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Knijnenburg, T.A. (author), De Winde, J.H. (author), Daran, J.M. (author), Daran-Lapujade, P. (author), Pronk, J.T. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)
journal article 2007
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Nijkamp, J.F. (author), Van den Broek, M.A. (author), Datema, E. (author), De Kok, S. (author), Bosman, L. (author), Luttik, M.A.H. (author), Daran-Lapujade, P.A.S. (author), Vongsangnak, W. (author), Nielsen, J. (author), Heijne, W.H.M. (author), Klaassen, P. (author), Paddon, C.J. (author), Platt, D. (author), Kötter, P. (author), Van Ham, R.C. (author), Reinders, M.J.T. (author), Pronk, J.T. (author), De Ridder, D. (author), Daran, J.M. (author)
Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization compared to the reference strain S. cerevisiae...
journal article 2012
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Tai, S.L. (author), Daran-Lapujade, P. (author), Walsh, M.C. (author), Pronk, J.T. (author), Daran, J.M. (author)
Effects of suboptimal temperatures on transcriptional regulation in yeast have been extensively studied in batch cultures. To eliminate indirect effects of specific growth rates that are inherent to batch-cultivation studies, genome-wide transcriptional responses to low temperatures were analyzed in steady-state chemostats, grown at a fixed...
journal article 2007
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Boender, L.G.M. (author), De Hulster, E.A.F. (author), Van Maris, A.J.A. (author), Daran-Lapujade, P.A.S. (author), Pronk, J.T. (author)
Growth at near-zero specific growth rates is a largely unexplored area of yeast physiology. To investigate the physiology of Saccharomyces cerevisiae under these conditions, the effluent removal pipe of anaerobic, glucose-limited chemostat culture (dilution rate, 0.025 h–1) was fitted with a 0.22-µm-pore-size polypropylene filter unit. This...
journal article 2009
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Mendes, F. (author), Sieuwerts, S. (author), De Hulster, E. (author), Almering, M.J. (author), Luttik, M.A. (author), Pronk, J.T. (author), Smid, E.J. (author), Bron, P.A. (author), Daran-Lapujade, P. (author)
Mixed populations of Saccharomyces cerevisiae yeasts and lactic acid bacteria occur in many dairy, food, and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir...
journal article 2013
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Daran, J.M. (author), Bakker, B.M. (author), Pronk, J.T. (author), Westerhoff, H.V. (author), De Winde, J.H. (author), Heck, A.J.R. (author), Slijper, M. (author), De Groot, M.J.L. (author), Luttik, M.A.H. (author), Van Gulik, W.M. (author), Rossell, S. (author), Daran-Lapujade, P. (author)
Metabolic fluxes may be regulated ‘‘hierarchically,’’ e.g., by changes of gene expression that adjust enzyme capacities (Vmax) and/or ‘‘metabolically’’ by interactions of enzymes with substrates, products, or allosteric effectors. In the present study, a method is developed to dissect the hierarchical regulation into contributions by...
journal article 2007
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Fazio, A. (author), Jewett, M.C. (author), Daran-Lapujade, P. (author), Mustacchi, R. (author), Usaite, R. (author), Pronk, J.T. (author), Workman, C.T. (author), Nielsen, J. (author)
journal article 2008
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Boender, L.G.M. (author), Van Maris, A.J.A. (author), De Hulster, E.A.F. (author), Almering, M.J.H. (author), Van der Klei, I.J. (author), Veenhuis, M. (author), De Winde, J.H. (author), Pronk, J.T. (author), Daran-Lapujade, P.A.S. (author)
Extremely low specific growth rates (below 0.01 h?1) represent a largely unexplored area of microbial physiology. In this study, anaerobic, glucose-limited retentostats were used to analyse physiological and genome-wide transcriptional responses of Saccharomyces cerevisiae to cultivation at near-zero specific growth rates. While quiescence is...
journal article 2011
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Cruz, L.A.B. (author), Hebly, M. (author), Duong, G.H. (author), Wahl, S.A. (author), Pronk, J.T. (author), Heijnen, J.J. (author), Daran-Lapujade, P. (author), Van Gulik, W.M. (author)
Background Temperature strongly affects microbial growth, and many microorganisms have to deal with temperature fluctuations in their natural environment. To understand regulation strategies that underlie microbial temperature responses and adaptation, we studied glycolytic pathway kinetics in Saccharomyces cerevisiae during temperature changes....
