

    Genetic determinism of flowering regularity over years in an apple multi-family population
    Durand, J.B. ; Allard, A. ; Guitton, B. ; Weg, E. van de; Bink, M.C.A.M. ; Costes, E. - \ 2018
    In: International Symposium on Flowering, Fruit Set and Alternate Bearing. - ISHS (Acta Horticulturae 1229) - ISBN 9789462612266 - p. 15 - 22.
    Bayes factor - Biennial bearing - Entropy - Floral induction - Malus × domestica - Markov models - Pedigree based analysis

    Irregular flowering over years is commonly observed in fruit trees and is assumed to be, at least partly, under genetic control. This study aimed at predicting genotype flowering behaviours and at detecting QTL associated to regularity, in a multi-family apple tree population. Successions of vegetative and floral annual shoots (AS) were observed along axes in trees belonging to five apple related full-sib families, observed at two experimental sites. Sequences were analysed using Markovian and linear mixed models including year and site effects. Indices of flowering regularity, periodicity and synchronicity were estimated, at tree and axis scales. First indices were derived from the biennial bearing index (BBI). A second index was the autoregressive correlation coefficient between flowering in consecutive years. A third index quantified the synchronicity of meristems within the trees through the measure of differences in the predictability of flowering over years, from a probabilistic viewpoint. These three types of indices were used to predict tree behaviour and to detect QTL with a Bayesian pedigree-based analysis, using an integrated genetic map containing 6,849 SNPs. The combination of the three indices efficiently predicted and classified the genotype behaviours despite few miss-classifications. Four common QTLs for BBIs and auto-regressive coefficient were highlighted (on LG4, 5, 8 and 10) and one for synchronicity (on LG9) in the integrated multi-family map, thus revealing the complex genetic architecture of the considered traits. This study proposes a posteriori sampling of axes within trees as a relevant and time-saving method to estimate tree flowering behaviours. Coupled to appropriate statistical indices, it is efficient to evaluate the tree breeding values for flowering regularity. In apple tree, biennial bearing appeared to result from high AS synchronism in flowering i.e., with all axes alternatively flowering or not in a given year, whereas regularity resulted from either asynchronous alternating or regular flowering of AS.

    Erratum to: The sponge microbiome project
    Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2018
    GigaScience 7 (2018)12. - ISSN 2047-217X
    The sponge microbiome project
    Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2017
    GigaScience 6 (2017)10. - ISSN 2047-217X
    16S rRNA gene - Archaea - Bacteria - Marine sponges - Microbial diversity - Microbiome - Symbiosis
    Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.
    Study of the three-way interaction between Trichoderma atroviride, plant and fungal pathogens by using a proteomic approach
    Marra, Roberta ; Ambrosino, Patrizia ; Carbone, Virginia ; Vinale, Francesco ; Woo, Sheridan L. ; Ruocco, Michelina ; Ciliento, Rosalia ; Lanzuise, Stefania ; Ferraioli, Simona ; Soriente, Ida ; Gigante, Sarah ; Turrà, David ; Fogliano, Vincenzo ; Scala, Felice ; Lorito, Matteo - \ 2006
    Current Genetics 50 (2006)5. - ISSN 0172-8083 - p. 307 - 321.
    Differential proteins - Fungal pathogens - Plant - Proteomics - Three-way interactions - Trichoderma

    The main molecular factors involved in the complex interactions occurring between plants (bean), two different fungal pathogens (Botrytis cinerea, Rhizoctonia solani) and an antagonistic strain of the genus Trichoderma were investigated. Two-dimensional (2-D) electrophoresis was used to analyze separately collected proteomes from each single, two- or three-partner interaction (i.e., plant, pathogenic and antagonistic fungus alone and in all possible combinations). Differential proteins were subjected to mass spectrometry and in silico analysis to search for homologies with known proteins. In the plant proteome, specific pathogenesis-related proteins and other disease-related factors (i.e., potential resistance genes) seem to be associated with the interaction with either one of the two pathogens and/ or T. atroviride. This finding is in agreement with the demonstrated ability of Trichoderma spp. to induce systemic resistance against various microbial pathogens. On the other side, many differential proteins obtained from the T. atroviride interaction proteome showed interesting homologies with a fungal hydrophobin, ABC transporters, etc. Virulence factors, like cyclophilins, were up-regulated in the pathogen proteome during the interaction with the plant alone or with the antagonist too. We isolated and confidently identified a large number of protein factors associated to the multi-player interactions examined.

