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Different resource allocation in a bacillus subtilis population displaying bimodal motility

Syvertsson, S. (author), Wang, B. (author), Staal, J. (author), Gao, Y. (author), Kort, R. (author), Hamoen, L.W. (author)

To cope with sudden changes in their environment, bacteria can use a bet-hedging strategy by dividing the population into cells with different properties. This so-called bimodal or bistable cellular differentiation is generally controlled by positive feedback regulation of transcriptional activators. Due to the continuous increase in cell volume...

article 2021

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NF-B-mediated metabolic remodelling in the inflamed heart in acute viral myocarditis

Remels, A.H.V. (author), Derks, W.J.A. (author), Cillero-Pastor, B. (author), Verhees, K.J.P. (author), Kelders, M.C. (author), Heggermont, W. (author), Carai, P. (author), Summer, G. (author), Ellis, S.R. (author), de Theije, C.C. (author), Heeren, R.M.A. (author), Heymans, S. (author), Papageorgiou, A.P. (author), van Bilsen, M. (author)

Acute viral myocarditis (VM), characterised by leukocyte infiltration and dysfunction of the heart, is an important cause of sudden cardiac death in young adults. Unfortunately, to date, the pathological mechanisms underlying cardiac failure in VM remain incompletely understood. In the current study, we investigated if acute VM leads to cardiac...

article 2018

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Factors of concern in a human 3D cellular airway model to aerosols of nanoparticles

Kooter, I.M. (author), Grollers-Mulderij, M. (author), Duistermaat, E. (author), Kuper, C.F. (author)

Mucilair 3D bronchial airway models, cultured at an air-liquid interface, were exposed to aerosols of copper oxide (CuO) nanoparticles in Vitrocell air exposure modules. Four cell donors, four exposure modules and four exposure concentrations were varied within four different exposure sessions using a statistical experimental design called a...

article 2017

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Functions of the CCCH type zinc finger protein OsGZF1 in regulation of the seed storage protein GluB-1 from rice

Chen, Y. (author), Sun, A. (author), Wang, M. (author), Zhu, Z. (author), Ouwerkerk, P.B.F. (author), Centraal Instituut voor Voedingsonderzoek TNO (author)

Glutelins are the most abundant storage proteins in rice grain and can make up to 80 % of total protein content. The promoter region of GluB-1, one of the glutelin genes in rice, has been intensively used as a model to understand regulation of seed-storage protein accumulation. In this study, we describe a zinc finger gene of the Cys3His1 (CCCH...

article 2014

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The probiotic mixture VSL#3 mediates both pro- and anti-inflammatory responses in bone marrow-derived dendritic cells from C57BL/6 and BALB/c mice

Mariman, R. (author), Kremer, S.H.A. (author), Koning, F. (author), Nagelkerken, L. (author)

Probiotic bacteria express a wide range of molecular structures that bind to receptors on innate immune cells and mediate health-promoting effects in the host. We have recently demonstrated in a colitis model that favourable effects of the probiotic mixture VSL#3 may in part be due to the suppression of intestinal chemokine expression. To obtain...

article 2014

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Beneficial microbes. Foreword.

Venema, K. (author)

article 2012

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Quantitative analysis of flux regulation through hierarchical regulation analysis

van Eunen, K. (author), Rossell, S. (author), Bouwman, J. (author), Westerhoff, H.V. (author), Bakker, B.M. (author), Centraal Instituut voor Voedingsonderzoek TNO (author)

Regulation analysis is a methodology that quantifies to what extent a change in the flux through a metabolic pathway is regulated by either gene expression or metabolism. Two extensions to regulation analysis were developed over the past years: (i) the regulation of Vmax can be dissected into the various levels of the gene-expression cascade,...

conference paper 2011

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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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Epigenetic histone acetylation modifiers in vascular remodelling: New targets for therapy in cardiovascular disease

Pons, D. (author), de Vries, F.R. (author), van den Elsen, P.J. (author), Heijmans, B.T. (author), Quax, P.H.A. (author), Jukema, J.W. (author), TNO Kwaliteit van Leven (author)

Significant progress has been made in the clinical management of a variety of cardiovascular diseases. Nevertheless, the therapeutic efficacy of the current treatment modalities for atherosclerosis and restenosis is not fully sufficient in a large proportion of patients. One of the major contributing factors is the clinical and biological...

