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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    Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
    Lieven, Christian ; Beber, Moritz E. ; Olivier, Brett G. ; Bergmann, Frank T. ; Ataman, Meric ; Babaei, Parizad ; Bartell, Jennifer A. ; Blank, Lars M. ; Chauhan, Siddharth ; Correia, Kevin ; Diener, Christian ; Dräger, Andreas ; Ebert, Birgitta E. ; Edirisinghe, Janaka N. ; Faria, José P. ; Feist, Adam M. ; Fengos, Georgios ; Fleming, Ronan M.T. ; García-Jiménez, Beatriz ; Hatzimanikatis, Vassily ; Helvoirt, Wout van; Henry, Christopher S. ; Hermjakob, Henning ; Herrgård, Markus J. ; Kaafarani, Ali ; Kim, Hyun Uk ; King, Zachary ; Klamt, Steffen ; Klipp, Edda ; Koehorst, Jasper J. ; König, Matthias ; Lakshmanan, Meiyappan ; Lee, Dong Yup ; Lee, Sang Yup ; Lee, Sunjae ; Lewis, Nathan E. ; Liu, Filipe ; Ma, Hongwu ; Machado, Daniel ; Mahadevan, Radhakrishnan ; Maia, Paulo ; Mardinoglu, Adil ; Medlock, Gregory L. ; Monk, Jonathan M. ; Nielsen, Jens ; Nielsen, Lars Keld ; Nogales, Juan ; Nookaew, Intawat ; Palsson, Bernhard O. ; Papin, Jason A. ; Patil, Kiran R. ; Poolman, Mark ; Price, Nathan D. ; Resendis-Antonio, Osbaldo ; Richelle, Anne ; Rocha, Isabel ; Sánchez, Benjamín J. ; Schaap, Peter J. ; Malik Sheriff, Rahuman S. ; Shoaie, Saeed ; Sonnenschein, Nikolaus ; Teusink, Bas ; Vilaça, Paulo ; Vik, Jon Olav ; Wodke, Judith A.H. ; Xavier, Joana C. ; Yuan, Qianqian ; Zakhartsev, Maksim ; Zhang, Cheng - \ 2020
    Nature Biotechnology 38 (2020)4. - ISSN 1087-0156 - 1 p.

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    MEMOTE for standardized genome-scale metabolic model testing
    Lieven, Christian ; Beber, Moritz E. ; Olivier, Brett G. ; Bergmann, Frank T. ; Ataman, Meric ; Babaei, Parizad ; Bartell, Jennifer A. ; Blank, Lars M. ; Chauhan, Siddharth ; Correia, Kevin ; Diener, Christian ; Dräger, Andreas ; Ebert, Birgitta E. ; Edirisinghe, Janaka N. ; Faria, José P. ; Feist, Adam M. ; Fengos, Georgios ; Fleming, Ronan M.T. ; García-Jiménez, Beatriz ; Hatzimanikatis, Vassily ; Helvoirt, Wout van; Henry, Christopher S. ; Hermjakob, Henning ; Herrgård, Markus J. ; Kaafarani, Ali ; Kim, Hyun Uk ; King, Zachary ; Klamt, Steffen ; Klipp, Edda ; Koehorst, Jasper J. ; König, Matthias ; Lakshmanan, Meiyappan ; Lee, Dong Yup ; Lee, Sang Yup ; Lee, Sunjae ; Lewis, Nathan E. ; Liu, Filipe ; Ma, Hongwu ; Machado, Daniel ; Mahadevan, Radhakrishnan ; Maia, Paulo ; Mardinoglu, Adil ; Medlock, Gregory L. ; Monk, Jonathan M. ; Nielsen, Jens ; Nielsen, Lars Keld ; Nogales, Juan ; Nookaew, Intawat ; Palsson, Bernhard O. ; Papin, Jason A. ; Patil, Kiran R. ; Poolman, Mark ; Price, Nathan D. ; Resendis-Antonio, Osbaldo ; Richelle, Anne ; Rocha, Isabel ; Sánchez, Benjamín J. ; Schaap, Peter J. ; Malik Sheriff, Rahuman S. ; Shoaie, Saeed ; Sonnenschein, Nikolaus ; Teusink, Bas ; Vilaça, Paulo ; Vik, Jon Olav ; Wodke, Judith A.H. ; Xavier, Joana C. ; Yuan, Qianqian ; Zakhartsev, Maksim ; Zhang, Cheng - \ 2020
    Nature Biotechnology 38 (2020)3. - ISSN 1087-0156 - p. 272 - 276.
    Corrigendum to “Opinion paper about organic trace pollutants in wastewater: Toxicity assessment in a European perspective"
    Pedrazzani, Roberta ; Bertanza, Giorgio ; Brnardić, Ivan ; Cetecioglu, Zeynep ; Dries, Jan ; Dvarionienė, Jolanta ; García-Fernández, Antonio J. ; Langenhoff, Alette ; Libralato, Giovanni ; Lofrano, Giusy ; Škrbić, Biljana ; Martínez-López, Emma ; Meriç, Süreyya ; Mutavdžić Pavlović, Dragana ; Papa, Matteo ; Schröder, Peter ; Tsagarakis, Konstantinos P. ; Vogelsang, Christian - \ 2019
    Science of the Total Environment 669 (2019). - ISSN 0048-9697 - p. 1062 - 1062.

