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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    Inhibition of methyltransferase activity of enhancer of zeste 2 leads to enhanced lipid accumulation and altered chromatin status in zebrafish
    Broeder, Marjo J. den; Ballangby, Jarle ; Kamminga, Leonie M. ; Aleström, Peter ; Legler, Juliette ; Lindeman, Leif C. ; Kamstra, Jorke H. - \ 2020
    Epigenetics and Chromatin 13 (2020)1. - ISSN 1756-8935 - 1 p.
    ATAC-seq - Epigenetics - Histone methyl transferases - Metabolism - Zebrafish

    BACKGROUND: Recent studies indicate that exposure to environmental chemicals may increase susceptibility to developing metabolic diseases. This susceptibility may in part be caused by changes to the epigenetic landscape which consequently affect gene expression and lead to changes in lipid metabolism. The epigenetic modifier enhancer of zeste 2 (Ezh2) is a histone H3K27 methyltransferase implicated to play a role in lipid metabolism and adipogenesis. In this study, we used the zebrafish (Danio rerio) to investigate the role of Ezh2 on lipid metabolism and chromatin status following developmental exposure to the Ezh1/2 inhibitor PF-06726304 acetate. We used the environmental chemical tributyltin (TBT) as a positive control, as this chemical is known to act on lipid metabolism via EZH-mediated pathways in mammals. RESULTS: Zebrafish embryos (0-5 days post-fertilization, dpf) exposed to non-toxic concentrations of PF-06726304 acetate (5 μM) and TBT (1 nM) exhibited increased lipid accumulation. Changes in chromatin were analyzed by the assay for transposase-accessible chromatin sequencing (ATAC-seq) at 50% epiboly (5.5 hpf). We observed 349 altered chromatin regions, predominantly located at H3K27me3 loci and mostly more open chromatin in the exposed samples. Genes associated to these loci were linked to metabolic pathways. In addition, a selection of genes involved in lipid homeostasis, adipogenesis and genes specifically targeted by PF-06726304 acetate via altered chromatin accessibility were differentially expressed after TBT and PF-06726304 acetate exposure at 5 dpf, but not at 50% epiboly stage. One gene, cebpa, did not show a change in chromatin, but did show a change in gene expression at 5 dpf. Interestingly, underlying H3K27me3 marks were significantly decreased at this locus at 50% epiboly. CONCLUSIONS: Here, we show for the first time the applicability of ATAC-seq as a tool to investigate toxicological responses in zebrafish. Our analysis indicates that Ezh2 inhibition leads to a partial primed state of chromatin linked to metabolic pathways which results in gene expression changes later in development, leading to enhanced lipid accumulation. Although ATAC-seq seems promising, our in-depth assessment of the cebpa locus indicates that we need to consider underlying epigenetic marks as well.

    Neutrophils and macrophage cell count in the gut area of zebrafish larvae treated with antibiotics or saponin or a combination of treatments
    Lopez Nadal, Adria ; Brugman, Sylvia - \ 2019
    Wageningen University & Research
    Ciprofloxacin - Macrophages - Microbiota - Neutrophils - Oxytetracycline - Saponin - Zebrafish
    This data set contains data collected during zebrafish larvae experiments at the Wageningen University as part of Adrià López Nadal PhD Thesis. This study corresponds to the article: “Exposure to Antibiotics Affects Saponin Immersion-Induced Immune Stimulation and Shift in Microbial Composition in Zebrafish Larvae” published in Frontiers in Microbiology the 29th of October 2018.
    Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan
    Rougeot, Julien ; Chrispijn, Naomi D. ; Aben, Marco ; Elurbe, Dei M. ; Andralojc, Karolina M. ; Murphy, Patrick J. ; Jansen, Pascal W.T.C. ; Vermeulen, Michiel ; Cairns, Bradley R. ; Kamminga, Leonie M. - \ 2019
    Development 146 (2019)19. - ISSN 0950-1991
    ChIP-seq - Ezh2 - Polycomb - Proteomics - Transcriptomics - Zebrafish