    Evaluatie van de verzuringsdoelstellingen: de onderbouwing
    Albers, R. ; Beck, J. ; Bleeker, A. ; Bree, L. van; Dam, J. van; Eerden, L. v.d.; Freijer, J. ; Hinsberg, A. van; Marra, M. ; Salm, C. v.d.; Tonneijck, A. ; Vries, W. de; Wesselink, L. ; Woretelboer, F. - \ 2001
    Bilthoven : RIVM
    milieubeleid - evaluatie - milieueffect - zure depositie - waarden - modellen - nederland - terrestrische ecosystemen - atmosferische depositie - beleidsevaluatie - luchtverontreiniging - milieu - vegetatie - verzuring - environmental policy - evaluation - environmental impact - acid deposition - values - models - netherlands - terrestrial ecosystems
    Biochemical and morphological changes in lung tissue and isolated lung cells of rats induced by short-term nitrogen dioxide exposure
    Bree, L. van; Rietjens, I.M.C.M. ; Alink, G.M. ; Dormans, J.A.M.A. ; Marra, M. ; Rombout, P.J.A. - \ 2000
    Human and Experimental Toxicology 19 (2000). - ISSN 0960-3271 - p. 392 - 401.
    To investigate the effects of repeated exposure to nitrogen dioxide (NO2) on antioxidant enzymes in lung tissue and isolated lung cells, rats were continuously exposed to 20 mg/m3 NO2 (10.6 ppm) for 4 days. The activities of glucose-6-phosphate dehydrogenase (G6PDH), glutathione reductase (GR), and glutathione peroxidase (GSHPx) were measured in the cytosolic fraction of lung tissue of both control and NO2-exposed rats as well as in isolated alveolar macrophages (AMs) and type II cells. Qualitative and quantitative changes in AM and type II cells were studied by electron microscopy and by morphometric analyses using enzyme and immunohistochemistry. NO2 exposure resulted in significantly increased pulmonary activities of G6PDH, GR, and GSHPx, both expressed per lung and per gram of lung weight. Morphometric data show that NO2 exposure significantly increased the number of type II cells, predominantly in the centriacinar region, indicating proliferation of epithelium following cellular injury. Type II cells in lungs of NO2-exposed rats had a squamous, less cuboidal appearance with more lamellar bodies compared to type II cells in lungs of control rats. Compared to control lungs, a higher number of macrophages could be isolated from NO2-exposed lungs, while numbers of type II cells isolated from lungs of control and NO2-exposed rats were the same. Isolated type II cells from control and NO2-exposed rats were polymorphic, with a small number of lamellar bodies and without polarity. Isolated macrophages were rounded and contained many filopodia. NO2 exposure caused increases in the activities of G6PDH and GSHPx in isolated type II cells and of GSHPx in isolated macrophages, when expressed per number of cells. Macrophages and type II cells isolated from control and NO2-exposed rats and re-exposed in vitro to NO2, showed no differences in phagocytosis and viability features. Our results indicate that NO2-induced increases in pulmonary antioxidant enzymes are also reflected in isolated AM and type II cells. Since these lung cells do not display a decreased sensitivities toward an in vitro NO2 exposure, overall increase in antioxidant enzyme activities do not seem to play the most pivotal role in controlling cellular NO2 sensitivity and oxidant defence. Combined data from biochemical, morphological, and morphometric analyses of lungs and lung cells suggest that lung cell and tissue oxidant sensitivity and defence largely depends on the cell and tissue organisation, i.e., cell numbers and morphology as well as the ratio of surface area to cytoplasmic volume.
    Use of the lactococcal nisA promotor to regulate gene expression in gram-positive bacteria: comparison of induction level and promotor strength.
    Eichenbaum, Z. ; Federle, M.J. ; Marra, D. ; Vos, W.M. de; Kuipers, O.P. ; Kleerebezem, M. ; Scott, J.R. - \ 1998
    Applied and Environmental Microbiology 64 (1998). - ISSN 0099-2240 - p. 2763 - 2769.
    Respiratoire symptomen bij kinderen in relatie tot luchtverontreiniging door verkeer.
    Marra, M. ; Fischer, P.H. ; Lebret, E. ; Brunekreef, B. ; Wijnen, J.H. van - \ 1997
    Tijdschrift voor sociale geneeskunde 75 (1997)middenkatern. - ISSN 0040-7607 - p. 42 - 43.
    Glutathione pathway enzyme activities and the ozone sensitivity of lung cell populations derived from ozone exposed rats
    Rietjens, I.M.C.M. ; Bree, L. van; Marra, M. ; Poelen, M.C.M. ; Rombout, P.J.A. ; Alink, G.M. - \ 1985
    Toxicology 37 (1985). - ISSN 0300-483X - p. 205 - 214.
    Polyelectrolyte adsorption from saline solutions
    Marra, J. ; Schee, H.A. van der; Fleer, G.J. ; Lyklema, J. - \ 1983
    In: Adsorption from solution Academic Press - p. 245 - 258.
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