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Time-resolved and tissue-specific systems analysis of the pathogenesis of insulin resistance

TNO Kwaliteit van Leven (author), Kleemann, R. (author), van Erk, M. (author), Verschuren, L. (author), van den Hoek, A.M. (author), Koek, M. (author), Wielinga, P.Y. (author), Jie, A. (author), Pellis, L. (author), Bobeldijk-Pastorova, I. (author), Kelder, T. (author), Toet, K. (author), Wopereis, S. (author), Cnubben, N. (author), Evelo, C. (author), van Ommen, B. (author), Kooistra, T. (author)

BACKGROUND: The sequence of events leading to the development of insulin resistance (IR) as well as the underlying pathophysiological mechanisms are incompletely understood. As reductionist approaches have been largely unsuccessful in providing an understanding of the pathogenesis of IR, there is a need for an integrative, time-resolved approach...

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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Flexible biochips for detection of biomolecules

Peter, M. (author), Schüler, T. (author), Furthner, F. (author), Rensing, P.A. (author), van Heck, G.T. (author), Schoo, H.F.M. (author), Möllier, R. (author), Fritzsche, W. (author), van Breemen, A.J.J.M. (author), Meinders, E.R. (author), TNO Industrie en Techniek (author)

Miniaturization of biosensors is envisaged by the development of biochips consisting of parallel microarray patterns of binding sites on rigid substrates, such as glass or silicon. Thin plastic substrates are promising flexible alternatives because of the possibility for large-area roll-to-roll manufacturing of disposable chips at lower costs....

article 2009

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A Bifidobacterium mixed-species microarray for high resolution discrimination between intestinal bifidobacteria

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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TrgI, toluene repressed gene I, a novel gene involved in toluene-tolerance in Pseudomonas putida S12

Volkers, R.J.M. (author), Ballerstedt, H. (author), Ruijssenaars, H. (author), de Bont, J.A.M. (author), de Winde, J.H. (author), Wery, J. (author), TNO Kwaliteit van Leven (author)

Pseudomonas putida S12 is well known for its remarkable solvent tolerance. Transcriptomics analysis of this bacterium grown in toluene-containing chemostats revealed the differential expression of 253 genes. As expected, the genes encoding one of the major solvent tolerance mechanisms, the solvent efflux pump SrpABC and its regulatory genes...

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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Transcriptome analysis of sorbic acid-stressed Bacillus subtilis reveals a nutrient limitation response and indicates plasma membrane remodeling

ter Beek, A. (author), Keijser, B.J.F. (author), Boorsma, A. (author), Zakrzewska, A. (author), Orij, R. (author), Smits, G.J. (author), Brul, S. (author), TNO Kwaliteit van Leven (author)

The weak organic acid sorbic acid is a commonly used food preservative, as it inhibits the growth of bacteria, yeasts, and molds. We have used genome-wide transcriptional profiling of Bacillus subtilis cells during mild sorbic acid stress to reveal the growth-inhibitory activity of this preservative and to identify potential resistance...

article 2008

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Molecular characterization of trimellitic anhydride-induced respiratory allergy in Brown Norway rats

Kuper, C.F. (author), Heijne, W.H. (author), Dansen, M. (author), Verhoeckx, K.C. (author), Boorsma, A. (author), Radonjic, M. (author), Bruijntjes, J. (author), Stierum, R. (author), Muijser, H. (author), Arts, J.H. (author), TNO Kwaliteit van Leven (author)

To contribute to the hazard identification of low molecular weight (LMW) respiratory allergens, respiratory allergy induced by trimellitic anhydride (TMA) was characterized by whole genome analysis of lung tissue and blood proteomics in Brown Norway rats. Dermal sensitization (50% and 25% w/v) with TMA and an inhalation challenge of 15 mg/m(3)...

article 2008

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Interactions between polycyclic aromatic hydrocarbons in binary mixtures: Effects on gene expression and DNA adduct formation in precision-cut rat liver slices

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

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A framework to identify physiological responses in microarray-based gene expression studies: Selection and interpretation of biologically relevant genes

Rodenburg, W. (author), Heidema, A.G. (author), Boer, J.M.A. (author), Bovee-Oudenhoven, I.M.J. (author), Feskens, E.J.M. (author), Mariman, E.C.M. (author), Keijer, J. (author), TNO Kwaliteit van Leven (author)

In whole genome microarray studies major gene expression changes are easily identified, but it is a challenge to capture small, but biologically important, changes. Pathway-based programs can capture small effects but may have the disadvantage of being restricted to functionally annotated genes. A structured approach toward the identification of...

article 2008

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Transcriptional activity around bacterial cell death reveals molecular biomarkers for cell viability

TNO Kwaliteit van Leven (author), Kort, R. (author), Keijser, B.J. (author), Caspers, M.P.M. (author), Schuren, F.H. (author), Montijn, R. (author)