    Polycomb group (PcG) proteins are transcriptional repressors that are important regulators of cell fate during embryonic development. Among them, Ezh2 is responsible for catalyzing the epigenetic repressive mark H3K27me3 and is essential for animal development. The ability of zebrafish embryos lacking both maternal and zygotic ezh2 to form a normal body plan provides a unique model for comprehensively studying Ezh2 function during early development in vertebrates. By using a multi-omics approach, we found that Ezh2 is required for the deposition of H3K27me3 and is essential for proper recruitment of Polycomb group protein Rnf2. However, despite the complete absence of PcG-associated epigenetic mark and proteins, only minor changes in H3K4me3 deposition and gene and protein expression occur. These changes were mainly due to local dysregulation of transcription factors outside their normal expression boundaries. Altogether, our results in zebrafish show that Polycomb-mediated gene repression is important immediately after the body plan is formed to maintain spatially restricted expression profiles of transcription factors, and we highlight the differences that exist in the timing of PcG protein action between vertebrate species.

    A single meal containing phytosterols does not affect the uptake or tissue distribution of cholesterol in zebrafish (Danio rerio)
    Spankeren, Michel van; Sibinga, Nathaniel ; Reinshol, Øyvind ; Torstensen, Bente E. ; Sæle, Øystein ; Liland, Nina S. - \ 2019
    Frontiers in Marine Science 6 (2019). - ISSN 2296-7745
    Aquaculture - Cholesterol - Cholesterol uptake - Phytosterols - Zebrafish

    Increased plant oil inclusion in aquaculture feeds has led to higher dietary phytosterol concentrations and speculation about whether this affects the metabolism and health of the fish. The mechanisms of cholesterol absorption and how phytosterols may affect this is unknown in fish. Zebrafish (Danio rerio) were used to study the effects of phytosterols on the uptake and organ distribution of dietary cholesterol in fish. One meal of diets containing a constant addition of cholesterol (cold and [4- 14 C] cholesterol) and varying types and concentrations of phytosterols were fed to fish in individual compartments. The fish were not previously conditioned on the experimental diets. Activity of 14 C was then measured in water and fish tissues to quantify the tissue distribution and excretion of cholesterol. There were no effects of the moderate dietary concentrations of phytosterols on the excretion or tissue distribution of dietary cholesterol 24 h after the meal.

    Biomechanics of swimming in developing larval fish
    Voesenek, Cees J. ; Muijres, Florian T. ; Leeuwen, Johan L. Van - \ 2018
    Journal of Experimental Biology 221 (2018)1. - ISSN 0022-0949
    Cost of transport - Energetics of locomotion - Escape manoeuvre - Fluid dynamics - Muscle development - Zebrafish

    Most larvae of bony fish are able to swim almost immediately after hatching. Their locomotory system supports several vital functions: fish larvae make fast manoeuvres to escape from predators, aim accurately during suction feeding and maymigrate towards suitable future habitats. Owing to their small size and low swimming speed, larval fish operate in the intermediate hydrodynamic regime, which connects the viscous and inertial flow regimes. They experience relatively strong viscous effects at low swimming speeds, and relatively strong inertial effects at their highest speeds. As the larvae grow and increase swimming speed, a shift occurs towards the inertial flow regime. To compensate for sizerelated limitations on swimming speed, fish larvae exploit high tail beat frequencies at their highest speeds, made possible by their low body inertia and fast neuromuscular system. The shifts in flow regime and body inertia lead to changing functional demands on the locomotory system during larval growth. To reach the reproductive adult stage, the developing larvae need to adjust to and perform the functions necessary for survival. Just after hatching, many fish larvae rely on yolk and need to develop their feeding systems before the yolk is exhausted. Furthermore, the larvae need to develop and continuously adjust their sensory, neural and muscular systems to catch prey and avoid predation. This Review discusses the hydrodynamics of swimming in the intermediate flow regime, the changing functional demands on the locomotory system of the growing and developing larval fish, and the solutions that have evolved to accommodate these demands.

