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van der Veer, C. (author), Hertzberger, R.Y. (author), Bruisten, S.M. (author), Tytgat, H.L.P. (author), Swanenburg, J. (author), de Kat Angelino-Bart, A. (author), Schuren, F. (author), Molenaar, D. (author), Reid, G. (author), de Vries, H. (author), Kort, R. (author)Background: A vaginal microbiota dominated by lactobacilli (particularly Lactobacillus crispatus) is associated with vaginal health, whereas a vaginal microbiota not dominated by lactobacilli is considered dysbiotic. Here we investigated whether L. crispatus strains isolated from the vaginal tract of women with Lactobacillus-dominated vaginal...article 2019
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Rapid and generic identification of influenza A and other respiratory viruses with mass spectrometryMajchrzykiewicz-Koehorst, J.A. (author), Heikens, E. (author), Trip, H. (author), Hulst, A.G. (author), de Jong, A.L. (author), Viveen, M.C. (author), Sedee, N.J.A. (author), van der Plas, J. (author), Coenjaerts, F.E.J. (author), Paauw, A. (author)The rapid identification of existing and emerging respiratory viruses is crucial in combating outbreaks and epidemics. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid and reliable identification method in bacterial diagnostics, but has not been used in virological diagnostics. Mass...article 2015
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Roeselers, G. (author), Coolen, J. (author), van der Wielen, P.W. (author), Jaspers, M.C. (author), Atsma, A. (author), de Graaf, B. (author), Schuren, F. (author)In this study, we collected water from different locations in 32 drinking water distribution networks in the Netherlands and analysed the spatial and temporal variation in microbial community composition by high-throughput sequencing of 16S rRNA gene amplicons. We observed that microbial community compositions of raw source and processed water...article 2015
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van de Steeg, E. (author), Venhorst, J. (author), Jansen, H.T. (author), Nooijen, I.H.G. (author), Degroot, J. (author), Wortelboer, H.M. (author), Vlaming, M.L.H. (author)Human organic anion-transporting polypeptide 1B1 (OATP1B1) and OATP1B3 are important hepatic uptake transporters. Early assessment of OATP1B1/1B3-mediated drug-drug interactions (DDIs) is therefore important for successful drug development. A promising approach for early screening and prediction of DDIs is computational modeling. In this study...article 2015
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Majchrzykiewicz-Koehorst, J.A. (author), Heikens, E. (author), Trip, H. (author), Hulst, A.G. (author), de Jong, A.L. (author), Viveen, M.C. (author), Sedee, N.J.A. (author), van der Plas, J. (author), Coenjaerts, F.E.J. (author), Paauw, A. (author)Tested respiratory viruses: influenza A virus, respiratory syncytial virus (RSV) and human metapneumovirus (hMPV), were successfully identified directly from crude cell cultures using liquid chromatography-tandem MS (LC-MS/MS). The identification was preceded with the simple, generic and fast sample preparation method. The determined...conference paper 2014
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Lukovac, S. (author), Belzer, C. (author), Pellis, L. (author), Keijser, B.J. (author), de Vos, W.M. (author), Montijn, R.C. (author), Roeselers, G. (author)The gut microbiota is essential for numerous aspects of human health. However, the underlying mechanisms of many host-microbiota interactions remain unclear. The aim of this study was to characterize effects of the microbiota on host epithelium using a novel ex vivo model based on mouse ileal organoids. We have explored the transcriptional...article 2014
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Beker van Woudenberg, A. (author), Snel, C. (author), Rijkmans, E. (author), de Groot, D. (author), Bouma, M. (author), Hermsen, S. (author), Piersma, A. (author), Menke, A. (author), Wolterbeek, A. (author)To improve the predictability of the zebrafish embryotoxicity test (ZET) for developmental (neuro)toxicity screening, we used a multiple-endpoints strategy, including morphology, motor activity (MA), histopathology and kinetics. The model compounds used were antiepileptic drugs (AEDs): valproic acid (VPA), carbamazepine (CBZ), ethosuximide (ETH)...article 2014
