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Yuan, X.L. (author), Goosen, C. (author), Kools, H. (author), van der Maarel, M.J.E.C. (author), van den Hondel, C.A.M.J.J. (author), Dijkhuizen, L. (author), Ram, A.F.J. (author), TNO Kwaliteit van Leven (author)As a soil fungus, Aspergillus niger can metabolize a wide variety of carbon sources, employing sets of enzymes able to degrade plant-derived polysaccharides. In this study the genome sequence of A. niger strain CBS 513.88 was surveyed, to analyse the gene/enzyme network involved in utilization of the plant storage polymer inulin, and of sucrose,...article 2006
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van Erk, M.J. (author), Blom, W.A.M. (author), van Ommen, B. (author), Hendriks, H.F.J. (author), TNO Kwaliteit van Leven (author)Background: Application of transcriptomics technology in human nutrition intervention studies would allow for genome-wide screening of the effects of specific diets or nutrients and result in biomarker profiles. Objective: The aim was to evaluate the potential of gene expression profiling in blood cells collected in a human intervention study...article 2006
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de Boer, V.C.J. (author), van Schothorst, E.M. (author), Dihal, A.A. (author), van der Woude, H. (author), Arts, I.C.W. (author), Rietjens, I.M.C.M. (author), Hollman, P.C.H. (author), Keijer, J. (author), TNO Kwaliteit van Leven (author)Dietary quercetin intake is suggested to be health promoting, but this assumption is mainly based on mechanistic studies performed in vitro. Previously, we identified rat lung as a quercetin target tissue. To assess relevant in vivo health effects of quercetin, we analyzed mechanisms of effect in rat lungs of a chronic (41 weeks) 1% quercetin...article 2006
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Heijne, W.H.M. (author), Jonker, D. (author), Stierum, R.H. (author), van Ommen, B. (author), Groten, J.P. (author), TNO Kwaliteit van Leven (author)Benzene is an industrial chemical, component of automobile exhaust and cigarette smoke. After hepatic bioactivation benzene induces bone marrow, blood and hepatic toxicity. Using a toxicogenomics approach this study analysed the effects of benzene at three dose levels on gene expression in the liver after 28 daily doses. NMR based metabolomics...article 2005
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Meeuwsen, S. (author), Bsibsi, M. (author), Persoon-Deen, C. (author), Ravid, R. (author), van Noort, J.M. (author), TNO Preventie en Gezondheid (author)Objectives: Brain microglia are highly responsive cells in the central nervous system that exert key functions in host defense as well as in neuroprotection and regeneration. In this study the gene expression profiles for 268 cytokines, chemokines, growth factors and their receptors were examined in cultures of purified human adult microglia,...article 2005
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van Erk, M.J. (author), Krul, C.A.M. (author), Caldenhoven, E. (author), Stierum, R.H. (author), Peters, W.H. (author), Woutersen, R.A. (author), van Ommen, B. (author), TNO Kwaliteit van Leven TNO Voeding (author)Interest in mechanisms of colon cancer prevention by food compounds is strong and research in this area is often performed with cultured colon cancer cells. In order to assess utility for screening of potential cancer-preventive (food) compounds, expression profiles of 14 human cell lines derived from colonic tissue were measured using cDNA...article 2005
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te Biesebeke, R. (author), Levin, A. (author), Sagt, C. (author), Bartels, J. (author), Goosen, T. (author), Ram, A. (author), van den Hondel, C. (author), Punt, P. (author), TNO Kwaliteit van Leven (author)Aspergillus oryzae requires polarized growth for colonization of solid substrates, and this growth phenotype differs from that seen in liquid medium. Various experimental approaches were used to identify genes that are differentially expressed when A. oryzae is grown on wheat kernels and in a wheat-based liquid medium. Hybridization of A. oryzae...article 2005
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TNO Kwaliteit van Leven (author), Kralj, S. (author), Stripling, E. (author), Sanders, P. (author), van Geel-Schutten, G.H. (author), Dijkhuizen, L. (author)Lactobacillus reuteri strain ATCC 55730 (LB BIO) was isolated as a pure culture from a Reuteri tablet purchased from the BioGaia company. This probiotic strain produces a soluble glucan (reuteran), in which the majority of the linkages are of the alpha-(1→4) glucosidic type (∼70%). This reuteran also contains alpha-(1→6)-linked glucosyl units...article 2005
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TNO Kwaliteit van Leven TNO Voeding (author), Garosi, P. (author), de Filippo, C. (author), van Erk, M. (author), Rocca-Serra, P. (author), Sansone, S.A. (author), Elliott, R. (author)Microarrays represent a powerful tool for studies of diet-gene interactions. Their use is, however, associated with a number of technical challenges and potential pitfalls. The cost of microarrays continues to drop but is still comparatively high. This, coupled with the complex logistical issues associated with performing nutritional microarray...article 2005
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Clish, C.B. (author), Davidov, E. (author), Oresic, M. (author), Plasterer, T.N. (author), Lavine, G. (author), Londo, T. (author), Meys, M. (author), Snell, P. (author), Stochaj, W. (author), Adourian, A. (author), Zhang, X. (author), Morel, N. (author), Neumann, E. (author), Verheij, E. (author), Vogels, J.T.W.E. (author), Havekes, L.M. (author), Afeyan, N. (author), Regnier, F. (author), van der Greef, J. (author), Naylor, S. (author), TNO Preventie en Gezondheid (author)Integrative (or systems biology) is a new approach to analyzing biological entities as integrated systems of genetic, genomic, protein, metabolite, cellular, and pathway events that are in flux and interdependent. Here, we demonstrate the application of intregrative biological analysis to a mammalian disease model, the apolipoprotein E3-Leiden ...article 2004