    The authors regret that, despite thoroughly reviewing the manuscript, the content of a paragraph has been duplicated and has to be ignored .

    Opinion paper about organic trace pollutants in wastewater : Toxicity assessment in a European perspective
    Pedrazzani, Roberta ; Bertanza, Giorgio ; Brnardić, Ivan ; Cetecioglu, Zeynep ; Dries, Jan ; Dvarionienė, Jolanta ; García-Fernández, Antonio J. ; Langenhoff, Alette ; Libralato, Giovanni ; Lofrano, Giusy ; Škrbić, Biljana ; Martínez-López, Emma ; Meriç, Süreyya ; Pavlović, Dragana Mutavdžić ; Papa, Matteo ; Schröder, Peter ; Tsagarakis, Konstantinos P. ; Vogelsang, Christian - \ 2019
    Science of the Total Environment 651 (2019). - ISSN 0048-9697 - p. 3202 - 3221.
    Aquatic ecosystem - Bioassays - Ecotoxicity - Micro-pollutants - Risk assessment - Wastewater treatment

    This opinion paper focuses on the role of eco-toxicological tools in the assessment of possible impacts of emerging contaminants on the aquatic ecosystem, hence, on human health. Indeed, organic trace pollutants present in raw and treated wastewater are the pivot targets: a multidisciplinary approach allows defining the basic principles for managing this issue, from setting a proper monitoring campaign up to evaluating the optimal process treatment. Giving hints on trace pollutants fate and behaviour, attention is focused on the choice of the bioassay(s), by analysing the meaning of possible biological answers. Data interpretation and exploitation are detailed with the final goal of providing criteria in order to be able to select the best targeted treatment options. The manuscript deals with conventional and innovative analytical approaches for assessing toxicity, by reviewing laboratory and field assays; illustrative real scale and laboratory applications integrate and exemplify the proposed approach.

    Application of a decanter centrifuge for casein fractionation on pilot scale : Effect of operational parameters on total solid, purity and yield in solid discharge
    Schubert, Thomas ; Meric, Asutay ; Boom, Remko ; Hinrichs, Jörg ; Atamer, Zeynep - \ 2018
    International Dairy Journal 84 (2018). - ISSN 0958-6946 - p. 6 - 14.