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Chen, Y. (author), Sun, A. (author), Wang, M. (author), Zhu, Z. (author), Ouwerkerk, P.B.F. (author), Centraal Instituut voor Voedingsonderzoek TNO (author)Glutelins are the most abundant storage proteins in rice grain and can make up to 80 % of total protein content. The promoter region of GluB-1, one of the glutelin genes in rice, has been intensively used as a model to understand regulation of seed-storage protein accumulation. In this study, we describe a zinc finger gene of the Cys3His1 (CCCH...article 2014
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Hettne, K.M. (author), Boorsma, A. (author), van Dartel, D.A.M. (author), Goeman, J.J. (author), de Jong, E. (author), Piersma, A.H. (author), Stierum, R.H. (author), Kleinjans, J.C. (author), Kors, J.A. (author)Background: Availability of chemical response-specific lists of genes (gene sets) for pharmacological and/or toxic effect prediction for compounds is limited. We hypothesize that more gene sets can be created by next-generation text mining (next-gen TM), and that these can be used with gene set analysis (GSA) methods for chemical treatment...article 2013
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Terhal, P.A. (author), van Dommelen, P. (author), Le Merrer, M. (author), Zankl, A. (author), Simon, M.E. (author), Smithson, S.F. (author), Marcelis, C. (author), Kerr, B. (author), Kinning, E. (author), Mansour, S. (author), Hennekam, R.C. (author), van der Hout, A.H. (author), Cormier-Daire, V. (author), Lund, A.M. (author), Goodwin, L. (author), Mégarbané, A. (author), Lees, M. (author), Betz, R.C. (author), Tobias, E.S. (author), Coucke, P. (author), Mortier, G.R. (author)From data collected via a large international collaborative study, we have constructed a growth chart for patients with molecularly confirmed congenital spondylo-epiphyseal dysplasia (SEDC) and other COL2A1 related dysplasias. The growth chart is based on longitudinal height measurements of 79 patients with glycine substitutions in the triple...article 2012
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Koopman, F. (author), Wierckx, N. (author), de Winde, J.H. (author), Ruijssenaars, H.J. (author), TNO Kwaliteit van Leven (author)The toxic fermentation inhibitors in lignocellulosic hydrolysates pose significant problems for the production of second-generation biofuels and biochemicals. Among these inhibitors, 5-(hydroxymethyl) furfural (HMF) and furfural are specifically notorious. In this study, we describe the complete molecular identification and characterization of...article 2010
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Hamer, H.M. (author), Jonkers, D.M.A.E. (author), Renes, I.B. (author), Vanhoutvin, S.A.L.W. (author), Kodde, A. (author), Troost, F.J. (author), Venema, K. (author), Brummer, R.-J.M. (author), TNO Kwaliteit van Leven (author)INTRODUCTION: The colonic mucus layer plays an important role in the protection of the intestinal epithelium and mainly consists of mucin glycoproteins (primarily MUC2 in the colon) trefoil factor 3 (TFF3) and secretory IgA. Butyrate is a major end product of fermentation of dietary fibres and is associated with beneficial effects on colonic...article 2010
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TNO Kwaliteit van Leven (author), Wierckx, N. (author), Koopman, F. (author), Bandounas, L. (author), de Winde, J.H. (author), Ruijssenaars, H.J. (author)The formation of toxic fermentation inhibitors such as furfural and 5-hydroxy-2-methylfurfural (HMF) during acid (pre-)treatment of lignocellulose, calls for the efficient removal of these compounds. Lignocellulosic hydrolysates can be efficiently detoxified biologically with microorganisms that specifically metabolize the fermentation...article 2010
