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Li, A. (author), Pfelzer, N. (author), Zuijderwijk, R. (author), Brickwedde, A. (author), van Zeijl, C. (author), Punt, P. (author)Aspergillus niger has an extraordinary potential to produce organic acids as proven by its application in industrial citric acid production. Previously, it was shown that expression of the cis-aconitate decarboxylase gene (cadA) from Aspergillus terreus converted A. niger into an itaconic acid producer (Li et al., Fungal Genet Bio 48: 602-611,...article 2013
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Florian, B. (author), Noël, N. (author), Thyssen, C. (author), Felschau, I. (author), Sand, W. (author)Bacterial attachment and biofilm formation are important for microbial bioleaching of metal sulfides, however, many details of the role played by bacteria are still unknown. Attachment as the first step in biofilm formation is critical. Our investigations are focused on these processes to control bacterial bioleaching processes. In moderately...article 2011
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Rumbold, K. (author), van Buijsen, H.J.J. (author), Gray, V.M. (author), van Groenestijn, J.W. (author), Overkamp, K.M. (author), Slomp, R.S. (author), van der Werf, M.J. (author), Punt, P.J. (author), TNO Kwaliteit van Leven (author)Increasingly lignocellulosic biomass hydrolysates are used as the feedstock for industrial fermentations. These biomass hydrolysates consist of complex mixtures of different fermentable sugars, but also contain inhibitors and salts that affect the performance of the productgenerating microbes. The performance of six industrially relevant...article 2010
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Dieser, M. (author), Nocker, A. (author), Priscu, J.C. (author), Foreman, C.M. (author), TNO Kwaliteit van Leven (author)The permanent ice covers of the McMurdo Dry Valley lakes, Antarctica, are colonized by a diverse microbial assemblage. We collected ice cores from Lakes Fryxell, Hoare and Bonney. Propidium monoazide (PMA) was used in combination with quantitative PCR (qPCR) and denaturing gradient gel electrophoresis (DGGE) to examine membrane integrity of...article 2010
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Breier, J.M. (author), Gassmann, K. (author), Kayser, R. (author), Stegeman, H. (author), de Groot, D. (author), Fritsche, E. (author), Shafer, T.J. (author), TNO Kwaliteit van Leven (author)In vitro, high-throughput methods have been widely recommended as an approach to screen chemicals for the potential to cause developmental neurotoxicity and prioritize them for additional testing. The choice of cellular models for such an approach will have important ramifications for the accuracy, predictivity and sensitivity of the screening...article 2010
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Volkers, R.J.M. (author), Ballerstedt, H. (author), de Winde, J.H. (author), Ruijssenaars, H.J. (author), TNO Kwaliteit van Leven (author)Pseudomonas putida S12.49, a mutant stain of P. putida S12 that tolerates up to 20 mM benzene, was obtained by evolutionary selection. The genetic basis for the strongly enhanced benzene tolerance was investigated by proteome and transcriptome analysis. Indications were found that the highly benzene-tolerant phenotype is the resultant of...article 2010
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TNO Kwaliteit van Leven (author), van Ommen, B. (author), Bouwman, J. (author), Dragsted, L.O. (author), Drevon, C.A. (author), Elliott, R. (author), de Groot, P. (author), Kaput, J. (author), Mathers, J.C. (author), Müller, M. (author), Pepping, F. (author), Saito, J. (author), Scalbert, A. (author), Radonjic, M. (author), Rocca-Serra, P. (author), Travis, A. (author), Wopereis, S. (author), Evelo, C.T. (author)The challenge of modern nutrition and health research is to identify food-based strategies promoting life-long optimal health and well-being. This research is complex because it exploits a multitude of bioactive compounds acting on an extensive network of interacting processes. Whereas nutrition research can profit enormously from the revolution...article 2010
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Verouden, M.P.H. (author), Westerhuis, J.A. (author), van der Werf, M.J. (author), Smilde, A.K. (author), TNO Kwaliteit van Leven (author)In metabolomics research a large number of metabolites are measured that reflect the cellular state under the experimental conditions studied. In many occasions the experiments are performed according to an experimental design to make sure that sufficient variation is induced in the metabolite concentrations. However, as metabolomics is a...article 2009