    Individual casein fractions are of growing interest because of their multifunctional applications. The fractions of caseins (αS-, β- & κ-) possess a wide range of bio- and techno-functional properties. Although various isolation and purification methods to obtain casein fractions have been reported, there is still a need for improvement, especially on a technical scale. The aim of this study was to develop and establish a continuous process for the fractionation of caseins. The fractions were obtained from micellar casein by means of selective precipitation. The separation process was performed using a temperature-controlled decanter centrifuge. Enrichment of the fractions was optimised by altering the operational parameters of the decanter (inner weir diameter (Øweir), centrifugal force (FZ), differential speed (Δn), flow rate (V̇)). A 95% pure casein fraction containing αS- and β-casein was obtained. The purity and yield of the κ-casein fraction were 54% and 83%, respectively.

    Recent progress in understanding climate thresholds : Ice sheets, the Atlantic meridional overturning circulation, tropical forests and responses to ocean acidification
    Good, Peter ; Bamber, Jonathan ; Halladay, Kate ; Harper, Anna B. ; Jackson, Laura C. ; Kay, Gillian ; Kruijt, Bart ; Lowe, Jason A. ; Phillips, Oliver L. ; Ridley, Jeff ; Srokosz, Meric ; Turley, Carol ; Williamson, Phillip - \ 2018
    Progress in Physical Geography 42 (2018)1. - ISSN 0309-1333 - p. 24 - 60.
    Atlantic meridional overturning circulation - climate change - ice sheets - ocean acidification - thresholds - tropical forests
    This article reviews recent scientific progress, relating to four major systems that could exhibit threshold behaviour: ice sheets, the Atlantic meridional overturning circulation (AMOC), tropical forests and ecosystem responses to ocean acidification. The focus is on advances since the Intergovernmental Panel on Climate Change Fifth Assessment Report (IPCC AR5). The most significant developments in each component are identified by synthesizing input from multiple experts from each field. For ice sheets, some degree of irreversible loss (timescales of millennia) of part of the West Antarctic Ice Sheet (WAIS) may have already begun, but the rate and eventual magnitude of this irreversible loss is uncertain. The observed AMOC overturning has decreased from 2004–2014, but it is unclear at this stage whether this is forced or is internal variability. New evidence from experimental and natural droughts has given greater confidence that tropical forests are adversely affected by drought. The ecological and socio-economic impacts of ocean acidification are expected to greatly increase over the range from today’s annual value of around 400, up to 650 ppm CO2 in the atmosphere (reached around 2070 under RCP8.5), with the rapid development of aragonite undersaturation at high latitudes affecting calcifying organisms. Tropical coral reefs are vulnerable to the interaction of ocean acidification and temperature rise, and the rapidity of those changes, with severe losses and risks to survival at 2 °C warming above pre-industrial levels. Across the four systems studied, however, quantitative evidence for a difference in risk between 1.5 and 2 °C warming above pre-industrial levels is limited.
    E-course: Micropollutants in water
    Langenhoff, A.A.M. ; Meric, S. - \ 2017
    In: Innovative Wastewater Treatment Technologies & Resource Recovery Technologies / Lema, J.M., Suarez, S.S., London : IWA Publishing - ISBN 9781780407869 - p. 618 - 620.
    Comparative Genomics of Campylobacter fetus from Reptilesand Mammals Reveals Divergent Evolution in Host-Associated Lineages
    Gilbert, Maarten J. ; Miller, William G. ; Yee, Emma ; Zomer, Aldert ; Graaf-Van Bloois, Linda Van Der; Fitzgerald, C. ; Forbes, Ken J. ; Méric, Guillaume ; Sheppard, S. ; Wagenaar, J.A. ; Duim, Birgitta - \ 2016
    Genome Biology and Evolution 8 (2016)6. - ISSN 1759-6653 - p. 2006 - 2019.