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Boesten, R.J. (author), Schuren, F.H.J. (author), de Vos, W.M. (author), TNO Kwaliteit van Leven (author)A genomic DNA-based microarray was constructed containing over 6000 randomly cloned genomic fragments of approximately 1-2 kb from six mammalian intestinal Bifidobacterium spp. including B. adolescentis, B. animalis, B. bifidum, B. catenulatum, B. longum and B. pseudolongum. This Bifidobacterium Mixed-Species (BMS) microarray was used to...article 2009
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Hockley, S.L. (author), Mathijs, K. (author), Staal, Y.C.M. (author), Brewer, D. (author), Giddings, I. (author), van Delft, J.H.M. (author), Phillips, D.H. (author), TNO Kwaliteit van Leven (author)Microarray technology is being used increasingly to study gene expression of biological systems on a large scale. Both interlaboratory and interplatform differences are known to contribute to variability in microarray data. In this study we have investigated data from different platforms and laboratories on the transcriptomic profile of HepG2...article 2009
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TNO Kwaliteit van Leven (author), Klaassens, E.S. (author), Boesten, R.J. (author), Haarman, M. (author), Knol, J. (author), Schuren, F.H. (author), Vaughan, E.E. (author), Vos, W.M.de (author)Although their exact function remains enigmatic, bifidobacteria are among the first colonizers of the newborn infant gut and further develop into abundant communities, notably in response to diet. Therefore, the transcriptional responses of bifidobacteria in rapidly processed fecal samples from young infants that were fed either breast milk or a...article 2009
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Kovatcheva-Datchary, P. (author), Egert, M. (author), Maathuis, A. (author), Rajilić-Stojanović, M. (author), de Graaf, A.A. (author), Smidt, H. (author), de Vos, W.M. (author), Venema, K. (author), TNO Kwaliteit van Leven (author)Summary Carbohydrates, including starches, are an important energy source for humans, and are known for their interactions with the microbiota in the digestive tract. Largely, those interactions are thought to promote human health. Using 16S ribosomal RNA (rRNA)-based stable isotope probing (SIP), we identified starch-fermenting bacteria under...article 2009
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Yuan, X.-L. (author), van der Kaaij, R.M. (author), van den Hondel, C.A.M.J.J. (author), Punt, P.J. (author), van der Maarel, M.J.E.C. (author), Dijkhuizen, L. (author), Ram, A.F.J. (author), TNO Kwaliteit van Leven (author)The filamentous ascomycete Aspergillus niger is well known for its ability to produce a large variety of enzymes for the degradation of plant polysaccharide material. A major carbon and energy source for this soil fungus is starch, which can be degraded by the concerted action of α-amylase, glucoamylase and α-glucosidase enzymes, members of the...article 2008
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Weelink, S.A.B. (author), Tan, N.C.G. (author), ten Broeke, H. (author), van den Kieboom, C. (author), van Doesburg, W. (author), Langenhoff, A.A.M. (author), Gerritse, J. (author), Junca, H. (author), Stams, A.J.M. (author), TNO Bouw en Ondergrond (author)A bacterium, strain BC, was isolated from a benzene-degrading chlorate-reducing enrichment culture. Strain BC degrades benzene in conjunction with chlorate reduction. Cells of strain BC are short rods that are 0.6 μm wide and 1 to 2 μm long, are motile, and stain gram negative. Strain BC grows on benzene and some other aromatic compounds with...article 2008
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Staal, Y.C.M. (author), Pushparajah, D.S. (author), van Herwijnen, M.H.M. (author), Gottschalk, R.W.H. (author), Maas, L.M. (author), Ioannides, C. (author), van Schooten, F.J. (author), van Delft, J.H.M. (author), TNO Kwaliteit van Leven (author)Although exposure to polycyclic aromatic hydrocarbons (PAHs) occurs mostly through mixtures, hazard and risk assessment are mostly based on the effects caused by individual compounds. The objective of the current study was to investigate whether interactions between PAHs occur, focusing on gene expression (as measured by cDNA microarrays) and...article 2008