J J Heijnen

Summary

Affiliation: Delft University of Technology
Country: The Netherlands

Publications

  1. ncbi A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics
    I Emrah Nikerel
    Department of Biotechnology, TU Delft, Julianalaan 67, 2628 BC Delft, The Netherlands
    BMC Bioinformatics 7:540. 2006
  2. ncbi Approximative kinetic formats used in metabolic network modeling
    Joseph J Heijnen
    Department of Biotechnology, Kluyver Laboratory for Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BL, Delft, The Netherlands
    Biotechnol Bioeng 91:534-45. 2005
  3. ncbi Metabolic flux control analysis of branch points: an improved approach to obtain flux control coefficients from large perturbation data
    J J Heijnen
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
    Metab Eng 6:391-400. 2004
  4. ncbi Energetic and metabolic transient response of Saccharomyces cerevisiae to benzoic acid
    M T A P Kresnowati
    Department of Biotechnology, Delft University of Technology, The Netherlands
    FEBS J 275:5527-41. 2008
  5. ncbi Quantitative physiological study of the fast dynamics in the intracellular pH of Saccharomyces cerevisiae in response to glucose and ethanol pulses
    M T A P Kresnowati
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Metab Eng 10:39-54. 2008
  6. ncbi Application of metabolic flux analysis for the identification of metabolic bottlenecks in the biosynthesis of penicillin-G
    W M van Gulik
    Delft University of Technology, Kluyver Laboratory for Biotechnology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 68:602-18. 2000
  7. ncbi Generating short-term kinetic responses of primary metabolism of Penicillium chrysogenum through glucose perturbation in the bioscope mini reactor
    U Nasution
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Metab Eng 8:395-405. 2006
  8. ncbi Hydrolytic activity in baker's yeast limits the yield of asymmetric 3-oxo ester reduction
    I Chin-Joe
    Kluyver Laboratory for Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 69:370-6. 2000
  9. ncbi Dynamics of glycolytic regulation during adaptation of Saccharomyces cerevisiae to fermentative metabolism
    Joost van den Brink
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Appl Environ Microbiol 74:5710-23. 2008
  10. ncbi Use of sequential-batch fermentations to characterize the impact of mild hypothermic temperatures on the anaerobic stoichiometry and kinetics of Saccharomyces cerevisiae
    A L B Cruz
    Department of Biotechnology, Kluyver Centre for Genomics of Industrial Fermentation, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 109:1735-44. 2012

Collaborators

Detail Information

Publications100

  1. ncbi A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics
    I Emrah Nikerel
    Department of Biotechnology, TU Delft, Julianalaan 67, 2628 BC Delft, The Netherlands
    BMC Bioinformatics 7:540. 2006
    ..Recently, approximative rate equations, based on the linear logarithmic (linlog) format have been proposed as a suitable alternative with fewer parameters...
  2. ncbi Approximative kinetic formats used in metabolic network modeling
    Joseph J Heijnen
    Department of Biotechnology, Kluyver Laboratory for Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BL, Delft, The Netherlands
    Biotechnol Bioeng 91:534-45. 2005
    ....
  3. ncbi Metabolic flux control analysis of branch points: an improved approach to obtain flux control coefficients from large perturbation data
    J J Heijnen
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
    Metab Eng 6:391-400. 2004
    ..The improved calculation procedure is illustrated with four experimental cases...
  4. ncbi Energetic and metabolic transient response of Saccharomyces cerevisiae to benzoic acid
    M T A P Kresnowati
    Department of Biotechnology, Delft University of Technology, The Netherlands
    FEBS J 275:5527-41. 2008
    ..The intracellular metabolite profile in the new steady-state indicates increases in the glycolytic and tricarboxylic acid cycle fluxes, which are in agreement with the observed increases in specific glucose and O(2) uptake rates...
  5. ncbi Quantitative physiological study of the fast dynamics in the intracellular pH of Saccharomyces cerevisiae in response to glucose and ethanol pulses
    M T A P Kresnowati
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Metab Eng 10:39-54. 2008
    ..e. increase in glucose phosphorylation and accumulation of CO(2), is sufficient to explain the measured decrease in intracellular pH following a glucose pulse...
  6. ncbi Application of metabolic flux analysis for the identification of metabolic bottlenecks in the biosynthesis of penicillin-G
    W M van Gulik
    Delft University of Technology, Kluyver Laboratory for Biotechnology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 68:602-18. 2000
    ..This clearly shows that, in penicillin fermentation, possible limitations in primary metabolism reside in the supply/regeneration of cofactors (NADPH) rather than in the supply of carbon precursors...
  7. ncbi Generating short-term kinetic responses of primary metabolism of Penicillium chrysogenum through glucose perturbation in the bioscope mini reactor
    U Nasution
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Metab Eng 8:395-405. 2006
    ..Equilibrium conditions were confirmed to exist in the hexose-P pool, the glycolysis between F16bP and 2+3PG and in the C4 pool of the TCA cycle (fumarate, malate, oxaloacetate and aspartate)...