    Campylobacter fetus currently comprises three recognized subspecies, which display distinct host association. Campylobacter fetus subsp. fetus and C. fetus subsp. venerealis are both associated with endothermic mammals, primarily ruminants, whereas C. fetus subsp. testudinum is primarily associated with ectothermic reptiles. Both C. fetus subsp. testudinum and C. fetus subsp. fetus have been associated with severe infections, often with a systemic component, in immunocompromised humans. To study the genetic factors associated with the distinct host dichotomy in C. fetus, whole-genome sequencing and comparison of mammal- and reptile-associated C. fetus was performed. The genomes of C. fetus subsp. testudinum isolated from either reptiles or humans were compared with elucidate the genetic factors associated with pathogenicity in humans. Genomic comparisons showed conservation of gene content and organization among C. fetus subspecies, but a clear distinction between mammal- and reptile-associated C. fetus was observed. Several genomic regions appeared to be subspecies specific, including a putative tricarballylate catabolism pathway, exclusively present in C. fetus subsp. testudinum strains. Within C. fetus subsp. testudinum, sapA, sapB, and sapAB type strains were observed. The recombinant locus iamABC (mlaFED) was exclusively associated with invasive C. fetus subsp. testudinum strains isolated from humans. A phylogenetic reconstruction was consistent with divergent evolution in host-associated strains and the existence of a barrier to lateral gene transfer between mammal- and reptile-associated C. fetus. Overall, this study shows that reptile-associated C. fetus subsp. testudinum is genetically divergent from mammal-associated C. fetus subspecies.
    Mitigation of septic shock in mice and rhesus monkeys by human chorionic gonadotrophin-related oligopeptides
    Khan (Erasmus MC), N.A. ; Vierboom, M.P.M. ; Holten-Neelen, C. van; Breedveld, E. ; Zuiderwijk-Sick, E. ; Khan, A. ; Kondova, I. ; Braskamp, G. ; Savelkoul, H.F.J. ; Dik, W.A. ; Hart, B.A. 't; Benner, R. - \ 2010
    Clinical and Experimental Immunology 160 (2010)3. - ISSN 0009-9104 - p. 466 - 478.
    sepsis - pathophysiology - hcg - heterogeneity - inhibition - progress - gender - forms
    The marked improvement of several immune-mediated inflammatory diseases during pregnancy has drawn attention to pregnancy hormones as potential therapeutics for such disorders. Low molecular weight fractions derived from the pregnancy hormone human chorionic gonadotrophin (hCG) have remarkable potent immunosuppressive effects in mouse models of diabetes and septic shock. Based on these data we have designed a set of oligopeptides related to the primary structure of hCG and tested these in models of septic shock in mice and rhesus monkeys. We demonstrate that mice exposed to lipopolysaccharide (LPS) and treated subsequently with selected tri-, tetra-, penta- and hepta-meric oligopeptides (i.e. MTR, VVC, MTRV, LQGV, AQGV, VLPALP, VLPALPQ) are protected against fatal LPS-induced septic shock. Moreover, administration of a cocktail of three selected oligopeptides (LQGV, AQGV and VLPALP) improved the pathological features markedly and nearly improved haemodynamic parameters associated with intravenous Escherichia coli-induced septic shock in rhesus monkeys. These data indicate that the designed hCG-related oligopeptides may present a potential treatment for the initial hyperdynamic phase of septic shock in humans
    Introducing techniques to save water
    Balendonck, J. ; Tuzel, Hakki ; Tuzel, Y. ; Meric, K. ; Oztekin, G. - \ 2009
    FlowerTECH 12 (2009)3. - ISSN 1388-8439 - p. 24 - 25.
    Structural studies on dihydrolipoyl transacetylase : the core component of the pyruvate dehydrogenase complex of Azotobacter vinelandii
    Hanemaaijer, J.R.O. - \ 1988
    Agricultural University. Promotor(en): C. Veeger, co-promotor(en): A. de Kok. - S.l. : Hanemaaijer - 119
    azotobacter - koolhydraatmetabolisme - oxidoreductasen - azotobacter - carbohydrate metabolism - oxidoreductases
    The studies described in this thesis deal with the structure of the Azotobactervinelandii dihydrolipoyl transacetylase, the core component (E 2 ) of the pyruvate dehydrogenase complex. in all organisms the pyruvate dehydrogenase complex is closely related to the 2-oxoglutarate dehydrogenase complex and, if present, the branched-chain 2-oxoacid dehydrogenase complex. These enzyme complexes are large multimeric structures. The smallest known is the pyruvate dehydrogenase complex from A.vinelandii , Upon resolution of the other components, the tetrameric core component of this complex aggregates to a welldefined multimeric structure, resembling the structure from the large complexes from other organisms.. Therefore, it seems likely that the A.vinelandii complex could represent the model for the building unit of the large complexes from other organisms. Since the core component (E 2 ) carries all the information concerning the quaternary structure of the complex, we focussed our attention on this intriguing enzyme.

