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Suarez Mendez, C.A. (author), Hanemaaijer, M. (author), Ten Pierick, A. (author), Wolters, J.C. (author), Heijnen, J.J. (author), Wahl, S.A. (author)13C labeling experiments in aerobic glucose limited cultures of Saccharomyces cerevisiae at four different growth rates (0.054; 0.101, 0.207, 0.307 h?1) are used for calculating fluxes that include intracellular cycles (e.g., storage carbohydrate cycles, exchange fluxes with amino acids), which are rearranged depending on the growth rate. At low...journal article 2016
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Zhang, J. (author), Ten Pierick, A. (author), Van Rossum, H.M. (author), Maleki Seifar, R. (author), Daran, J.G. (author), Heijnen, J.J. (author), Wahl, S.A. (author)Eukaryotic metabolism is organised in complex networks of enzyme catalysed reactions which are distributed over different organelles. To quantify the compartmentalised reactions, quantitative measurements of relevant physiological variables in different compartments are needed, especially of cofactors. NADP(H) are critical components in cellular...journal article 2015
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Heeres, A.S. (author), Schroën, K. (author), Heijnen, J.J. (author), Van der Wielen, L.A.M. (author), Cuellar, M.C. (author)Developments in synthetic biology enabled the microbial production of long chain hydrocarbons, which can be used as advanced biofuels in aviation or transportation. Currently, these fuels are not economically competitive due to their production costs. The current process offers room for improvement: by utilizing lignocellulosic feedstock,...journal article 2015
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Lameiras, F. (author), Heijnen, J.J. (author), Van Gulik, W.M. (author)In view of the high citric acid production capacity of Aspergillus niger, it should be well suited as a cell factory for the production of other relevant acids as succinic, fumaric, itaconic and malic. Quantitative metabolomics is an important omics tool in a synthetic biology approach to develop A. niger for the production of these acids. Such...journal article 2015
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Suarez-Mendez, C.A. (author), Sousa, A. (author), Heijnen, J.J. (author), Wahl, S.A. (author)Microorganisms are constantly exposed to rapidly changing conditions, under natural as well as industrial production scale environments, especially due to large-scale substrate mixing limitations. In this work, we present an experimental approach based on a dynamic feast/famine regime (400 s) that leads to repetitive cycles with moderate changes...journal article 2014
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Jorda, J. (author), Suarez Mendez, C.A (author), Carnicer, M. (author), Ten Pierick, A. (author), Heijnen, J.J. (author), Van Gulik, W.M. (author), Ferrer, P. (author), Albiol, J. (author), Wahl, S.A. (author)Background Several studies have shown that the utilization of mixed carbon feeds instead of methanol as sole carbon source is beneficial for protein production with the methylotrophic yeast Pichia pastoris. In particular, growth under mixed feed conditions appears to alleviate the metabolic burden related to stress responses triggered by protein...journal article 2013
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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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Zhao, Z. (author), Ten Pierick, A. (author), De Jonge, L. (author), Heijnen, J.J. (author), Wahl, S.A. (author)Background Penicillium chrysogenum, the main production strain for penicillin-G, has a high content of intracellular carbohydrates, especially reduced sugars such as mannitol, arabitol, erythritol, as well as trehalose and glycogen. In previous steady state 13C wash-in experiments a delay of labeling enrichments in glycolytic intermediates was...journal article 2012
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Carnicer, M. (author), Ten Pierick, A. (author), Van Dam, J. (author), Heijnen, J.J. (author), Albiol, J. (author), Van Gulik, W. (author), Ferrer, P. (author)Background: Environmental and intrinsic stress factors can result in the global alteration of yeast physiology, as evidenced by several transcriptional studies. Hypoxia has been shown to have a beneficial effect on the expression of recombinant proteins in Pichia pastoris growing on glucose. Furthermore, transcriptional profiling analyses...journal article 2012
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Jamalzadeh, E. (author), Verheijen, P.J. (author), Heijnen, J.J. (author), Van Gulik, W.M. (author)Microbial production of C4 dicarboxylic acids from renewable resources has gained renewed interest. The yeast Saccharomyces cerevisiae is known as a robust microorganism and is able to grow at low pH, which makes it a suitable candidate for biological production of organic acids. However, a successful metabolic engineering approach for...journal article 2011