    Oxazolone-induced intestinal inflammation in adult zebrafish
    Brugman, Sylvia ; Nieuwenhuis, Edward E.S. - \ 2017
    In: Inflammation / Clausen, Björn E., Laman, Jon D., Humana Press Inc. (Methods in Molecular Biology ) - ISBN 9781493967841 - p. 311 - 318.
    Crohn’s disease - Granulocytes - Gut barrier function - IBD - Intestinal inflammation - Intra-rectal injection - Oxazolone - Ulcerative colitis - Zebrafish

    Zebrafish are an excellent model for the study of intestinal immunity. The availability of several transgenic reporter fish for different innate and adaptive immune cells and the high homology in terms of gut function and morphology enables in depth analysis of the process of intestinal inflammation. Here, we describe a method to induce intestinal inflammation by intra-rectal injection of the hapten oxazolone in adult zebrafish.

    Oral vaccination of fish : Lessons from humans and veterinary species
    Embregts, Carmen W.E. ; Forlenza, Maria - \ 2016
    Developmental and Comparative Immunology 64 (2016). - ISSN 0145-305X - p. 118 - 137.
    Adenoviruses - Adjuvants - Encapsulation - Live vaccines - M-like cells - Zebrafish

    The limited number of oral vaccines currently approved for use in humans and veterinary species clearly illustrates that development of efficacious and safe oral vaccines has been a challenge not only for fish immunologists. The insufficient efficacy of oral vaccines is partly due to antigen breakdown in the harsh gastric environment, but also to the high tolerogenic gut environment and to inadequate vaccine design. In this review we discuss current approaches used to develop oral vaccines for mass vaccination of farmed fish species. Furthermore, using various examples from the human and veterinary vaccine development, we propose additional approaches to fish vaccine design also considering recent advances in fish mucosal immunology and novel molecular tools. Finally, we discuss the pros and cons of using the zebrafish as a pre-screening animal model to potentially speed up vaccine design and testing for aquaculture fish species.

    The zebrafish as a model to study intestinal inflammation
    Brugman, Sylvia - \ 2016
    Developmental and Comparative Immunology 64 (2016). - ISSN 0145-305X - p. 82 - 92.
    Enterocolitis - Immunity - Inflammation - Intestines - Zebrafish

    Starting out as a model for developmental biology, during the last decade, zebrafish have also gained the attention of the immunologists and oncologists. Due to its small size, high fecundity and full annotation of its genome, the zebrafish is an attractive model system. The fact that fish are transparent early in life combined with the growing list of immune cell reporter fish, enables in vivo tracking of immune responses in a complete organism. Since zebrafish develop ex utero from a fertilized egg, immune development can be monitored from the start of life. Given that several gut functions and immune genes are conserved between zebrafish and mammals, the zebrafish is an interesting model organism to investigate fundamental processes underlying intestinal inflammation and injury. This review will first provide some background on zebrafish intestinal development, bacterial colonization and immunity, showing the similarities and differences compared to mammals. This will be followed by an overview of the existing models for intestinal disease, and concluded by future perspectives in light of the newest technologies and insights.

    Polarization of immune responses in fish : The 'macrophages first' point of view
    Wiegertjes, Geert F. ; Wentzel, Annelieke S. ; Spaink, Herman P. ; Elks, Philip M. ; Fink, Inge R. - \ 2016
    Molecular Immunology 69 (2016). - ISSN 0161-5890 - p. 146 - 156.
    Arginase - Fish - INOS - LPS - Macrophage polarization - Zebrafish