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Kralj, S. (author), van Geel-Schutten, G.H. (author), Dondorff, M.M.G. (author), Kirsanovs, S. (author), van der Maarel, M.J.E.C. (author), Dijkhuizen, L. (author), TNO Voeding Centraal Instituut voor Voedingsonderzoek TNO (author)Members of the genera Streptococcus and Leuconostoc synthesize various α-glucans (dextran, alternan and mutan). In Lactobacillus, until now, the only glucosyltransferase (GTF) enzyme that has been characterized is gtfA of Lactobacillus reuteri 121, the first GTF enzyme synthesizing a glucan (reuteran) that contains mainly α-(1 → 4) linkages...article 2004
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van Hijum, S.A.F.T. (author), Szalowska, E. (author), van der Maarel, M.J.E.C. (author), Dijkhuizen, L. (author), TNO Voeding Centraal Instituut voor Voedingsonderzoek TNO (author)Lactobacillus reuteri strain 121 employs a fructosyltransferase (FTF) to synthesize a fructose polymer [a fructan of the levan type, with β(2→6) linkages] from sucrose or raffinose. Purification of this FTF (a levansucrase), and identification of peptide amino acid sequences, allowed isolation of the first Lactobacillus levansucrase gene (lev),...article 2004
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Majhenič, A.Č. (author), Venema, K. (author), Allison, G.E. (author), Matijašić, B.B. (author), Rogelj, I. (author), Klaenhammer, T.R. (author), TNO Voeding (author)Lactobacillus gasseri LF221, an isolate from the feces of a child, produces two bacteriocins. Standard procedures for molecular techniques were used to locate, clone and sequence the fragments of LF221 chromosomal DNA carrying the acidocin LF221 A and B structural genes, respectively. Sequencing analysis revealed the gene of acidocin LF221 A to...article 2004
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Lüchtenborg, M. (author), Weijenberg, M.P. (author), Roemen, G.M.J.M. (author), de Bruïne, A.P. (author), van den Brandt, P.A. (author), Lentjes, M.H.F.M. (author), Brink, M. (author), van Engeland, M. (author), Goldbohm, R.A. (author), de Goeij, A.F.P.M. (author), TNO Voeding Centraal Instituut voor Voedingsonderzoek TNO (author)The adenomatous polyposis coli (APC) gene is considered to be a gatekeeper in colorectal tumourigenesis. Inactivating mutations in APC have been reported in 34-70% of sporadic colorectal cancer patients, the majority of which occur in the mutation cluster region (MCR). In this study, tumour tissue from 665 incident colorectal cancer patients,...article 2004
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Verhoeckx, K.C.M. (author), Bijlsma, S. (author), Jespersen, S. (author), Ramaker, R. (author), Verheij, E.R. (author), Witkamp, R.F. (author), van der Greef, J. (author), Rodenburg, R.J.T. (author), TNO Voeding Centraal Instituut voor Voedingsonderzoek TNO (author)The discovery of new anti-inflammatory drugs is often based on an interaction with a specific target, although other pathways often play a primary or secondary role. Anti-inflammatory drugs can be categorized into classes, based on their mechanism of action. In this article we investigate the possibility to characterize novel anti-inflammatory...article 2004
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Jonker, D. (author), Freidig, A.P. (author), Groten, J.P. (author), de Hollander, A.E.M. (author), Stierum, R.H. (author), Woutersen, R.A. (author), Feron, V.J. (author), TNO Voeding (author)Recent developments in hazard identification and risk assessment of chemical mixtures are reviewed. Empirical, descriptive approaches to study and characterize the toxicity of mixtures have dominated during the past two decades, but an increasing number of mechanistic approaches have made their entry into mixture toxicology. A series of...article 2004
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Heijne, W.H.M. (author), Slitt, A.L. (author), van Bladeren, P.J. (author), Groten, J.P. (author), Klaassen, C.D. (author), Stierum, R.H. (author), van Ommen, B. (author), TNO Voeding Centraal Instituut voor Voedingsonderzoek TNO (author)Rats were exposed to three levels of bromobenzene, sampled at 6, 24, and 48 h, and liver gene expression profiles were determined to identify dose and time-related changes. Expression of many genes changed transiently, and dependent on the dose. Few changes were identified after 6 h, but many genes were differentially expressed after 24 h, while...article 2004
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Nieuwenhuizen, W.F. (author), van Leeuwen, S. (author), Jack, R.W. (author), Egmond, M.R. (author), Götz, F. (author)Ceramidase (CDase) hydrolyzes the amide bond in ceramides to yield free fatty acid and sphingosine. From a 3-L Pseudomonas aeruginosa PA01 culture, 70 μg of extracellular alkaline, Ca2+-dependent CDase, was purified to homogeneity, the N-terminal sequence was determined, and the CDase gene was cloned. The CDase gene encodes a 670 amino acid...article 2003
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Kralj, S. (author), Geel van - Schutten, G.H. (author), van der Maarel, M.J.E.C. (author), Dijkhuizen, L. (author)Limited information is available about homopolysaccharide synthesis in the genus Lactobacillus. Using efficient screening techniques, extracellular glucosyltransferase (GTF) enzyme activity, resulting in α-glucan synthesis from sucrose, was detected in various lactobacilli. PCR with degenerate primers based on homologous boxes of known...article 2003
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Heijne, W.H.M. (author), Stierum, R.H. (author), Slijper, M. (author), van Bladeren, P.J. (author), van Ommen, B. (author)Toxicogenomics is a novel approach integrating the expression analysis of thousands of genes (transcriptomics) or proteins (proteomics) with classical methods in toxicology. Effects at the molecular level are related to pathophysiological changes of the organisms, enabling detailed comparison of mechanisms and early detection and prediction of...article 2003