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De Jonge, L.P. (author), Douma, R.D. (author), Heijnen, J.J. (author), Van Gulik, W.M. (author)A sampling procedure for quantitative metabolomics in Penicillium chrysogenum based on cold aqueous methanol quenching was re-evaluated and optimized to reduce metabolite leakage during sample treatment. The optimization study included amino acids and intermediates of the glycolysis and the TCA-cycle. Metabolite leakage was found to be minimal...journal article 2011
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Douma, R.D. (author), Batista, J.M. (author), Touw, K.M. (author), Kiel, J.A.K.W. (author), Krikken, A.M. (author), Zhao, Z. (author), Veiga, T. (author), Klaassen, P. (author), Bovenberg, R.A.L. (author), Daran, J.M. (author), Heijnen, J.J. (author), Van Gulik, W.M. (author)Background In microbial production of non-catabolic products such as antibiotics a loss of production capacity upon long-term cultivation (for example chemostat), a phenomenon called strain degeneration, is often observed. In this study a systems biology approach, monitoring changes from gene to produced flux, was used to study degeneration of...journal article 2011
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Carnicer,, M. (author), Canelas, A.B. (author), Ten Pierick, A. (author), Zeng, Z. (author), Van Dam, J. (author), Albiol, J. (author), Ferrer, P. (author), Heijnen, J.J. (author), Van Gulik, W. (author)Accurate, reliable and reproducible measurement of intracellular metabolite levels has become important for metabolic studies of microbial cell factories. A first critical step for metabolomic studies is the establishment of an adequate quenching and washing protocol, which ensures effective arrest of all metabolic activity and removal of...journal article 2011
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Waegeman, H. (author), Beauprez, J. (author), Moens, H. (author), Maertens, J. (author), De Mey, M. (author), Foulquié-Moreno, M.R. (author), Heijnen, J.J. (author), Charlier, D. (author), Soetaert, W. (author)Background: Gene expression is regulated through a complex interplay of different transcription factors (TFs) which can enhance or inhibit gene transcription. ArcA is a global regulator that regulates genes involved in different metabolic pathways, while IclR as a local regulator, controls the transcription of the glyoxylate pathway genes of the...journal article 2011
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Zhao, Z. (author), Kuijvenhoven, K. (author), Van Gulik, W.M. (author), Heijnen, J.J. (author), Van Winden, W.A. (author), Verheijen, P.J.T. (author)The in vivo flux through the oxidative branch of the pentose phosphate pathway (oxPPP) in Penicillium chrysogenum was determined during growth in glucose/ethanol carbon-limited chemostat cultures, at the same growth rate. Non-stationary 13C flux analysis was used to measure the oxPPP flux. A nearly constant oxPPP flux was found for all glucose...journal article 2010
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Van der Wielen, L.A.M. (author), Heijnen, J.J. (author)The present invention is directed to a process for the continuous biological production of lipids, hydrocarbons, hydrocarbon like material or mixtures thereof by conversion of a suitable substrate using micro-organisms, in which process the said substrate is continuously, anaerobically fermented to produce lipids, hydrocarbons, hydrocarbon like...patent 2010
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Heijnen, J.J. (author)It is shown that properties of biological systems which are relevant for systems biology motivated mathematical modelling are strongly shaped by general thermodynamic principles such as osmotic limit, Gibbs energy dissipation, near equilibria and thermodynamic driving force. Each of these aspects will be demonstrated both theoretically and...journal article 2010
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Baart, G.J.E. (author), Beauprez, J.J.R. (author), Foulquie, M.M.R. (author), Heijnen, J.J. (author), Maertens, J. (author)The present invention relates to a method for obtaining enhanced metabolite production in micro-organisms, and to mutants and/or transformants obtained with said method. More particularly, it relates to bacterial mutants and/or transformants for enhanced succinate production, especially mutants and/or transformants that are affected in the...patent 2010
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Canelas, A.B. (author), Ras, C. (author), Ten Pierick, A. (author), Van Dam, J.C. (author), Heijnen, J.J. (author), Van Gulik, W.M. (author)Accurate determination of intracellular metabolite levels requires reliable, reproducible techniques for sampling and sample treatment. Quenching in 60% (v/v) methanol at ?40°C is currently the standard method for sub-second arrest of metabolic activity in microbial metabolomics but there have been contradictory reports in the literature on...journal article 2008
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- Mashego, M.R. (author), Rumbold, K. (author), De Mey, M. (author), Vandamme, E. (author), Soetaert, W. (author), Heijnen, J.J. (author) journal article 2007
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