  8. ncbi Hydrolytic activity in baker's yeast limits the yield of asymmetric 3-oxo ester reduction
    I Chin-Joe
    Kluyver Laboratory for Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 69:370-6. 2000
    ..Improvement of the efficiency of the reduction and hence the reduction/hydrolysis ratio should lead to a further increase in yield...
  9. ncbi Dynamics of glycolytic regulation during adaptation of Saccharomyces cerevisiae to fermentative metabolism
    Joost van den Brink
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Appl Environ Microbiol 74:5710-23. 2008
    ..cerevisiae to fermentative conditions and provides a better understanding of the roles of different regulatory mechanisms that influence the dynamics of yeast glycolysis...
  10. ncbi Use of sequential-batch fermentations to characterize the impact of mild hypothermic temperatures on the anaerobic stoichiometry and kinetics of Saccharomyces cerevisiae
    A L B Cruz
    Department of Biotechnology, Kluyver Centre for Genomics of Industrial Fermentation, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 109:1735-44. 2012
    ..Most interesting was to find that most of the biomass-specific rates have the same temperature dependency, leading to a near temperature independent batch stoichiometry...
  11. ncbi A priori analysis of metabolic flux identifiability from (13)C-labeling data
    W A Van Winden
    Department of Bioprocess Technology, Faculty of Applied Sciences, Delft University of Technology, The Netherlands
    Biotechnol Bioeng 74:505-16. 2001
    ....
  12. ncbi New experimental and theoretical tools for metabolic engineering of micro-organisms
    J J Heijnen
    Kluyverlaboratory for Biotechnology, Technical University Delft, Delft, The Netherlands
    Meded Rijksuniv Gent Fak Landbouwkd Toegep Biol Wet 66:11-30. 2001
    ..At this moment these tools are being applied in metabolic engineering studies of Saccharomyces cerevisiae and Penicillin chrysogenum...
  13. ncbi Measurement of intracellular metabolites of primary metabolism and adenine nucleotides in chemostat cultivated Penicillium chrysogenum
    U Nasution
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 94:159-66. 2006
    ..A comparison of the metabolite levels between Saccharomyces cerevisiae and Penicillium chrysogenum showed both significant similarities and large differences, which seem to be related to the presence of the penicillin pathway...
  14. ncbi Improved rapid sampling for in vivo kinetics of intracellular metabolites in Saccharomyces cerevisiae
    H C Lange
    Kluyver Laboratory for Biotechnology, Delft University of Technology, Julianalaan 67, 2628BC Delft, The Netherlands
    Biotechnol Bioeng 75:406-15. 2001
    ..The presented system is capable of reliably dealing with fermenter samples as small as 1-g with a variation of less than 3%, and is thus ideally suited for intracellular measurements on small, lab-scale fermenters...
  15. ncbi Determination of in vivo oxygen uptake and carbon dioxide evolution rates from off-gas measurements under highly dynamic conditions
    L Wu
    Kluyver Laboratory for Biotechnology, Delft University of Technology, The Netherlands
    Biotechnol Bioeng 81:448-58. 2003
    ..The estimated in vivo OUR and CER provide valuable insights into the complex dynamic behavior of yeast and are essential for the establishment and validation of in vivo kinetic models of primary metabolism...
  16. ncbi A metabolome study of the steady-state relation between central metabolism, amino acid biosynthesis and penicillin production in Penicillium chrysogenum
    Uly Nasution
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Metab Eng 10:10-23. 2008
    ....
  17. ncbi Three-dimensional dual-morphotype species modeling of activated sludge flocs
    António M P Martins
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Environ Sci Technol 38:5632-41. 2004
    ..The model suggests that attachment has a very strong effect on floc structure, leading to enhancement of the effect of substrate microgradients...
  18. ncbi Energetics of growth and penicillin production in a high-producing strain of Penicillium chrysogenum
    W M vanGulik
    Delft University of Technology, Kluyver Laboratory for Biotechnology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 72:185-93. 2001
    ..This finding has been confirmed in independent experiments and has been shown to result in a significantly lower estimate for the maximum theoretical yield of penicillin-G on the carbon source...
  19. ncbi When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation
    M T A P Kresnowati
    Department of Biotechnology, Bioprocess Technology Section, Delft University of Technology, Delft, The Netherlands
    Mol Syst Biol 2:49. 2006
    ..This acceleration of mRNA decay can be interpreted both as an additional nucleotide salvage pathway and an additional level of glucose-induced regulation of gene expression...
  20. ncbi Stoichiometry and kinetics of poly-beta-hydroxybutyrate metabolism in aerobic, slow growing, activated sludge cultures
    J J Beun
    Kluyver Laboratory for Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 67:379-89. 2000
    ..PHB consumption in the famine period could best be described kinetically with a nth-order degradation equation in PHB concentration. The obtained results are discussed in the context of the general activated sludge models...