    The domain structure of E 2 has been examined by limited proteolysis of E 2 , as described in chapter 2. After limited proteolysis with trypsin two stable domains were obtained. The lipoyl domain carries the lipoyl groups which are concerned with the transport of the substrates between the active sites of the different components. The catalytic domain possesses the transacetylase active site and the E 2 -intersubunit binding sites, responsible for the quaternary structure of E 2 . The binding sites for the E 1 and E 3 components are lost during proteolysis.

    The cloning and sequencing of the gene encoding dihydrolipoyl transacetylase have been described in chapter 3. The gene, located downstream of the gene encoding the PDC E 1 component, does not possess an own promoter, but is probably regulated by the E 1 -promoter. The gene possesses a strong terminating sequence. Downstream the gene encoding E 2 no open reading frame, that codes for the E 3 component, has been identified, as has been found in E.coli . The primary structure of E 2 , derived from the DNA sequence, is homologous to that of E 2 from E.coli . The lipoyl domain, located at the N-terminus, is built from three repeating sequences, separated by regions which are very rich in alanine and proline residues. The catalytic domain, located at the C-terminus, comprises the transacetylase active site and the E 2 intersubunit binding sites. The region, located between the lipoyl and the catalytic domain contains many charged amino acid residues and is thought to possess the E 1 and E 3 binding sites. The expression of the gene encoding E 2 , located on plasmid pRA282 and cloned in E.coli , has been described in chapter 4. A high production of E 2 was obtained. The production raised dramatically when the cells were in the stationery phase of the growth-cycle. The percentage active E 2 varied strongly per culture. The inactivation was found to be caused by formation of intramolecular or intermolecular S-S-bridges, resulting in incorrect folding of the catalytic domain. An activation and an isolation procedure have been described.

    Mobility of the repeating units within the lipoyl domain has been studied using time-resolved fluorescence, as described in chapter 5. It has been shown that the repeats show no independent rotational mobility, but rotate as one unit, serving the active sites of the different components.

    Internal mobility within the lipoyl domain has been observed by 1H-NMR experiments, as described in chapter 6. Probably this internal mobility, that is ascribed to the alanine-proline rich region, does not result into an independent mobility of the three repeats. The catalytic domain, despite its compact structure, still possesses a certain amount of internal mobility. This can partly be ascribed to alanine and proline residues, probably the N-terminal region of the domain, which is rich in these residues. In the spectrum of E 2 sharp resonances have been observed that can be ascribed to mobility of the E 1 and E 3 binding domain. Such mobility has not been found after binding of E 1 and E 3 components, in the whole complex.

    The molecular mass of the native catalytic domain and of the single polypeptide chain have been determined, and from this and light-scattering and crosslinking experiments it has been concluded that the large multimeric structure of the isolated catalytic domain (and of E 2 ) is built from 24 subunits in contrast to a 32-meric structure as proposed previously. A model has been presented for the quaternary structure of E 2 , in which it is assumed that the multimeric E 2 -core is built from six tetrameric morphological subunits, forming the lateral faces of the cubic 24-mer.

    These tetrameric subunits represent the E2-core of the intact complex. Compared to other 2-oxoacid dehydrogenase complexes, the A.vinelandii PDC contains one additional binding site for E 1 per E 2 tetramer. It is assumed that this extra binding site becomes available during dissociation, resulting in the unique small PDC of A.vinelandii .

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