Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA
Brinkrolf C, Henke NA, Ochel L, Pucker B, Kruse O, Lutter P (2018)
Journal of Integrative Bioinformatics 15(3): 20180018.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
Download
10.1515_jib-2018-0018.pdf
2.29 MB
Autor*in
Brinkrolf, ChristophUniBi;
Henke, Nadja AlinaUniBi;
Ochel, Lennart;
Pucker, BoasUniBi 
;
Kruse, OlafUniBi ;
Lutter, PetraUniBi
;
Kruse, OlafUniBi ;
Lutter, PetraUniBiEinrichtung
Technische Fakultät > AG Bioinformatik
Centrum für Biotechnologie > Arbeitsgruppe V. Wendisch
Centrum für Biotechnologie > Arbeitsgruppe B. Weisshaar
Fakultät für Biologie > Proteom- und Metabolomforschung
Fakultät für Biologie > Algenbiotechnologie
Fakultät für Biologie > Genetik der Prokaryoten
Fakultät für Biologie > Genetik und Genomik der Pflanzen
Technische Fakultät > Int. Graduiertenkolleg DiDy (GRK 1906)
Centrum für Biotechnologie > Arbeitsgruppe O. Kruse
Centrum für Biotechnologie > Arbeitsgruppe V. Wendisch
Centrum für Biotechnologie > Arbeitsgruppe B. Weisshaar
Fakultät für Biologie > Proteom- und Metabolomforschung
Fakultät für Biologie > Algenbiotechnologie
Fakultät für Biologie > Genetik der Prokaryoten
Fakultät für Biologie > Genetik und Genomik der Pflanzen
Technische Fakultät > Int. Graduiertenkolleg DiDy (GRK 1906)
Centrum für Biotechnologie > Arbeitsgruppe O. Kruse
Abstract / Bemerkung
In this work we present new concepts of VANESA, a tool for modeling and simulation in systems biology. We provide a convenient way to handle mathematical expressions and take physical units into account. Simulation and result management has been improved, and syntax and consistency checks, based on physical units, reduce modeling errors. As a proof of concept, essential components of the aerobic carbon metabolism of the green microalga Chlamydomonas reinhardtii are modeled and simulated. The modeling process is based on xHPN Petri net formalism and simulation is performed with OpenModelica, a powerful environment and compiler for Modelica. VANESA, as well as OpenModelica, is open source, free-of-charge for non-commercial use, and is available at: http://agbi.techfak.uni-bielefeld.de/vanesa.
Stichworte
petri net;
Chlamydomonas reinhardtii
Erscheinungsjahr
2018
Zeitschriftentitel
Journal of Integrative Bioinformatics
Band
15
Ausgabe
3
Art.-Nr.
20180018
Urheberrecht / Lizenzen
ISSN
1613-4516
eISSN
1613-4516
Page URI
https://pub.uni-bielefeld.de/record/2931064
Zitieren
Brinkrolf C, Henke NA, Ochel L, Pucker B, Kruse O, Lutter P. Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. Journal of Integrative Bioinformatics. 2018;15(3): 20180018.
Brinkrolf, C., Henke, N. A., Ochel, L., Pucker, B., Kruse, O., & Lutter, P. (2018). Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. Journal of Integrative Bioinformatics, 15(3), 20180018. https://doi.org/10.1515/jib-2018-0018
Brinkrolf, Christoph, Henke, Nadja Alina, Ochel, Lennart, Pucker, Boas, Kruse, Olaf, and Lutter, Petra. 2018. “Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA”. Journal of Integrative Bioinformatics 15 (3): 20180018.
Brinkrolf, C., Henke, N. A., Ochel, L., Pucker, B., Kruse, O., and Lutter, P. (2018). Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. Journal of Integrative Bioinformatics 15:20180018.
Brinkrolf, C., et al., 2018. Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. Journal of Integrative Bioinformatics, 15(3): 20180018.
C. Brinkrolf, et al., “Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA”, Journal of Integrative Bioinformatics, vol. 15, 2018, : 20180018.