  21. ncbi Aerobic granulation in a sequencing batch airlift reactor
    J J Beun
    Kluyverlaboratory for Biotechnology, Delft University of Technology, The Netherlands
    Water Res 36:702-12. 2002
    ..It is discussed that this could be due to the fact that the SBAR is intermittently fed, while the BASR is continuously fed...
  22. ncbi Hydrodynamic characteristics and gas-liquid mass transfer in a biofilm airlift suspension reactor
    C Nicolella
    Kluyver Institute for Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 60:627-35. 1998
    ..To evaluate scale effects, experimental results were compared with theoretical and empirical models proposed for similar systems...
  23. ncbi N-removal in a granular sludge sequencing batch airlift reactor
    J J Beun
    Kluyverlaboratory for Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 75:82-92. 2001
    ..In particular, PHB is stored in bacteria situated in deeper layers of the granules below where the autotrophic activity occurs, serves as a C-source for denitrification...
  24. ncbi Development of (R)-4-hydroxymandelonitrile synthesis in an aqueous-organic biphasic stirred tank batch reactor
    W F Willeman
    Delft University of Technology, Kluyver Laboratory for Biotechnology, Julianalaan 67, NL-2628 BC Delft, The Netherlands
    Biotechnol Bioeng 79:154-64. 2002
    ..6 g/L aqueous phase. At the predicted optimum, the synthesis was performed experimentally and the results were in accordance with the simulation regarding the extent of conversion and the enantiomeric excess...
  25. ncbi Characterization of an experimental miniature bioreactor for cellular perturbation studies
    Fredrick O Aboka
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 95:1032-42. 2006
    ....
  26. ncbi Influence of the ethanol and glucose supply rate on the rate and enantioselectivity of 3-oxo ester reduction by baker's yeast
    I Chin-Joe
    Kluyver Laboratory for Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 75:29-38. 2001
    ..In contrast to batchwise conversions with excess glucose as the electron donor, this strategy prevented by-product formation and biomass increase, and resulted in a low oxygen requirement...
  27. ncbi Mathematical modeling of biofilm structure with a hybrid differential-discrete cellular automaton approach
    C Picioreanu
    Delft University of Technology, Department of Biochemical Engineering, Kluyver Laboratory for Biotechnology, Julianalaan 67, 2628 BC Delft, The
    Biotechnol Bioeng 58:101-16. 1998
    ....
  28. ncbi Effect of dissolved oxygen concentration on sludge settleability
    A M P Martins
    Kluyver Laboratory for Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Appl Microbiol Biotechnol 62:586-93. 2003
    ....
  29. ncbi Equilibrium modeling of extractive enzymatic hydrolysis of penicillin G with concomitant 6-aminopenicillanic acid crystallization
    M B Diender
    Delft University of Technology, Kluyver Laboratory for Biotechnology, Julianalaan 67, NL-2628 BC Delft, The Netherlands
    Biotechnol Bioeng 78:395-402. 2002
    ..The model predicted the equilibrium conversion of Pen G quite reasonably for different values of pH, initial penicillin G concentration and phase volume ratio. The model can be used as a tool for optimizing the enzymatic hydrolysis...
  30. ncbi Poly-beta-hydroxybutyrate metabolism in dynamically fed mixed microbial cultures
    J J Beun
    Kluyver Laboratory for Biotechnology, Delft University of Technology, The Netherlands
    Water Res 36:1167-80. 2002
    ..The kinetic descriptions can be used to predict PHB production and consumption in general in dynamic fed wastewater treatment systems, and they provide some trends for modeling purposes...
  31. ncbi Metabolic flux analysis of a glycerol-overproducing Saccharomyces cerevisiae strain based on GC-MS, LC-MS and NMR-derived C-labelling data
    Roelco J Kleijn
    Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
    FEMS Yeast Res 7:216-31. 2007
    ....
  32. ncbi Determination of the cytosolic free NAD/NADH ratio in Saccharomyces cerevisiae under steady-state and highly dynamic conditions
    André B Canelas
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628BC Delft, The Netherlands
    Biotechnol Bioeng 100:734-43. 2008
    ..This approach provides a new experimental tool for quantitative physiology and opens new possibilities in the study of energy and redox metabolism in S. cerevisiae. The same strategy should also be applicable to other microorganisms...
  33. ncbi Aerobic batch cultivation in micro bioreactor with integrated electrochemical sensor array
    Michiel van Leeuwen
    Dept of Biotechnology, Delft University of Technology and Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC, Delft, The Netherlands
    Biotechnol Prog 26:293-300. 2010
    ..g. using the 96-well microtiterplate format...
  34. ncbi Dynamic in vivo metabolome response of Saccharomyces cerevisiae to a stepwise perturbation of the ATP requirement for benzoate export
    M T A P Kresnowati
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 99:421-41. 2008
    ..The new dynamic metabolite datasets obtained in this study will prove of great value in developing kinetic models...
  35. ncbi A theoretical study on the effect of surface roughness on mass transport and transformation in biofilms
    C Picioreanu
    Department of Biochemical Engineering, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 68:355-69. 2000
    ....
