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Krishnan, S. (author), Vermeulen, R. (author), Pronk, A. (author), Gyori, B.M. (author), Bachman, J.A. (author), Vlaanderen, J. (author), Stierum, R. (author)BACKGROUND: Mechanistic data is increasingly used in hazard identification of chemicals. However, the volume of data is large, challenging the efficient identification and clustering of relevant data. OBJECTIVES: We investigated whether evidence identification for hazard assessment can become more efficient and informed through an automated...article 2022
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Jagadeesan, B. (author), Gerner-Smidt, P. (author), Allard, M.W. (author), Leuillet, S. (author), Winkler, A. (author), Xiao, Y. (author), Chaffron, S. (author), Chaffron, S. (author), Tang, S. (author), Katase, M. (author), McClure, P. (author), Kimura, B. (author), Chai, L. Ching (author), Chapman, J. (author), Grant, K. (author)Next Generation Sequencing (NGS) combined with powerful bioinformatic approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of single isolates allows the most detailed comparison possible hitherto of individual strains. The two principle approaches for strain discrimination, single nucleotide polymorphism (SNP) analysis...article 2019
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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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Changing the field of carcinogenicity testing of human pharmaceuticals by emphasizing mode of actionvan der Laan, J.W. (author), Duijndam, B. (author), van den Hoorn, T. (author), Woutersen, R. (author), van de Water, B. (author)Lifetime testing for carcinogenicity of pharmaceuticals in rodents has been a controversial issue since the start of the International Conference on Harmonisation in 1990. Since 2010 the debate reached a new level following the proposal that a negative outcome of carcinogenicity studies can be predicted based upon the findings of 6 months...article 2017
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Fiamoncini, J. (author), Yiorkas, A.M. (author), Gedrich, K. (author), Rundle, M. (author), Alsters, S.I. (author), Roeselers, G. (author), van den Broek, T.J. (author), Clavel, T. (author), Lagkouvardos, I. (author), Wopereis, S. (author), Frost, G. (author), van Ommen, B. (author), Blakemore, A.I. (author), Daniel, H. (author)Bile acids (BA) are signaling molecules with a wide range of biological effects, also identified among the most responsive plasma metabolites in the postprandial state. We here describe this response to different dietary challenges and report on key determinants linked to its interindividual variability. Healthy men and women (n = 72, 62 ± 8 yr,...article 2017
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van Genabeek, J.A.G.M. (author), Gijsbers, G.W. (author), Esmeijer, J. (author), van der Klauw, D.M. (author), Wevers, C.W.J. (author)Deze studie verkent de relatie tussen technologie, innovatie en maatschappelijke ontwikkelingen, met name wat betreft de gezondheid, de (gezondheids)zorg en de (arbeids)participatie van mensen. We stellen ons de vraag hoe technologie de vermogens van mensen om deel te nemen aan arbeid en maatschappij kan versterken en beperken. We onderzoeken...report 2016
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Gruben, B.S. (author), Zhou, M. (author), Wiebenga, A. (author), Ballering, J. (author), Overkamp, K.M. (author), Punt, P.J. (author), de Vries, R.P. (author)The genome of the filamentous fungus Aspergillus niger is rich in genes encoding pectinases, a broad class of enzymes that have been extensively studied due to their use in industrial applications. The sequencing of the A. niger genome provided more knowledge concerning the individual pectinolytic genes, but little is known about the regulatory...article 2014
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Blatchford, P. (author), Ansell, J. (author), de Godoy, M.R.C. (author), Fahey, G. (author), Garcia-Mazcorro, J.F. (author), Gibson, G.R. (author), Goh, Y.J. (author), Hotchkiss, A.T. (author), Hutkins, R. (author), LaCroix, C. (author), Rastall, R.A. (author), Reimer, R.A. (author), Schoterman, M. (author), Van Sinderen, D. (author), Venema, K. (author), Whelan, K. (author)In October 2012, a group of scientists met at the 10th Meeting of the International Scientific Association of Probiotics and Prebiotics (ISAPP) in Cork, Ireland to discuss issues surrounding prebiotics and their development. This article summarises outputs from the meeting. Various prebiotic definitions were discussed and how the concept has...article 2013
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Ramautar, R. (author), Berger, R. (author), van der Greef, J. (author), Hankemeier, T. (author)Metabolomics provides a direct functional read-out of the physiological status of an organism and is in principle ideally suited to describe someone's health status. Whereas only a limited number of small metabolites are used in the clinics, in inborn errors of metabolism an extensive repertoire of metabolites are used as biomarkers. We discuss...article 2013
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- Cesuroglu, T. (author), van Ommen, B. (author), Malats, N. (author), Sudbrak, R. (author), Lehrach, H. (author), Brand, A. (author) article 2012
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Mariman, R. (author), Kremer, S.H.A. (author), van Erk, M. (author), Lagerweij, T. (author), Koning, F. (author), Nagelkerken, L. (author)Background: Host-microbiota interactions in the intestinal mucosa play a major role in intestinal immune homeostasis and control the threshold of local inflammation. The aim of this study was to evaluate the efficacy of probiotics in the recurrent trinitrobenzene sulfonic acid (TNBS)-induced colitis model and gain more insight into protective...article 2012