Background: In bacteriology, the ability to grow in selective media and to form colonies on nutrient agar plates is routinely used as a retrospective criterion for the detection of living bacteria. However, the utilization of indicators for bacterial viability-such as the presence of specific transcripts or membrane integrity-would overcome bias...

article 2008

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Dynamics in prophage content of invasive and noninvasive M1 and M28 Streptococcus pyogenes isolates in the Netherlands from 1959 to 1996

Vlaminckx, B.J.M. (author), Schuren, F.H.J. (author), Montijn, R.C. (author), Caspers, M.P.M. (author), Beitsma, M.M. (author), Wannet, W.J.B. (author), Schouls, L.M. (author), Verhoef, J. (author), Jansen, W.T.M. (author), TNO Kwaliteit van Leven (author)

Invasive group A streptococcal (GAS) disease reemerged in The Netherlands in the late 1980s. To seek an explanation for this resurgence, the genetic compositions of 22 M1 and 19 M28 GAS strains isolated in The Netherlands between 1960s and the mid-1990s were analyzed by using a mixed-genome DNA microarray. During this four-decade period, M1 and...

article 2007

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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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Analysis of temporal gene expression during Bacillus subtilis spore germination and outgrowth

Keijser, B.J.F. (author), ter Beek, A. (author), Rauwerda, H. (author), Schuren, F. (author), Montijn, R. (author), van der Spek, H. (author), Brul, S. (author), TNO Kwaliteit van Leven (author)

Bacillus subtilis forms dormant spores upon nutrient depletion. Under favorable environmental conditions, the spore breaks its dormancy and resumes growth in a process called spore germination and outgrowth. To elucidate the physiological processes that occur during the transition of the dormant spore to an actively growing vegetative cell, we...

article 2007

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Determination of the relationship between group A streptococcal genome content, M type, and toxic shock syndrome by a mixed genome microarray

Vlaminckx, B.J.M. (author), Schuren, F.H.J. (author), Montijn, R.C. (author), Caspers, M.P.M. (author), Fluit, A.C. (author), Wannet, W.J.B. (author), Schouls, L.M. (author), Verhoef, J. (author), Jansen, W.T.M. (author), TNO Kwaliteit van Leven (author)

Group A streptococci (GAS), or Streptococcus pyogenes, are associated with a remarkable variety of diseases, ranging from superficial infections to life-threatening diseases such as toxic-shock-like syndrome (TSS). GAS strains belonging to M types M1 and M3 are associated with TSS. This study aims to obtain insight into the gene profiles...

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

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Pathway and single gene analyses of inhibited Caco-2 differentiation by ascorbate-stabilized quercetin suggest enhancement of cellular processes associated with development of colon cancer

Dihal, A.A. (author), Tilburgs, C. (author), van Erk, M.J. (author), Rietjens, I.M.C.M. (author), Woutersen, R.A. (author), Stierum, R.H. (author), TNO Kwaliteit van Leven (author)

The aim was to investigate mechanisms contributing to quercetin's previously described effects on cell-proliferation and -differentiation, which contradicted its proposed anticarcinogenic potency. In a 10-day experiment, 40 μM quercetin stabilized by 1 mM ascorbate reduced Caco-2 differentiation up to 50% (p < 0.001). Caco-2 RNA from days 5 and...

article 2007

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Wnt but not BMP signaling is involved in the inhibitory action of sclerostin on BMP-stimulated bone formation

van Bezooijen, R.L. (author), Svensson, J.P. (author), Eefting, D. (author), Visser, A. (author), van der Horst, G. (author), Karperien, M. (author), Quax, P.H.A. (author), Vrieling, H. (author), Papapoulos, S.E. (author), ten Dijke, P. (author), Löwik, W.G.M.C. (author), TNO Kwaliteit van Leven (author)

Sclerostin is an osteocyte-derived negative regulator of bone formation. It inhibits BMP-stimulated bone formation both in vitro and in vivo but has no direct effect on BMP signaling. Instead, sclerostin inhibits Wnt signaling that is required for BMP-stimulated osteoblastic differentiation. Introduction: Sclerostin is a member of the Dan family...

article 2007

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A sandwich-cultured rat hepatocyte system with increased metabolic competence evaluated by gene expression profiling

Kienhuis, A.S. (author), Wortelboer, H.M. (author), Maas, W.J. (author), van Herwijnen, M. (author), Kleinjans, J.C.S. (author), van Delft, J.H.M. (author), Stierum, R.H. (author), TNO Kwaliteit van Leven (author)

A rapid decline of cytochrome P450 (CYP450) enzyme activities remains a drawback of rat hepatocyte-based in vitro cultures. Consequently, judgment of the toxic potential of compounds that need bioactivation by CYP450s may not be adequate using this model. In the present study, an improved hepatocyte-based in vitro system was developed with...

article 2007