  36. ncbi Bio-augmentation by nitrification with return sludge
    S Salem
    Kluyver Laboratory for Biotechnology, Department of Biochemical Engineering, Delft, University of Technology, Julianalaan 67, 2628 BC, The Netherlands
    Water Res 37:1794-804. 2003
    ..The results of this study give a quantitative basis for the design of process internal bio-augmentation processes and the effect on the N-removal capacity of the treatment plant...
  37. ncbi Modelling of activated sludge processes with structured biomass
    M C M van Loosdrecht
    Kluyverlaboratory for Biotechnology, Delft University of Technology, The Netherlands
    Water Sci Technol 45:13-23. 2002
    ..However especially the growth rate in the famine phase seems to be overestimated. The model defined here is a contribution to a further development of mechanistically based models for activated sludge processes...
  38. ncbi High-rate acidophilic ferrous iron oxidation in a biofilm airlift reactor and the role of the carrier material
    S Ebrahimi
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 90:462-72. 2005
    ..ferrooxidans species could out-compete A. ferrooxidans due to the low Fe(2+) and high Fe(3+) concentrations...
  39. ncbi Mathematical modelling of biofilm structures
    M C M van Loosdrecht
    Kluvverlaboratory for Biotechnology, Delft University of Technology, The Netherlands
    Antonie Van Leeuwenhoek 81:245-56. 2002
    ..Biofilm structure results from the interplay between these interactions (mass transfer, conversion rates, detachment forces) making it difficult to study systems taking only one of these factors into account...
  40. ncbi Metabolic modelling of full-scale biological nitrogen and phosphorus removing wwtp's
    S C Meijer
    Kluyver Laboratory, Delft University of Technology, Netherlands
    Water Res 35:2711-23. 2001
    ..Therefore, operational data should be evaluated, or considered in model calibration over the use of kinetic and stoichiometric parameters...
  41. ncbi Electrospray ionization mass spectrometry, circular dichroism and SAXS studies of the (S)-hydroxynitrile lyase from Hevea brasiliensis
    U Hanefeld
    Kluyverlaboratorium voor Biotecnologie, Techische Universiteit Delft, The Netherlands
    Biochim Biophys Acta 1544:133-42. 2001
    ..Unfolding can also be observed by CD spectroscopy, and there is a clear correlation between enzyme activity and unfolding as detected by ESI-MS and CD...
  42. ncbi Impact of thermodynamic principles in systems biology
    J J Heijnen
    Department Biotechnology, Bioprocess Technology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
    Adv Biochem Eng Biotechnol 121:139-62. 2010
    ..Each of these aspects will be demonstrated both theoretically and experimentally...
  43. ncbi Critical evaluation of sampling techniques for residual glucose determination in carbon-limited chemostat culture of Saccharomyces cerevisiae
    M R Mashego
    Kluyver Laboratory for Biotechnology, 67 Julianalaan, 2628BC Delft, The Netherlands
    Biotechnol Bioeng 83:395-9. 2003
    ....
  44. ncbi Dynamic gene expression regulation model for growth and penicillin production in Penicillium chrysogenum
    Rutger D Douma
    Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 106:608-18. 2010
    ....
  45. ncbi Intracellular metabolite determination in the presence of extracellular abundance: Application to the penicillin biosynthesis pathway in Penicillium chrysogenum
    Rutger D Douma
    Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, BC Delft, The Netherlands
    Biotechnol Bioeng 107:105-15. 2010
    ....
  46. ncbi Revisiting the 13C-label distribution of the non-oxidative branch of the pentose phosphate pathway based upon kinetic and genetic evidence
    Roelco J Kleijn
    Department of Biotechnology, Delft University of Technology, The Netherlands
    FEBS J 272:4970-82. 2005
    ..Results show that the inclusion of isoenzymes affects the ensuing flux estimates...
  47. ncbi In vivo kinetics of primary metabolism in Saccharomyces cerevisiae studied through prolonged chemostat cultivation
    Liang Wu
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
    Metab Eng 8:160-71. 2006
    ..Metabolome measurements during the transient indicate that the differences might be due to a reduced ATP regeneration capacity in prolonged cultures...
  48. ncbi Quantitative evaluation of intracellular metabolite extraction techniques for yeast metabolomics
    André B Canelas
    Department of Biotechnology, Kluyver Centre for Genomics of Industrial Fermentation, Delft University of Technology, Julianalaan 67, 2628 BC, The Netherlands
    Anal Chem 81:7379-89. 2009
    ..According to our results, AANM performs poorly in yeast and FTM cannot be considered adequate as an extraction method, as it does not ensure inactivation of enzymatic activity...
  49. ncbi In vivo kinetics with rapid perturbation experiments in Saccharomyces cerevisiae using a second-generation BioScope
    Mlawule R Mashego
    Faculty of Applied Sciences, Department of Biotechnology, Technical University of Delft, Julianalaan 67, 2628BC Delft, The Netherlands
    Metab Eng 8:370-83. 2006
    ..It was observed that the dynamic metabolite concentration profiles obtained from both perturbations were nearly the same, with the exception of the C4 metabolites of the TCA cycle, which might be due to differences in culture age...