Brinkrolf, C., Henke, N.A., Ochel, L., Pucker, B., Kruse, O., Lutter, P.: Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. Journal of Integrative Bioinformatics. 15, : 20180018 (2018).
Brinkrolf, Christoph, Henke, Nadja Alina, Ochel, Lennart, Pucker, Boas, Kruse, Olaf, and Lutter, Petra. “Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA”. Journal of Integrative Bioinformatics 15.3 (2018): 20180018.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Creative Commons Namensnennung - Nicht kommerziell - Keine Bearbeitungen 4.0 International (CC BY-NC-ND 4.0):
Volltext(e)
Name
10.1515_jib-2018-0018.pdf
2.29 MB
Access Level
Open Access
Zuletzt Hochgeladen
2021-06-10T06:10:38Z
MD5 Prüfsumme
f60c95770d442290c6bb564bb09ddbce
Daten bereitgestellt von European Bioinformatics Institute (EBI)
Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
44 References
Daten bereitgestellt von Europe PubMed Central.
KEGG for integration and interpretation of large-scale molecular data sets.
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22080510
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22080510
Levels of nicotinamide nucleotide coenzymes in lactic acid bacteria
Takebe, J Gen Appl Microbiol 9(), 1963
Takebe, J Gen Appl Microbiol 9(), 1963
Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets
Goss, Proc Natl Acad Sci 5(), 1998
Goss, Proc Natl Acad Sci 5(), 1998
Heterotrophic growth of Chlamydomonas reinhardtii on acetate in chemostat culture
Chen, Process Biochemistry 31(), 1996
Chen, Process Biochemistry 31(), 1996
Full-scale model of glycolysis in Saccharomyces cerevisiae.
Hynne F, Dano S, Sorensen PG., Biophys. Chem. 94(1-2), 2001
PMID: 11744196
Hynne F, Dano S, Sorensen PG., Biophys. Chem. 94(1-2), 2001
PMID: 11744196
Knock-Down of the IFR1 Protein Perturbs the Homeostasis of Reactive Electrophile Species and Boosts Photosynthetic Hydrogen Production in Chlamydomonas reinhardtii.
Venkanna D, Sudfeld C, Baier T, Homburg SV, Patel AV, Wobbe L, Kruse O., Front Plant Sci 8(), 2017
PMID: 28824682
Venkanna D, Sudfeld C, Baier T, Homburg SV, Patel AV, Wobbe L, Kruse O., Front Plant Sci 8(), 2017
PMID: 28824682
The free NADH concentration is kept constant in plant mitochondria under different metabolic conditions.
Kasimova MR, Grigiene J, Krab K, Hagedorn PH, Flyvbjerg H, Andersen PE, Moller IM., Plant Cell 18(3), 2006
PMID: 16461578
Kasimova MR, Grigiene J, Krab K, Hagedorn PH, Flyvbjerg H, Andersen PE, Moller IM., Plant Cell 18(3), 2006
PMID: 16461578
Continuous bioluminescent monitoring of cytoplasmic ATP in single isolated rat hepatocytes during metabolic poisoning
Koop, Biochem J (), 1993
Koop, Biochem J (), 1993
Redox control of exocytosis: regulatory role of NADPH, thioredoxin, and glutaredoxin.
Ivarsson R, Quintens R, Dejonghe S, Tsukamoto K, in 't Veld P, Renstrom E, Schuit FC., Diabetes 54(7), 2005
PMID: 15983215
Ivarsson R, Quintens R, Dejonghe S, Tsukamoto K, in 't Veld P, Renstrom E, Schuit FC., Diabetes 54(7), 2005
PMID: 15983215
Intracellular compartmentalization of adenosine triphosphate
Miller, J Biol Chem 5(), 1986
Miller, J Biol Chem 5(), 1986
Flux balance analysis reveals acetate metabolism modulates cyclic electron flow and alternative glycolytic pathways in Chlamydomonas reinhardtii.