    In this review, we support taking polarized immune responses in teleost fish from a 'macrophage first' point of view, a hypothesis that reverts the dichotomous T helper (TH)1 and TH2 driving forces by building on the idea of conservation of innate immune responses in lower vertebrates. It is plausible that the initial trigger for macrophage polarization into M1 (inflammation) or M2 (healing) could rely only on sensing microbial/parasite infection or other innate danger signals, without the influence of adaptive immunity. Given the long and ongoing debate on the presence/absence of a typical TH1 cytokine environment and, in particular, TH2 cytokine environment in fish immune responses, it stands out that the presence of macrophages with polarized phenotypes, alike M1 and M2, have been relatively easy to demonstrate for fish. We summarize in short present knowledge in teleost fish on those cytokines considered most critical to the dichotomous development of TH1/M1 and TH2/M2 polarization, in particular, but not exclusively, interferon-γ and interleukin (IL)-4/IL-13. We review, in more detail, polarization of fish immune responses taken from the macrophage point of view for which we adopted the simple nomenclature of M1 and M2. We discuss inducible nitric oxide synthase, or NOS-2, as a reliable M1 marker and arginase-2 as a reliable M2 marker for teleost fish and discuss the value of these macrophage markers for the generation of zebrafish reporter lines to study M1/M2 polarization in vivo.

    Vitamin K reduces hypermineralisation in zebrafish models of PXE and GACI
    Mackay, Eirinn W. ; Apschner, Alexander ; Schulte-Merker, Stefan - \ 2015
    Development 142 (2015)6. - ISSN 0950-1991 - p. 1095 - 1101.
    ABCC6 - Mineralisation - PXE - Vitamin K - Zebrafish

    The mineralisation disorder pseudoxanthoma elasticum (PXE) is associated with mutations in the transporter protein ABCC6. Patients with PXE suffer from calcified lesions in the skin, eyes and vasculature, and PXE is related to a more severe vascular calcification syndrome called generalised arterial calcification of infancy (GACI). Mutations in ABCC6 are linked to reduced levels of circulating vitamin K. Here, we describe a mutation in the zebrafish (Danio rerio) orthologue abcc6a, which results in extensive hypermineralisation of the axial skeleton. Administration of vitamin K to embryos was sufficient to restore normal levels of mineralisation. Vitamin K also reduced ectopic mineralisation in a zebrafish model of GACI, and warfarin exacerbated the mineralisation phenotype in both mutant lines. These data suggest that vitamin K could be a beneficial treatment for human patients with PXE or GACI. Additionally, we found that abcc6a is strongly expressed at the site of mineralisation rather than the liver, as it is in mammals, which has significant implications for our understanding of the function of ABCC6.

    Early life exposure to PCB126 results in delayed mortality and growth impairment in the zebrafish larvae
    Paolo, Carolina Di; Groh, Ksenia J. ; Zennegg, Markus ; Vermeirssen, Etiënne L.M. ; Murk, Albertinka J. ; Eggen, Rik I.L. ; Hollert, Henner ; Werner, Inge ; Schirmer, Kristin - \ 2015
    Aquatic Toxicology 169 (2015). - ISSN 0166-445X - p. 168 - 178.
    Delayed effects - Early life stages - Growth - PCB126 - Sublethal effects - Zebrafish

    The occurrence of chronic or delayed toxicity resulting from the exposure to sublethal chemical concentrations is an increasing concern in environmental risk assessment. The Fish Embryo Toxicity (FET) test with zebrafish provides a reliable prediction of acute toxicity in adult fish, but it cannot yet be applied to predict the occurrence of chronic or delayed toxicity. Identification of sublethal FET endpoints that can assist in predicting the occurrence of chronic or delayed toxicity would be advantageous. The present study characterized the occurrence of delayed toxicity in zebrafish larvae following early exposure to PCB126, previously described to cause delayed effects in the common sole. The first aim was to investigate the occurrence and temporal profiles of delayed toxicity during zebrafish larval development and compare them to those previously described for sole to evaluate the suitability of zebrafish as a model fish species for delayed toxicity assessment. The second aim was to examine the correlation between the sublethal endpoints assessed during embryonal and early larval development and the delayed effects observed during later larval development. After exposure to PCB126 (3-3000. ng/L) until 5 days post fertilization (dpf), larvae were reared in clean water until 14 or 28 dpf. Mortality and sublethal morphological and behavioural endpoints were recorded daily, and growth was assessed at 28 dpf. Early life exposure to PCB126 caused delayed mortality (300. ng/L and 3000. ng/L) as well as growth impairment and delayed development (100. ng/L) during the clean water period. Effects on swim bladder inflation and cartilaginous tissues within 5 dpf were the most promising for predicting delayed mortality and sublethal effects, such as decreased standard length, delayed metamorphosis, reduced inflation of swim bladder and column malformations. The EC50 value for swim bladder inflation at 5 dpf (169. ng/L) was similar to the LC50 value at 8 dpf (188 and 202. ng/L in two experiments). Interestingly, the patterns of delayed mortality and delayed effects on growth and development were similar between sole and zebrafish. This indicates the comparability of critical developmental stages across divergent fish species such as a cold water marine flatfish and a tropical freshwater cyprinid. Additionally, sublethal effects in early embryo-larval stages were found promising for predicting delayed lethal and sublethal effects of PCB126. Therefore, the proposed method with zebrafish is expected to provide valuable information on delayed mortality and delayed sublethal effects of chemicals and environmental samples that may be extrapolated to other species.

    Carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase (cad) regulates Notch signaling and vascular development in zebrafish
    Coxam, Baptiste ; Neyt, Christine ; Grassini, D.R. ; Guen, Ludovic Le; Smith, K.A. ; Schulte-Merker, Stefan ; Hogan, B.M. - \ 2015
    Developmental Dynamics 244 (2015)1. - ISSN 1058-8388 - p. 1 - 9.
    Angiogenesis - Glycosylation - Lymphangiogenesis - Notch - Vegfc - Zebrafish

    Background: The interplay between Notch and Vegf signaling regulates angiogenesis in the embryo. Notch signaling limits the responsiveness of endothelial cells to Vegf to control sprouting. Despite the importance of this regulatory relationship, much remains to be understood about extrinsic factors that modulate the pathway. Results: During a forward genetic screen for novel regulators of lymphangiogenesis, we isolated a mutant with reduced lymphatic vessel development. This mutant also exhibited hyperbranching arteries, reminiscent of Notch pathway mutants. Positional cloning identified a missense mutation in the carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase (cad) gene. Cad is essential for UDP biosynthesis, which is necessary for protein glycosylation and de novo biosynthesis of pyrimidine-based nucleotides. Using a transgenic reporter of Notch activity, we demonstrate that Notch signaling is significantly reduced in cadhu10125 mutants. In this context, genetic epistasis showed that increased endothelial cell responsiveness to Vegfc/Vegfr3 signaling drives excessive artery branching. Conclusions: These findings suggest important posttranslational modifications requiring Cad as an unappreciated mechanism that regulates Notch/Vegf signaling during angiogenesis.

    An un-momentous start to life: Can hydrodynamics explain why fish larvae change swimming style?
    Müller, Ulrike K. ; Leeuwen, Johan L. van; Duin, Stephan van; Liu, Hao - \ 2009
    Journal of Biomechanical Science and Engineering 4 (2009)1. - ISSN 1880-9863 - p. 37 - 53.
    Burst and coast - Danio Rerio - Fish larvae - Intermittent swimming - Viscous flow regime - Zebrafish

    In this study, we explore mechanical constraints on the swimming performance of zebrafish larvae (Danio rerio) that might explain why larvae switch from sustained swimming to the more efficient burst & coast as they grow. Two hypotheses have been proposed to explain why young fish larvae perform poorly at burst & coast. First, their initial momentum might be low; second, their drag coefficient might be high. To test the two hypotheses, this study makes a quantitative comparison between experimental observations of swimming fish larvae and a CFD model of a self-propelled fish. The study focuses on larvae of the crucial age and size range in which zebrafish switch swimming style. Our studies show that hatchlings perform poorly not only because they cannot accelerate to a high initial coasting speed and hence do not gain enough initial momentum. But they also suffer higher decelerations while coasting due to a high drag coefficient. Overall, the fivefold difference in coasting distance between hatchlings and older larvae corresponds closely to a threefold difference in the time constant of the speed decay and a threefold difference in initial momentum. Our data also show that swimming speed does not decay exponentially, as predicted by the drag-speed relationship in the viscous flow regime, but hyperbolically, due to flow phenomena developing in the boundary layer during the coast.

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