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Correction to: Toxicogenomics directory of chemically exposed human hepatocytes

Grinberg, M. (author), Stöber, R.M. (author), Edlund, K. (author), Rempel, E. (author), Godoy, P. (author), Reif, R. (author), Widera, A. (author), Madjar, K. (author), Schmidt-Heck, W. (author), Marchan, R. (author), Sachinidis, A. (author), Spitkovsky, D. (author), Hescheler, J. (author), Carmo, H. (author), Arbo, M.D. (author), van de Water, B. (author), Wink, S. (author), Vinken, M. (author), Rogiers, V. (author), Escher, S. (author), Hardy, B. (author), Mitic, D. (author), Myatt, G. (author), Waldmann, T. (author), Mardinoglu, A. (author), Damm, G. (author), Seehofer, D. (author), Nüssler, A. (author), Weiss, T.S. (author), Oberemm, A. (author), Lampen, A. (author), Schaap, M.M. (author), Luijten, M. (author), van Steeg, H. (author), Thasler, W.E. (author), Kleinjans, J.C.S. (author), Stierum, R.H. (author), Leist, M. (author), Rahnenführer, J. (author), Hengstler, J.G. (author)

Correction to: Arch Toxicol (2014) 88:2261–2287 https://doi.org/10.1007/s00204-014-1400-x.

article 2022

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Plasticity of lifelong calorie-restricted C57BL/6J mice in adapting to a medium-fat diet intervention at old age

Rusli, F. (author), Boekschoten, M.V. (author), Borelli, V. (author), Sun, C. (author), Lute, C. (author), Menke, A.L. (author), van den Heuvel, J. (author), Salvioli, S. (author), Franceschi, C. (author), Müller, M. (author), Steegenga, W.T. (author)

Calorie restriction (CR) is a dietary regimen that supports healthy aging. In this study, we investigated the systemic and liver-specific responses caused by a diet switch to a medium-fat (MF) diet in 24-month-old lifelong, CR-exposed mice. This study aimed to increase the knowledge base on dietary alterations of gerontological relevance. Nine...

article 2018

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The probiotic mixture VSL#3 has differential effects on intestinal immune parameters in healthy female BALB/c and C57BL/6 mice

Mariman, R. (author), Tielen, F. (author), Koning, F. (author), Nagelkerken, L. (author)

Background: Probiotic bacteria may render mice resistant to the development of various inflammatory and infectious diseases. Objective: This study aimed to identify mechanisms by which probiotic bacteria may influence intestinal immune homeostasis in noninflammatory conditions. Methods: The effect of VSL#3, a mixture of 8 probiotic bacteria, on...

article 2015

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A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal

Goelela, V.S. (author), Kelder, T. (author), Adriaens, M.E. (author), Evelo, C.T. (author), Radonijc, M. (author)

Background Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and...

article 2015

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Anacetrapib reduces (V)LDL-cholesterol by inhibition of CETP activity and reduction of plasma PCSK9

van der Tuin, S.J. (author), Kühnast, S. (author), Berbée, J. (author), Verschuren, L. (author), Pieterman, E.J. (author), Havekes, L.M. (author), van der Hoorn, J.W. (author), Rensen, P.C. (author), Jukema, J.W. (author), Princen, H.M. (author), Willems van Dijk, K. (author), Wang, Y. (author)

Recently, we showed in APOE*3-Leiden.CETP mice that anacetrapib attenuated atherosclerosis development by reducing (V)LDL-C rather than by raising HDL-C. Here, we investigated the mechanism by which anacetrapib reduces (V)LDL-C and whether this effect was dependent on the inhibition of CETP. APOE*3-Leiden.CETP mice were fed a Western type diet...

article 2015

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The impact of hormonal contraception and pregnancy on sexually transmitted infections and on cervicovaginal microbiota in african sex workers

Borgdorff, H. (author), Verwijs, M.C. (author), Wit, F.W.N.M. (author), Tsivtsivadze, E. (author), Ndayisaba, G.F. (author), Verhelst, R. (author), Schuren, F.H. (author), van de Wijgert, J.H.H.M. (author)

Background The observed association between Depo-Provera injectable use and increased HIV acquisition may be caused by hormone-induced increased susceptibility to other sexually transmitted infections (STIs) or changes in the cervicovaginal microbiota (VMB), accompanied by genital immune activation and/or mucosal remodeling. Methods Rwandan...

article 2015

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Toxicogenomics directory of chemically exposed human hepatocytes

Grinberg, M. (author), Stöber, R.M. (author), Edlund, K. (author), Rempel, E. (author), Godoy, P. (author), Reif, R. (author), Widera, A. (author), Madjar, K. (author), Schmidt-Heck, W. (author), Marchan, R. (author), Sachinidis, A. (author), Spitkovsky, D. (author), Hescheler, J. (author), Carmo, H. (author), Arbo, M.D. (author), van de Water, B. (author), Wink, S. (author), Vinken, M. (author), Rogiers, V. (author), Escher, S. (author), Hardy, B. (author), Mitic, D. (author), Myatt, G. (author), Waldmann, T. (author), Mardinoglu, A. (author), Damm, G. (author), Seehofer, D. (author), Nüssler, A. (author), Weiss, T.S. (author), Oberemm, A. (author), Lampen, A. (author), Schaap, M.M. (author), Luijten, M. (author), van Steeg, H. (author), Thasler, W.E. (author), Kleinjans, J.C.S. (author), Stierum, R.H. (author), Leist, M. (author), Rahnenführer, J. (author), Hengstler, J.G. (author)

A long-term goal of numerous research projects is to identify biomarkers for in vitro systems predicting toxicity in vivo. Often, transcriptomics data are used to identify candidates for further evaluation. However, a systematic directory summarizing key features of chemically influenced genes in human hepatocytes is not yet available. To bridge...