journal article 2012
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Tai, S.L. (author), Daran-Lapujade, P. (author), Luttik, M.A. (author), Walsh, M.C. (author), Diderich, J.A. (author), Krijger, G.C. (author), Van Gulik, W.M. (author), Pronk, J.T. (author), Daran, J.M. (author)
journal article 2007
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Hebly, M. (author), De Ridder, D. (author), De Hulster, E.A. (author), De la Torre Cortes, P. (author), Pronk, J.T. (author), Daran-Lapujade, P.A.S. (author)
Diurnal temperature cycling is an intrinsic characteristic of many exposed microbial ecosystems. However, its influence on yeast physiology and the yeast transcriptome has not been studied in detail. In this study, 24-h sinusoidal temperature cycles, oscillating between 12°C and 30°C, were imposed on anaerobic, glucose-limited chemostat cultures...
journal article 2014
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Solis-Escalante, D. (author), Kuijpers, N.G.A. (author), Barrajon-Simancas, N. (author), Van den Broek, M. (author), Pronk, J.T. (author), Daran, J.M. (author), Daran-Lapujade, P. (author)
As a result of ancestral whole-genome and small-scale duplication events, the genomes of Saccharomyces cerevisiae and many eukaryotes still contain a substantial fraction of duplicated genes. In all investigated organisms, metabolic pathways, and more particularly glycolysis, are specifically enriched for functionally redundant paralogs. In...
journal article 2015
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Vos, T. (author), De la Torre Cortes, P. (author), Van Gulik, W.M. (author), Pronk, J.T. (author), Daran-Lapujade, P.A.S. (author)
Introduction: Saccharomyces cerevisiae has become a popular host for production of non-native compounds. The metabolic pathways involved generally require a net input of energy. To maximize the ATP yield on sugar in S. cerevisiae, industrial cultivation is typically performed in aerobic, sugar-limited fed-batch reactors which, due to constraints...
journal article 2015
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Ercan, O. (author), Bisschops, M.M. (author), Overkamp, W. (author), Jørgensen, T.R. (author), Rama, A.F. (author), Smid, E.J. (author), Pronk, J.T. (author), Kuipers, O.P. (author), Daran-Lapujade, P. (author), Kleerebezem, M. (author)
The current knowledge of the physiology and gene expression of industrially relevant microorganisms is largely based on laboratory studies under conditions of rapid growth and high metabolic activity. However, in natural ecosystems and industrial processes, microbes frequently encounter severe calorie restriction. As a consequence, microbial...
journal article 2015
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Jansen, M.L.A. (author), Daran-Lapujade, P. (author), de Winde, J.H. (author), Piper, M.D. (author), Pronk, J.T. (author)
journal article 2004
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Kuijpers, N.G.A. (author), Chroumpi, S. (author), Vos, T. (author), Solis-Escalante, D. (author), Bosman, D. (author), Pronk, J.T. (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)
In vivo assembly of overlapping fragments by homologous recombination in Saccharomyces cerevisiae is a powerful method to engineer large DNA constructs. Whereas most in vivo assembly methods reported to date result in circular vectors, stable integrated constructs are often preferred for metabolic engineering as they are required for large-scale...
journal article 2013
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Knijnenburg, T.A. (author), De Winde, J.H. (author), Daran, J.M. (author), Daran-Lapujade, P. (author), Pronk, J.T. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)
journal article 2007
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Mans, R. (author), Van Rossum, H.M. (author), Wijsman, M. (author), Backx, A. (author), Kuijpers, N.G.A. (author), van den Broek, M. (author), Daran-Lapujade, P.A.S. (author), Pronk, J.T. (author), Van Maris, A.J.A. (author), Daran, J.G. (author)
A variety of techniques for strain engineering in Saccharomyces cerevisiae have recently been developed. However, especially when multiple genetic manipulations are required, strain construction is still a time-consuming process. This study describes new CRISPR/Cas9-based approaches for easy, fast strain construction in yeast and explores their...
journal article 2015
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Jansen, M.L.A. (author), Diderich, J.A. (author), Mashego, M. (author), Hassane, A. (author), de Winde, J.H. (author), Daran-Lapujade, P. (author), Pronk, J.T. (author)
journal article 2005
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Van Den Brink, J. (author), Daran-Lapujade, P. (author), Pronk, J.T. (author), De Winde, J.H. (author)
OA Fund
journal article 2008
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