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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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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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Heijnen, J.J. (author), Daran, J.M. (author), Pronk, J.T. (author), Daran-Lapujade, P. (author), Knijnenburg, T.A. (author), Ras, C. (author), Ten Pierick, A. (author), Akmering, M.J. (author), Van Winden, W.A. (author), Kresnowati, M.T. (author)
Within the first 5 min after a sudden relief from glucose limitation, Saccharomyces cerevisiae exhibited fast changes of intracellular metabolite levels and a major transcriptional reprogramming. Integration of transcriptome and metabolome data revealed tight relationships between the changes at these two levels. Transcriptome as well as...
journal article 2006
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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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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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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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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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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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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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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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Knijnenburg, T.A. (author), Daran, J.M.G. (author), Van den Broek, M.A. (author), Daran-Lapujade, P.A.S. (author), De Winde, J.H. (author), Pronk, J.T. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)
OA Fund TU delft Background: Microorganisms adapt their transcriptome by integrating multiple chemical and physical signals from their environment. Shake-flask cultivation does not allow precise manipulation of individual culture parameters and therefore precludes a quantitative analysis of the (combinatorial) influence of these parameters on...
journal article 2009
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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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Hazelwood, L.A. (author), Walsh, M.C. (author), Luttik, M.A.H. (author), Daran-Lapujade, P. (author), Pronk, J.T. (author), Daran, J.M. (author)
OA Fund TU Delft Accumulation of glycogen and trehalose in nutrient-limited cultures of Saccharomyces cerevisiae is negatively correlated with the specific growth rate. Additionally, glucose-excess conditions (i.e., growth limitation by nutrients other than glucose) are often implicated in high-level accumulation of these storage carbohydrates....
journal article 2009
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Boender, L.G.M. (author), Almering, M.J.H. (author), Dijk, M. (author), Van Maris, A.J.A. (author), De Winde, J.H. (author), Pronk, J.T. (author), Daran-Lapujade, P. (author)
Cultivation methods used to investigate microbial calorie restriction often result in carbon and energy starvation. This study aims to dissect cellular responses to calorie restriction and starvation in Saccharomyces cerevisiae by using retentostat cultivation. In retentostats, cells are continuously supplied with a small, constant carbon and...
journal article 2011
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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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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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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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Solis-Escalante, D. (author), Kuijpers, N.G.A. (author), Bongaerts, N. (author), Bolat, I. (author), Bosman, L. (author), Pronk, J.T. (author), Daran, J.M. (author), Daran-Lapujade, P.A.S. (author)
Despite the large collection of selectable marker genes available for Saccharomyces cerevisiae, marker availability can still present a hurdle when dozens of genetic manipulations are required. Recyclable markers, counterselectable cassettes that can be removed from the targeted genome after use, are therefore valuable assets in ambitious...
journal article 2012
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Kuijpers, N.G. (author), Solis-Escalante, D. (author), Bosman, L. (author), Van den Broek, M. (author), Pronk, J.T. (author), Daran, J.M. (author), Daran-Lapujade, P.A.S. (author)
Background: In vivo recombination of overlapping DNA fragments for assembly of large DNA constructs in the yeast Saccharomyces cerevisiae holds great potential for pathway engineering on a small laboratory scale as well as for automated high-throughput strain construction. However, the current in vivo assembly methods are not consistent with...
journal article 2013
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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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