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Zhang, T. (author), Wu, Z. (author), Runge, Jurgen H. (author), Lavini, Cristina (author), Stoker, Jaap (author), Van Gulik, Thomas (author), Cieslak, Kasia P. (author), van Vliet, L.J. (author), Vos, F.M. (author)
The Couinaud classification of hepatic anatomy partitions the liver into eight functionally independent segments. Detection and segmentation of the hepatic vein (HV), portal vein (PV) and inferior vena cava (IVC) plays an important role in the subsequent delineation of the liver segments. To facilitate pharmacokinetic modeling of the liver...
conference paper 2018
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Zhang, T. (author), Li, Z. (author), Runge, Jurgen H. (author), Lavini, Cristina (author), Stoker, Jaap (author), Van Gulik, Thomas (author), van Vliet, L.J. (author), Vos, F.M. (author)
In Dynamic Contrast-Enhanced MRI (DCE-MRI) of the liver, a series of images is acquired over a period of 20 minutes. Due to the patient's breathing, the liver is subject to a substantial displacement between acquisitions. Furthermore, due to its location in the abdomen, the liver also undergoes marked deformation. The large deformations...
conference paper 2016
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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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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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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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Zhou, J. (author), Olson, D.G. (author), Argyros, D.A. (author), Deng, Y. (author), Van Gulik, W.M. (author), Van Dijken, J.P. (author), Lynd, L.R. (author)
Cofactor specificities of glycolytic enzymes in Clostridium thermocellum were studied with cellobiose-grown cells from batch cultures. Intracellular glucose was phosphorylated by glucokinase using GTP rather than ATP. Although phosphofructokinase typically uses ATP as a phosphoryl donor, we found only pyrophosphate (PPi)-linked activity....
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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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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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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Gidijala, L. (author), Kiel, J.A.K.W. (author), Douma, R.D. (author), Seifar, R.M. (author), Van Gulik, W.M. (author), Bovenberg, R.A.L. (author), Veenhuis, M. (author), Van Klei, I.J. (author)
This study aimed at developing an alternative host for the production of penicillin (PEN). As yet, the industrial production of this β-lactam antibiotic is confined to the filamentous fungus Penicillium chrysogenum. As such, the yeast Hansenula polymorpha, a recognized producer of pharmaceuticals, represents an attractive alternative....
journal article 2009
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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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Roa Engel, C.A. (author), Straathof, A.J.J. (author), Zijlmans, T.W. (author), Van Gulik, W.M. (author), Van der Wielen, L.A.M. (author)
Abstract The potential of fumaric acid as a raw material in the polymer industry and the increment of cost of petroleum-based fumaric acid raises interest in fermentation processes for production of this compound from renewable resources. Although the chemical process yields 112% w/w fumaric acid from maleic anhydride and the fermentation...
journal article 2008
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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), 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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Nikerel, I.E. (author), Van Winden, W. (author), Van Gulik, W.M. (author), Heijnen, J.J. (author)
Background: Dynamic modeling of metabolic reaction networks under in vivo conditions is a crucial step in order to obtain a better understanding of the (dis)functioning of living cells. So far dynamic metabolic models generally have been based on mechanistic rate equations which often contain so many parameters that their identifiability from...
journal article 2006
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Van Gulik, W.M. (author)
doctoral thesis 1990
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