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van den Berg, R.A. (author), Rubingh, C.M. (author), Westerhuis, J.A. (author), van der Werf, M.J. (author), Smilde, A.K. (author), TNO Kwaliteit van Leven (author)In metabolomics research, it is often important to focus the data analysis to specific areas of interest within the metabolome. In this paper, we describe the application of consensus principal component analysis (CPCA) and canonical correlation analysis (CCA) as a means to explore the relation between metabolome data and (i) biochemically...article 2009
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van Wietmarschen, H. (author), Yuan, K. (author), Lu, C. (author), Gao, P. (author), Wang, J. (author), Xiao, C. (author), Yan, X. (author), Wang, M. (author), Schroën, J. (author), Lu, A. (author), Xu, G. (author), van der Greef, J. (author), TNO Kwaliteit van Leven (author)BACKGROUND: Complex chronic diseases such as rheumatoid arthritis have become a major challenge in medicine and for the pharmaceutical industry. New impulses for drug development are needed. OBJECTIVE: A systems biology approach is explored to find subtypes of rheumatoid arthritis patients enabling a development towards more personalized...article 2009
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Kienhuis, A.S. (author), van de Poll, M.C.G. (author), Wortelboer, H. (author), van Herwijnen, M. (author), Gottschalk, R. (author), de Jong, C.H.C. (author), Boorsma, A. (author), Paules, R.S. (author), Kleinjans, J.C.S. (author), Stierum, R.H. (author), van Delft, J.H.M. (author), TNO Kwaliteit van Leven (author)The frequent use of rodent hepatic in vitro systems in pharmacological and toxicological investigations challenges extrapolation of in vitro results to the situation in vivo and interspecies extrapolation from rodents to humans. The toxicogenomics approach may aid in evaluating relevance of these model systems for human risk assessment by direct...article 2009
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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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Welling, M.M. (author), Ferro-Flores, G. (author), Pirmettis, I. (author), Brouwer, C.P.J.M. (author)Infection specific radiopharmaceuticals can be used for diagnosis, decision-making in therapy and treatment follow-up. Research has been ongoing to develop infection specific markers since clinically used tracers cannot discriminate between infection and inflammation. A specific radiopharmaceutical for infection imaging should satisfy the...article 2009
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Rodriguez, V. (author), TNO Kwaliteit van Leven (author)The aim of this article is to put into critical perspective the empirical findings on secrecy and withholding in research. In other words, by taking existing empirical literature into account, it is intended that a crucial question is answered: Is secrecy and withholding in research harmful or innocuous to science? To understand how secrecy and...article 2009
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TrgI, toluene repressed gene I, a novel gene involved in toluene-tolerance in Pseudomonas putida S12Volkers, 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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- Russo Wortman, J. (author), Driessen, A.J.M. (author), Punt, P.J. (author), Ram, A.F.J. (author), TNO Kwaliteit van Leven (author) article 2009
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Braaksma, M. (author), Smilde, A.K. (author), van der Werf, M.J. (author), Punt, P.J. (author), TNO Kwaliteit van Leven (author)Proteolytic degradation by host proteases is one of the key issues in the application of filamentous fungi for non-fungal protein production. In this study the influence of several environmental factors on the production of extracellular proteases of Aspergillus niger was investigated systematically in controlled batch cultures. Of all factors...article 2009
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TNO Kwaliteit van Leven (author), Verhoef, S. (author), Wierckx, N. (author), Westerhof, R.G.M. (author), Winde, J.H.de (author), Ruijssenaars, H.J. (author)Two solvent-tolerant Pseudomonas putida S12 strains, originally designed for phenol and p-coumarate production, were engineered for efficient production of p-hydroxystyrene from glucose. This was established by introduction of the genes pal and pdc encoding L-phenylalanine/L-tyrosine ammonia lyase and p-coumaric acid decarboxylase, respectively....article 2009
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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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van Groenestijn, J.W. (author), Geelhoed, J.S. (author), Goorissen, H.P. (author), Meesters, K.P.M. (author), Stams, A.J.M. (author), Claassen, P.A.M. (author), TNO Kwaliteit van Leven (author)Non-axenic operation of a 400 L trickle bed reactor inoculated with the thermophile Caldicellulosiruptor saccharolyticus, yielded 2.8 molH 2mol hexose converted. The reactor was fed with a complex medium with sucrose as the main substrate, continuously flushed with nitrogen gas, and operated at 73°C. The volumetric productivity was 22 mmolH2(L...article 2009