  50. ncbi A comprehensive method for the quantification of the non-oxidative pentose phosphate pathway intermediates in Saccharomyces cerevisiae by GC-IDMS
    Chiara Cipollina
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    J Chromatogr B Analyt Technol Biomed Life Sci 877:3231-6. 2009
    ....
  51. ncbi 13C-labeled gluconate tracing as a direct and accurate method for determining the pentose phosphate pathway split ratio in Penicillium chrysogenum
    Roelco J Kleijn
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Appl Environ Microbiol 72:4743-54. 2006
    ....
  52. ncbi Microbial metabolomics: past, present and future methodologies
    Mlawule R Mashego
    Department of Biotechnology, Faculty of Applied Sciences, Technical University of Delft, Delft, The Netherlands
    Biotechnol Lett 29:1-16. 2007
    ....
  53. ncbi Simultaneous quantification of free nucleotides in complex biological samples using ion pair reversed phase liquid chromatography isotope dilution tandem mass spectrometry
    Reza M Seifar
    Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Julianalaan 67, Delft, The Netherlands
    Anal Biochem 388:213-9. 2009
    ..Uniformly (13)C-labeled isotopes of nucleotides were used as internal standards for both extraction and quantification of intracellular nucleotides. The method was validated by determining the linearity, sensitivity, and repeatability...
  54. ncbi Dynamic 13C-tracer study of storage carbohydrate pools in aerobic glucose-limited Saccharomyces cerevisiae confirms a rapid steady-state turnover and fast mobilization during a modest stepup in the glucose uptake rate
    Fredrick O Aboka
    Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
    FEMS Yeast Res 9:191-201. 2009
    ..This study shows that for accurate in vivo kinetic interpretation of rapid pulse experiments, glycogen and trehalose metabolism must be taken into account...
  55. ncbi Metabolome dynamic responses of Saccharomyces cerevisiae to simultaneous rapid perturbations in external electron acceptor and electron donor
    Mlawule R Mashego
    Department of Biotechnology, Faculty of Applied Sciences, Technical University of Delft, Julianalaan, Delft, The Netherlands
    FEMS Yeast Res 7:48-66. 2007
    ..Surprisingly, trehalose was not mobilized in the time frame of 180 s...
  56. ncbi Quantitative analysis of metabolites in complex biological samples using ion-pair reversed-phase liquid chromatography-isotope dilution tandem mass spectrometry
    Reza M Seifar
    Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, 67 Julianalaan, 2628 BC Delft, The Netherlands
    J Chromatogr A 1187:103-10. 2008
    ..The method showed excellent precision (relative standard deviation (RSD)<or=11%, except for PIO and 8-HPA) in present of interferences from sample matrix. Limits of quantification (LOQs) for all metabolites were below 1 microM level...
  57. ncbi Model reduction and a priori kinetic parameter identifiability analysis using metabolome time series for metabolic reaction networks with linlog kinetics
    I Emrah Nikerel
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Metab Eng 11:20-30. 2009
    ..We illustrated the methodology on model reduction and theoretical/practical identifiability analysis on an example system representing the glycolysis in Saccharomyces cerevisiae cells...
  58. ncbi Isotopic non-stationary 13C gluconate tracer method for accurate determination of the pentose phosphate pathway split-ratio in Penicillium chrysogenum
    Zheng Zhao
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628BC Delft, The Netherlands
    Metab Eng 10:178-86. 2008
    ..2+/-0.6%) using the novel approach, shows statistically no difference with the split-ratio obtained from the originally proposed isotopic stationary gluconate tracing method...
  59. ncbi Application of metabolome data in functional genomics: a conceptual strategy
    Liang Wu
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
    Metab Eng 7:302-10. 2005
    ..We demonstrate in silico that changes in enzyme activities can be accurately predicted by this approach, even in 'silent mutants'...
  60. ncbi Correcting mass isotopomer distributions for naturally occurring isotopes
    Wouter A van Winden
    Department of Bioprocess Technology, Faculty of Applied Sciences, Delft University of Technology, The Netherlands
    Biotechnol Bioeng 80:477-9. 2002
    ..Furthermore, it is shown that the source of information with respect to isotopic compositions of the elements needs to be chosen with care...
  61. ncbi Effect of feeding pattern and storage on the sludge settleability under aerobic conditions
    António M P Martins
    Department of Biochemical Engineering, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Water Res 37:2555-70. 2003
    ..Where presence of filamentous bacteria is related to process conditions, the presence of a specific filament is likely due to presence of a specific limiting substrate...
  62. ncbi Cumulative bondomers: a new concept in flux analysis from 2D [13C,1H] COSY NMR data
    Wouter A van Winden
    Department of Bioprocess Technology, Faculty of Applied Sciences, Delft University of Technology, The Netherlands
    Biotechnol Bioeng 80:731-45. 2002
    ..The combinations of 2D [(13)C,(1)H] COSY NMR data that allow identification of all metabolic fluxes in these pathways are analyzed, and it is found that the NMR data contain less information than was previously expected...