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Euser, S.M. (author), Nagelkerke, N.J. (author), Schuren, F. (author), Jansen, R. (author), den Boer, J.W. (author)Background: Legionella, the causative agent for Legionnaires' disease, is ubiquitous in both natural and man-made aquatic environments. The distribution of Legionella genotypes within clinical strains is significantly different from that found in environmental strains. Developing novel genotypic methods that offer the ability to distinguish...article 2012
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Boesten, R. (author), Schuren, F. (author), Wind, R.D. (author), Knol, J. (author), de Vos, W.M. (author)A total of 20 Bifidobacterium strains were isolated from fecal samples of 4 breast- and bottle-fed infants and all were characterized as Bifidobacterium breve based on 16S rRNA gene sequence and metabolic analysis. These isolates were further characterized and compared to the type strains of B. breve and 7 other Bifidobacterium spp. by...article 2011
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Punt, A. (author), Schiffelers, M.J.W.A. (author), Jean Horbach, G. (author), van de Sandt, J.J.M. (author), Groothuis, G.M.M. (author), Rietjens, I.M.C.M. (author), Blaauboer, B.J. (author)The present paper aims at identifying strategies to increase the impact and applicability of alternative testing strategies in risk assessment. To this end, a quantitative and qualitative literature evaluation was performed on (a) current research efforts in the development of in vitro methods aiming for alternatives to animal testing, (b) the...article 2011
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van der Vossen, J. (author), Keijser, B. (author), Schuren, F. (author), Nocker, A. (author), Montijn, R. (author)Thermophilic Campylobacter species are the most common cause of gastroenteritis in developed countries. Campylobacter spp. are ubiquitous in nature and widespread in livestock. Infections occur sporadically, and are believed to occur through consumption of contaminated meat products and from environmental sources. DNA-based techniques are...conference paper 2011
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Respiratory sensitization: Advances in assessing the risk of respiratory inflammation and irritationVandebriel, R. (author), Callant Cransveld, C. (author), Crommelin, D. (author), Diamant, Z. (author), Glazenburg, B. (author), Joos, G. (author), Kuper, F. (author), Natsch, A. (author), Nijkamp, F. (author), Noteborn, H. (author), Pieters, R. (author), Roberts, D. (author), Roggen, E. (author), Rorije, E. (author), Seed, M. (author), Sewald, K. (author), van den Heuvel, R. (author), van Engelen, J. (author), Verstraelen, S. (author), van Loveren, H. (author)Respiratory sensitization provides a case study for a new approach to chemical safety evaluation, as the prevalence of respiratory sensitization has increased considerably over the last decades, but animal and/or human experimental/predictive models are not currently available. Therefore, the goal of a working group was to design a road map to...article 2011
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van Batenburg, M.F. (author), Coulier, L. (author), van Eeuwijk, F. (author), Smilde, A.K. (author), Westerhuis, J.A. (author)In the field of metabolomics, hundreds of metabolites are measured simultaneously by analytical platforms such as gas chromatography/mass spectrometry (GC/MS), liquid chromatography/mass spectrometry (LC/MS) and NMR to obtain their concentration levels in a reliable way. Analytical repeatability (intrabatch precision) is a common figure of merit...article 2011
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Brul, S. (author), van Beilen, J. (author), Caspers, M. (author), O'Brien, A. (author), de Koster, C. (author), Oomes, S. (author), Smelt, J. (author), Kort, R. (author), ter Beek, A. (author)Bacterial spore formers are prime organisms of concern in the food industry. Spores from the genus Bacillus are extremely stress resistant, most notably exemplified by high thermotolerance. This sometimes allows surviving spores to germinate and grow out to vegetative cells causing food spoilage and possible intoxication. Similar issues though...article 2011
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van der Horst, E. (author), Peironcely, J.E. (author), van Westen, G.J.P. (author), van den Hoven, O.O. (author), Galloway, W.R.J.D. (author), Spring, D.R. (author), Wegner, J.K. (author), van Vlijmen, H.W.T. (author), Ijzerman, A.P. (author), Overington, J.P. (author), Bender, A. (author)Chemogenomic approaches, which link ligand chemistry to bioactivity against targets (and, by extension, to phenotypes) are becoming more and more important due to the increasing number of bioactivity data available both in proprietary databases as well as in the public domain. In this article we review chemogenomics approaches applied in four...article 2011
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Caspers, M.P.M. (author), Schuren, F.H.J. (author), van Zuijlen, A.C.M. (author), Brul, S. (author), Montijn, R.C. (author), Abee, T. (author), Kort, R. (author)Failure of food preservation is frequently caused by thermostable spores of members of the Bacillaceae family, which show a wide spectrum of resistance to cleaning and preservation treatments. We constructed and validated a mixed-species genotyping array for 6 Bacillus species, including Bacillus subtilis, Bacillus licheniformis, Bacillus...article 2011