article 2014

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Aspergillus niger RhaR, a regulator involved in L-rhamnose release and catabolism

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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Gene expression profiling identifies mechanisms of protection to recurrent trinitrobenzene sulfonic acid colitis mediated by probiotics

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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Genome Analysis of Legionella pneumophila Strains Using a Mixed-Genome Microarray

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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A combined transcriptomics and lipidomics analysis of subcutaneous, epididymal and mesenteric adipose tissue reveals marked functional differences

TNO Kwaliteit van Leven (author), Caesar, R. (author), Manieri, M. (author), Kelder, T. (author), Boekschoten, M. (author), Evelo, C. (author), Müller, M. (author), Kooistra, T. (author), Cinti, S. (author), Kleemann, R. (author), Drevon, C.A. (author)

Depot-dependent differences in adipose tissue physiology may reflect specialized functions and local interactions between adipocytes and surrounding tissues. We combined time-resolved microarray analyses of mesenteric- (MWAT), subcutaneous- (SWAT) and epididymal adipose tissue (EWAT) during high-fat feeding of male transgenic ApoE3Leiden mice...

article 2010

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Early gene expression changes during embryonic stem cell differentiation into cardiomyocytes and their modulation by monobutyl phthalate

van Dartel, D.A.M. (author), Pennings, J.L.A. (author), Hendriksen, P.J.M. (author), van Schooten, F.J. (author), Piersma, A.H. (author), TNO Kwaliteit van Leven (author)

The Embryonic Stem cell Test (EST) is an in vitro alternative test designed for the prediction of embryotoxicity. The endpoint of the test is the interference with mesoderm-derived cardiac muscle differentiation observed under the microscope as beating muscle foci. The relative subjectivity of this endpoint, as well as the applicability domain...

article 2009

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Interlaboratory and interplatform comparison of microarray gene expression analysis of HepG2 cells exposed to benzo(a)pyrene

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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Mixed-species genomic microarray analysis of fecal samples reveals differential transcriptional responses of bifidobacteria in breast- And formula-fed infants

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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Aspergillus niger genome-wide analysis reveals a large number of novel alpha-glucan acting enzymes with unexpected expression profiles

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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The contact allergen dinitrochlorobenzene (DNCB) and respiratory allergy in the Th2-prone Brown Norway rat

Kuper, C.F. (author), Stierum, R.H. (author), Boorsma, A. (author), Schijf, M.A. (author), Prinsen, M. (author), Bruijntjes, J.P. (author), Bloksma, N. (author), Arts, J.H.E. (author), TNO Kwaliteit van Leven (author)

All LMW respiratory allergens known to date can also induce skin allergy in test animals. The question here was if in turn skin allergens can induce allergy in the respiratory tract. Respiratory allergy was tested in Th2-prone Brown Norway (BN) rats by dermal sensitization with the contact allergen dinitrochlorobenzene (DNCB; 1%, day 0; 0.5%,...

article 2008

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Genomic diversity within the enterobacter cloacae complex

TNO Kwaliteit van Leven (author), Paauw, A. (author), Caspers, M.P.M. (author), Schuren, F.H.J. (author), Leverstein-van Hall, M.A. (author), Delétoile, A. (author), Montijn, R.C. (author), Verhoef, J. (author), Fluit, A.C. (author)

Background: Isolates of the Enterobacter cloacae complex have been increasingly isolated as nosocomial pathogens, but phenotypic identification of the E. cloacae complex is unreliable and irreproducible. Identification of species based on currently available genotyping tools is already superior to phenotypic identification, but the taxonomy of...

article 2008

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Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA

Nueda, M.J. (author), Conesa, A. (author), Westerhuis, J.A. (author), Hoefsloot, H.C.J. (author), Smilde, A.K. (author), Talón, M. (author), Ferrer, A. (author), TNO Kwaliteit van Leven (author)

Motivation: Designed microarray experiments are used to investigate the effects that controlled experimental factors have on gene expression and learn about the transcriptional responses associated with external variables. In these datasets, signals of interest coexist with varying sources of unwanted noise in a framework of (co)relation among...

article 2007

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Genomotyping of Pseudomonas putida strains using P. putida KT2440-based high-density DNA microarrays: Implications for transcriptomics studies

Ballerstedt, H. (author), Volkers, R.J.M. (author), Mars, A.E. (author), Hallsworth, J.E. (author), Santos, V.A.M.D. (author), Puchalka, J. (author), van Duuren, J. (author), Eggink, G. (author), Timmis, K.N. (author), de Bont, J.A.M. (author), Wery, J. (author), TNO Kwaliteit van Leven (author)

Pseudomonas putida KT2440 is the only fully sequenced P. putida strain. Thus, for transcriptomics and proteomics studies with other P. putida strains, the P. putida KT2440 genomic database serves as standard reference. The utility of KT2440 whole-genome, high-density oligonucleotide microarrays for transcriptomics studies of other Pseudomonas...

article 2007

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Transcriptomics analysis of interactive effects of benzene, trichloroethylene and methyl mercury within binary and ternary mixtures on the liver and kidney following subchronic exposure in the rat

Hendriksen, P.J.M. (author), Freidig, A.P. (author), Jonker, D. (author), Thissen, U. (author), Bogaards, J.J.P. (author), Mumtaz, M.M. (author), Groten, J.P. (author), Stierum, R.H. (author), TNO Kwaliteit van Leven (author)

The present research aimed to study the interaction of three chemicals, methyl mercury, benzene and trichloroethylene, on mRNA expression alterations in rat liver and kidney measured by microarray analysis. These compounds were selected based on presumed different modes of action. The chemicals were administered daily for 14 days at the Lowest...

article 2007