  63. ncbi Filamentous bulking sludge--a critical review
    António M P Martins
    Department of Biochemical Engineering, Delft University of Technology, Julianalaan, The Netherlands
    Water Res 38:793-817. 2004
    ..Several theories for bulking sludge are discussed. Based on these theories the application and associated problems with the use of biological selectors are critically evaluated. Finally, a set of open research questions is identified...
  64. ncbi A new framework for the estimation of control parameters in metabolic pathways using lin-log kinetics
    Liang Wu
    Department of Biotechnology, Delft University of Technology, The Netherlands
    Eur J Biochem 271:3348-59. 2004
    ....
  65. ncbi Metabolic flux and metabolic network analysis of Penicillium chrysogenum using 2D [13C, 1H] COSY NMR measurements and cumulative bondomer simulation
    Wouter A van Winden
    Bioprocestechnology Group, Faculty of Applied Sciences, Delft University of Technology, The Netherlands
    Biotechnol Bioeng 83:75-92. 2003
    ..Strict statistical testing of the outcomes of (13)C-labeling based flux analysis using realistic measurement errors is demonstrated to be of prime importance for verifying the assumed metabolic model...
  66. ncbi Quantitative analysis of the microbial metabolome by isotope dilution mass spectrometry using uniformly 13C-labeled cell extracts as internal standards
    Liang Wu
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
    Anal Biochem 336:164-71. 2005
    ..In conclusion, the method presented leads to less workload, more robustness, and a higher precision in metabolome analysis...
  67. ncbi Changes in the metabolome of Saccharomyces cerevisiae associated with evolution in aerobic glucose-limited chemostats
    Mlawule R Mashego
    Department of Biotechnology, Faculty of Applied Sciences, Technical University of Delft, 67 Julianalaan, 2628 BC Delft, The Netherlands
    FEMS Yeast Res 5:419-30. 2005
    ..The driving force is proposed to be a growth advantage in the absence of these metabolic overcapacities...
  68. ncbi Determination of elasticities, concentration and flux control coefficients from transient metabolite data using linlog kinetics
    M T A Penia Kresnowati
    Department of Biotechnology, TU Delft, Julianalaan 67, 2628 BC Delft, The Netherlands
    Metab Eng 7:142-53. 2005
    ....
  69. ncbi Metabolic-flux analysis of Saccharomyces cerevisiae CEN.PK113-7D based on mass isotopomer measurements of (13)C-labeled primary metabolites
    Wouter A van Winden
    Kluyver Laboratory for Biotechnology, Department of Biotechnology, Faculty of Applied Sciences, Bioprocess Technology Group, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    FEMS Yeast Res 5:559-68. 2005
    ..Furthermore, it is found that turnover of storage carbohydrates occurs. Inclusion of this turnover in the model leads to a large confidence interval of the estimated split ratio...
  70. ncbi Statistical reconciliation of the elemental and molecular biomass composition of Saccharomyces cerevisiae
    H C Lange
    Delft University of Technology, Kluyver Laboratory for Biotechnology, Delft, The Netherlands
    Biotechnol Bioeng 75:334-44. 2001
    ....
  71. ncbi Study of the (S)-hydroxynitrile lyase from Hevea brasiliensis: mechanistic implications
    U Hanefeld
    Kluyver Laboratory for Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
    Biochim Biophys Acta 1432:185-93. 1999
    ..Therefore the earlier postulated reaction intermediate as well as the proposed action of the catalytic triad have to be reevaluated. The calculated molecular mass could be confirmed by mass spectroscopy...
  72. ncbi Model-based evaluation of a new upgrading concept for N-removal
    S Salem
    Kluyver Laboratory for Biotechnology, Delft University of Technology, The Netherlands
    Water Sci Technol 45:169-76. 2002
    ..Based on the modelling results a decision was made to implement the bioaugmentation concept at full scale without further pilot scale testing, thereby strongly decreasing the scale-up period for this process...
  73. ncbi Study on the use of NADH fluorescence measurements for monitoring wastewater treatment systems
    G Farabegoli
    Department of Biochemical Engineering, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Water Res 37:2732-8. 2003
    ..In the near zero concentration ranges of oxygen and nitrate (0.1-0.5mg/l) the signal changes only slightly in the opposite direction to the redox trend...
  74. ncbi Degradation of polymers in a biofilm airlift suspension reactor
    A Mosquera-Corral
    Kluyverlaboratory for Biotechnology, Department of Biochemical Engineering, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Water Res 37:485-92. 2003
    ..During unstable conditions or start-up significant hydrolytic activity occurred outside the biofilm...
  75. ncbi Bulking sludge in biological nutrient removal systems
    António M P Martins
    Department of Biochemical Engineering, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 86:125-35. 2004
    ....
  76. ncbi Development of a system for the on-line measurement of carbon dioxide production in microbioreactors: application to aerobic batch cultivations of Candida utilis
    Michiel van Leeuwen
    Dept of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Prog 25:892-7. 2009
    ..The measurements showed that on-line measurement of the CO(2) production rate in microbioreactors can provide essential data for quantitative physiological studies and provide better understanding of microscale cultivations...