article 2009

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Combined TLR2 and TLR4 ligation in the context of bacterial or helminth extracts in human monocyte derived dendritic cells: Molecular correlates for Th1/Th2 polarization

van Riet, E. (author), Everts, B. (author), Retra, K. (author), Phylipsen, M. (author), van Hellemond, J.J. (author), Tielens, A.G.M. (author), van der Kleij, D. (author), Hartgers, F.C. (author), Yazdanbakhsh, M. (author), TNO Defensie en Veiligheid (author)

Background: Recognition of pathogens by dendritic cells (DCs) through interaction with pattern recognition receptors, including Toll like receptors (TLR), is crucial for the initiation of appropriate polarized T helper (Th) cell responses. Yet, the characteristics and differences in molecular profiles of DCs with different T cell polarizing...

article 2009

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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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Potency of isothiocyanates to induce luciferase reporter gene expression via the electrophile-responsive element from murine glutathione S-transferase Ya

Vermeulen, M. (author), Boerboom, A.M.M.J.F. (author), Blankvoort, B.M.G. (author), Aarts, J.M.M.J.G. (author), Rietjens, I.M.C.M. (author), van Bladeren, P.J. (author), Vaes, W.H.J. (author), TNO Kwaliteit van Leven (author)

Isothiocyanates are electrophiles that are able to induce phase II biotransformation enzyme gene expression via an electrophile-responsive element (EpRE) in the gene regulatory region. To study the potency of different isothiocyanates to induce the expression of EpRE-regulated genes, a Hepa-1c1c7 luciferase reporter cell line was exposed to...

article 2009

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Doxycycline therapy for abdominal aneurysm: Improved proteolytic balance through reduced neutrophil content

Abdul-Hussien, H. (author), Hanemaaijer, R. (author), Verheijen, J.H. (author), van Bockel, J.H. (author), Geelkerken, R.H. (author), Lindeman, J.H.N. (author), TNO Kwaliteit van Leven (author)

Background: Matrix metalloproteinase-9 (MMP-9) is thought to play a central role in abdominal aortic aneurysm (AAA) initiation. Doxycycline, a tetracycline analogue, has direct MMP-9-inhibiting properties in vitro, and it effectively suppresses AAA development in rodents. Observed inhibition of AAA progression, and contradictory findings in...

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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β1 integrins regulate chondrogenesis and rock signaling in adipose stem cells

Lu, Z.F. (author), Doulabi, B.Z. (author), Huang, C.L. (author), Bank, R.A. (author), Helder, M.N. (author), TNO Kwaliteit van Leven (author)

β1 integrins play a controversial role during chondrogenesis. Since the maturation of chondrocytes relies on a signaling switch from cell-cell to cell-matrix interactions, we hypothesized that β1 integrins play a different role at the earlier (mainly cell-cell interaction) from the later stage (mainly cell-matrix interaction) of chondrogenesis....

article 2008

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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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Comprehensive analysis of the metabolome of Pseudomonas putida S12 grown on different carbon sources

van der Werf, M.J. (author), Overkamp, K.M. (author), Muilwijk, B. (author), Koek, M.M. (author), van der Werff van der - Vat, B.J.C. (author), Jellema, R.H. (author), Coulier, L. (author), Hankemeier, T. (author), TNO Kwaliteit van Leven (author)

Metabolomics is an emerging, powerful, functional genomics technology that involves the comparative non-targeted analysis of the complete set of metabolites in an organism. We have set-up a robust quantitative metabolomics platform that allows the analysis of 'snapshot' metabolomes. In this study, we have applied this platform for the...

article 2008

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Transcriptome analysis of a phenol-producing Pseudomonas putida S12 construct: Genetic and physiological basis for improved production

Wierckx, N.J.P. (author), Ballerstedt, H. (author), de Bont, J.A.M. (author), de Winde, J.H. (author), Ruijssenaars, H.J. (author), Wery, J. (author), TNO Kwaliteit van Leven (author)

The unknown genetic basis for improved phenol production by a recombinant Pseudomonas putida S12 derivative bearing the tpl (tyrosine-phenol lyase) gene was investigated via comparative transcriptomics, nucleotide sequence analysis, and targeted gene disruption. We show upregulation of tyrosine biosynthetic genes and possibly decreased...

article 2008