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Correlates of the molecular vaginal microbiota composition of African women

TNO Kwaliteit van Leven (author), Gautam, R. (author), Borgdorff, H. (author), Jespers, V. (author), Francis, S.C. (author), Verhelst, R. (author), Mwaura, M. (author), Delany-Moretlwe, S. (author), Ndayisaba, G. (author), Kyongo, J.K. (author), Hardy, L. (author), Menten, HJ. (author), Crucitti, T. (author), Tsivtsivadze, E. (author), Schuren, F. (author), van de Wijgert, J.H.R.M. (author), Vaginal biomarkers Study Group, (author)

Background: Sociodemographic, behavioral and clinical correlates of the vaginal microbiome (VMB) as characterized by molecular methods have not been adequately studied. VMB dominated by bacteria other than lactobacilli may cause inflammation, which may facilitate HIV acquisition and other adverse reproductive health outcomes. Methods: We...

article 2015

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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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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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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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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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Effect of body fat distribution on the transcription response to dietary fat interventions

TNO Kwaliteit van Leven (author), Radonjic, M. (author), van Erk, M.J. (author), Pasman, W.J. (author), Wortelboer, H.M. (author), Hendriks, H.F.J. (author), van Ommen, B. (author)

Combination of decreased energy expenditure and increased food intake results in fat accumulation either in the abdominal site (upper body obesity, UBO) or on the hips (lower body obesity, LBO). In this study, we used microarray gene expression profiling of adipose tissue biopsies to investigate the effect of body fat distribution on the...

article 2009

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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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Transcriptome analysis provides new insights into liver changes induced in the rat upon dietary administration of the food additives butylated hydroxytoluene, curcumin, propyl gallate and thiabendazole

Stierum, R. (author), Conesa, A. (author), Heijne, W. (author), Ommen, B.v. (author), Junker, K. (author), Scott, M.P. (author), Price, R.J. (author), Meredith, C. (author), Lake, B.G. (author), Groten, J. (author), TNO Kwaliteit van Leven (author), KvL (author)

Transcriptomics was performed to gain insight into mechanisms of food additives butylated hydroxytoluene (BHT), curcumin (CC), propyl gallate (PG), and thiabendazole (TB), additives for which interactions in the liver can not be excluded. Additives were administered in diets for 28 days to Sprague-Dawley rats and cDNA microarray experiments were...

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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Interleukin 10: A new risk marker for the development of restenosis after percutaneous coronary intervention

Monraats, P.S. (author), Kurreeman, F.A.S. (author), Pons, D. (author), Sewgobind, V.D.K.D. (author), de Vries, F.R. (author), Zwinderman, A.H. (author), de Maat, M.P.M. (author), Doevendans, P.A. (author), de Winter, R.J. (author), Tio, R.A. (author), Waltenberger, J. (author), Huizinga, T.W.J. (author), Eefting, D. (author), Quax, P.H.A. (author), Frants, R.R. (author), van der Laarse, A. (author), van der Wall, E.E. (author), Jukema, J.W. (author), TNO Kwaliteit van Leven (author)

Genetic factors appear to be important in the process of restenosis after percutaneous coronary intervention (PCI), as well as in inflammation, a pivotal factor in restenosis. An important mediator in the inflammatory response is interleukin (IL)-10. Our aim was to study whether genetic variants in IL-10 predispose to the risk of restenosis. The...

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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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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Towards understanding molecular modes of probiotic action

Marco, M.L. (author), Pavan, S. (author), Kleerebezem, M. (author), TNO Kwaliteit van Leven (author)

The possibility that certain microorganisms might be beneficial to human health is highlighted by the numerous consumer products containing probiotic bacteria. Probiotics are typically administered in food that, following entry into the gastro-intestinal tract, results in measurable health-promoting effects. Although there is a growing list of...

article 2006

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The impact of functional genomics on microbiological food quality and safety

Brul, S. (author), Schuren, F. (author), Montijn, R. (author), Keijser, B.J.F. (author), van der Spek, H. (author), Oomes, S.J.C.M. (author), TNO Kwaliteit van Leven (author)

In the food processing industry, unwanted occurrence and growth of spoilage and pathogenic microorganisms is a key concern. A prime example is the extremely heat resistant bacterial endospores, microbial survival structures, that create problems due to their ability to survive classical thermal treatments and their ability to subsequently...

article 2006