  77. ncbi The mathematics of metabolic control analysis revisited
    Diana Visser
    Kluyverlaboratory for Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Metab Eng 4:114-23. 2002
    ..The value of our approach is its simplicity: the derivation is straightforward and therefore easy to follow. It can serve as a compact introduction to the mathematical basis of MCA...
  78. ncbi Measurement of fast dynamic intracellular pH in Saccharomyces cerevisiae using benzoic acid pulse
    M T A P Kresnowati
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 97:86-98. 2007
    ..The low concentration benzoic acid pulse which was implemented in the method avoids the undesirable effects that may be introduced by benzoic acid to cell metabolism...
  79. ncbi A quantitative approach to characterizing cell lysis caused by mechanical agitation of Streptomyces clavuligerus
    J A Roubos
    Control Laboratory, Faculty of Information Technology and Systems, Delft University of Technology, P.O. Box 5031, 2600 GA Delft, The Netherlands
    Biotechnol Prog 17:336-47. 2001
    ..07 h(-1), when the gassed power input increases above 1.1, 1.7, or 2.0 kW/m(3), respectively, depending on the medium composition. The overall biomass yield on substrate is dramatically reduced in all experiments (>30%)...
  80. ncbi 13C-Labeled metabolic flux analysis of a fed-batch culture of elutriated Saccharomyces cerevisiae
    Roeland Costenoble
    Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
    FEMS Yeast Res 7:511-26. 2007
    ....
  81. ncbi Development of a process model to describe the synthesis of (R)-mandelonitrile by Prunus amygdalus hydroxynitrile lyase in an aqueous-organic biphasic reactor
    Wouter F Willeman
    Delft University of Technology, Kluyver Laboratory for Biotechnology, Julianalaan 67, NL-2628 BC Delft, The Netherlands
    Biotechnol Bioeng 77:239-47. 2002
    ..To synthesize cyanohydrins with a high enantiomeric excess, the enzyme is required to work at mass transfer limited conditions. The developed process model will be used to investigate other process concepts and other substrates...
  82. ncbi Genome-derived minimal metabolic models for Escherichia coli MG1655 with estimated in vivo respiratory ATP stoichiometry
    Hilal Taymaz-Nikerel
    Department of Biotechnology, Delft University of Technology, Julianalaan BC Delft, The Netherlands
    Biotechnol Bioeng 107:369-81. 2010
    ..The resulting metabolic network model only requires the specific rate of growth, micro, as an input in order to accurately predict all other fluxes and yields...
  83. ncbi Sensitivity analysis of a biofilm model describing a one-stage completely autotrophic nitrogen removal (CANON) process
    Xiaodi Hao
    Kluyver Laboratory for Biotechnology, Department of Biochemical Engineering, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
    Biotechnol Bioeng 77:266-77. 2002
    ..It can be concluded that a one-stage process is probably not optimal if a good nitrogen effluent is required. A two-stage process like the combined SHARON and ANAMMOX process would be advised for complete nitrogen removal...
  84. ncbi Quantitative determination of glucose transfer between concurrent laminar water streams in a H-shaped microchannel
    Michiel van Leeuwen
    Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
    Biotechnol Prog 25:1826-32. 2009
    ..The results obtained in this work show the applicability of LFDI for the controlled diffusive supply of a solute to a water stream, with as possible application substrate and/or precursor feeding to microreactors...
  85. ncbi Simultaneous COD, nitrogen, and phosphate removal by aerobic granular sludge
    M K de Kreuk
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628BC Delft, The Netherlands
    Biotechnol Bioeng 90:761-9. 2005
    ..Monitoring the laboratory scale reactors for a long period showed that N-removal efficiency highly depends on the diameter of the granules...
  86. ncbi MIRACLE: mass isotopomer ratio analysis of U-13C-labeled extracts. A new method for accurate quantification of changes in concentrations of intracellular metabolites
    M R Mashego
    Kluyver Laboratory for Biotechnology, 67 Julianalaan, 2628BC Delft, The Netherlands
    Biotechnol Bioeng 85:620-8. 2004
    ..e., no spiking and standard additions). By coextracting a known amount of U-13C labeled cells with the unlabeled samples, metabolite losses occurring during the sample extraction procedure are corrected for...
  87. ncbi Potential application of monolith packed columns as bioreactors, control of biofilm formation
    Sirous Ebrahimi
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 93:238-45. 2006
    ..Periodic biofilm removal could straightforwardly be achieved by rinsing with water at moderate pressures and allows for stable operation for prolonged periods of time...
  88. ncbi In situ product removal using a crystallization loop in asymmetric reduction of 4-oxoisophorone by Saccharomyces cerevisiae
    Evelyn M Buque-Taboada
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Biotechnol Bioeng 86:795-800. 2004
    ..An almost sixfold reduction in biocatalyst consumption per kilogram product was achieved, which also can contribute to the minimization of waste streams...
  89. ncbi Model-based evaluation of temperature and inflow variations on a partial nitrification-ANAMMOX biofilm process
    Xiaodi Hao
    Department of Biochemical Engineering, Delft University of Technology, The Netherlands
    Water Res 36:4839-49. 2002
    ..At T = 20 degrees C, an N-removal efficiency of 88% is possible at ASL = 0.5 g NH4+ - N/mr2 d, in a biofilm of at least 0.7 mm thickness and a DO level of 0.3 g O2/m3 in the bulk liquid...
  90. ncbi Cytosolic NADPH metabolism in penicillin-G producing and non-producing chemostat cultures of Penicillium chrysogenum
    Roelco J Kleijn
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    Metab Eng 9:112-23. 2007
    ..chrysogenum was obtained by comparing the PPP fluxes from the gluconate-tracer experiment to oxidative PPP fluxes derived via metabolic flux analysis, using different assumptions for the stoichiometry of NADPH consumption and production...
  91. ncbi Development and application of a differential method for reliable metabolome analysis in Escherichia coli
    Hilal Taymaz-Nikerel
    Department of Biotechnology, Delft University of Technology, BC Delft, The Netherlands
    Anal Biochem 386:9-19. 2009
    ....
  92. ncbi Clavulanic acid degradation in Streptomyces clavuligerus fed-batch cultivations
    Johannes A Roubos
    Control Systems Engineering, Faculty of Information Technology and Systems, Delft University of Technology, P O Box 5031, 2600 GA Delft, The Netherlands
    Biotechnol Prog 18:451-7. 2002
    ..Finally, a linear and a fuzzy logic model were made to predict CA degradation rates in these fed-batches...
  93. ncbi In situ product recovery (ISPR) by crystallization: basic principles, design, and potential applications in whole-cell biocatalysis
    Evelyn M Buque-Taboada
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
    Appl Microbiol Biotechnol 71:1-12. 2006
    ..This leads to an economically more interesting process alternative. Finally, a general outlook on the various research aspects of ISPR by crystallization is given...
  94. ncbi Lab-scale fermentation tests of microchip with integrated electrochemical sensors for pH, temperature, dissolved oxygen and viable biomass concentration
    Erik E Krommenhoek
    MESA Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
    Biotechnol Bioeng 99:884-92. 2008
    ..1 pH unit. The platinum thin-film temperature resistor followed temperature changes with approximately 0.1 degrees C accuracy. The dimensions of the multi sensor chip are chosen as such that it is compatible with the 96-well plate format...
  95. ncbi Dynamics of intracellular metabolites of glycolysis and TCA cycle during cell-cycle-related oscillation in Saccharomyces cerevisiae
    Christoph Wittmann
    Biochemical Engineering, Saarland University, POB 151150, 66123 Saarbrucken, Germany
    Biotechnol Bioeng 89:839-47. 2005
    ..Oscillations in intracellular amino acids might therefore be, at least partly, following oscillations of their anabolic precursors...
  96. ncbi Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics
    Diana Visser
    PURAC, P O Box 21, 4200 AA Gorinchem, The Netherlands
    Metab Eng 5:164-76. 2003
    ..Results show that the linlog approximation is able to describe the non-linear dynamics of this pathway very well for concentration changes up to a factor 20. Also the metabolic design equation was tested successfully...
  97. ncbi Short-term metabolome dynamics and carbon, electron, and ATP balances in chemostat-grown Saccharomyces cerevisiae CEN.PK 113-7D following a glucose pulse
    Liang Wu
    DSM Anti Infectives, P O Box 525, 2613 AX Delft, The Netherlands
    Appl Environ Microbiol 72:3566-77. 2006
    ..The identified metabolic processes involving major carbon, electron, and energy sinks must be taken into account in in vivo kinetic models based on short-term dynamic metabolome responses...
  98. ncbi Analysis of in vivo kinetics of glycolysis in aerobic Saccharomyces cerevisiae by application of glucose and ethanol pulses
    Diana Visser
    PURAC, P O Box 21, 4200 AA Gorinchem, The Netherlands
    Biotechnol Bioeng 88:157-67. 2004
    ..Our results confirm that FBP stimulates pyruvate kinase and suggest that this effect is pronounced. Furthermore, it appears that PEP does not play an important role in the allosteric regulation of phosphofructo kinase...
  99. ncbi Rapid sampling for analysis of in vivo kinetics using the BioScope: a system for continuous-pulse experiments
    Diana Visser
    Puroc, P O Box 21, 4200AA Gorinchem, The Netherlands
    Biotechnol Bioeng 79:674-81. 2002
    ..The agreement between the results demonstrates that the BioScope is indeed a promising device for studying in vivo kinetics...
  100. ncbi Optimal re-design of primary metabolism in Escherichia coli using linlog kinetics
    Diana Visser
    PURAC, Research, Development and Technology, P O Box 21, Arkelsedijk 46, 4200 AA Gorinchem, The Netherlands
    Metab Eng 6:378-90. 2004
    ....