Chapman SP, Paget CM, Johnson GN, Schwartz JM., Front Plant Sci 6(), 2015
PMID: 26175742
Chapman SP, Paget CM, Johnson GN, Schwartz JM., Front Plant Sci 6(), 2015
PMID: 26175742
Bioluminescent measurement in single cardiomyocytes of sudden cytosolic ATP depletion coincident with rigor.
Bowers KC, Allshire AP, Cobbold PH., J. Mol. Cell. Cardiol. 24(3), 1992
PMID: 1625346
Bowers KC, Allshire AP, Cobbold PH., J. Mol. Cell. Cardiol. 24(3), 1992
PMID: 1625346
A purification of microsomal glucose - - phosphatase from human tissue
Reczek, Biochem Biophys Res Commun (), 1982
Reczek, Biochem Biophys Res Commun (), 1982
Human Protein Reference Database--2009 update.
Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18988627
Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18988627
Metabolic engineering for higher alcohol production.
Nozzi NE, Desai SH, Case AE, Atsumi S., Metab. Eng. 25(), 2014
PMID: 25080238
Nozzi NE, Desai SH, Case AE, Atsumi S., Metab. Eng. 25(), 2014
PMID: 25080238
MINT, the molecular interaction database: 2012 update.
Licata L, Briganti L, Peluso D, Perfetto L, Iannuccelli M, Galeota E, Sacco F, Palma A, Nardozza AP, Santonico E, Castagnoli L, Cesareni G., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22096227
Licata L, Briganti L, Peluso D, Perfetto L, Iannuccelli M, Galeota E, Sacco F, Palma A, Nardozza AP, Santonico E, Castagnoli L, Cesareni G., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22096227
Tailored carbon partitioning for phototrophic production of (E)-α-bisabolene from the green microalga Chlamydomonas reinhardtii.
Wichmann J, Baier T, Wentnagel E, Lauersen KJ, Kruse O., Metab. Eng. 45(), 2017
PMID: 29258965
Wichmann J, Baier T, Wentnagel E, Lauersen KJ, Kruse O., Metab. Eng. 45(), 2017
PMID: 29258965
de Optimizing the distribution of resources between enzymes of carbon metabolism can dramatically in - crease photosynthetic rate : a numerical simulation using an evolutionary algorithm
Zhu, Plant Physiol 26(), 2007
Zhu, Plant Physiol 26(), 2007
Efficient phototrophic production of a high-value sesquiterpenoid from the eukaryotic microalga Chlamydomonas reinhardtii.
Lauersen KJ, Baier T, Wichmann J, Wordenweber R, Mussgnug JH, Hubner W, Huser T, Kruse O., Metab. Eng. 38(), 2016
PMID: 27474353
Lauersen KJ, Baier T, Wichmann J, Wordenweber R, Mussgnug JH, Hubner W, Huser T, Kruse O., Metab. Eng. 38(), 2016
PMID: 27474353
The kinetic mechanism of yeast phosphoenolpyruvate carboxykinase
Jabalquinto, Biochim Biophys Acta (), 1993
Jabalquinto, Biochim Biophys Acta (), 1993
Regulation of NAD - and NADP - dependent isocitrate dehydrogenases by reduction levels of pyridine nucleotides in mitochondria and cytosol of pea leaves
Igamberdiev, Biochim Biophys Acta Bioenerg 25(), 2003
Igamberdiev, Biochim Biophys Acta Bioenerg 25(), 2003
Central carbon metabolism and electron transport in Chlamydomonas reinhardtii: metabolic constraints for carbon partitioning between oil and starch.
Johnson X, Alric J., Eukaryotic Cell 12(6), 2013
PMID: 23543671
Johnson X, Alric J., Eukaryotic Cell 12(6), 2013
PMID: 23543671
Petri nets : an introduction Vol of EATCS Monographs on Theoretical Germany : Springer - Verlag Berlin Heidelberg
Reisig, Computer Science (), 1985
Reisig, Computer Science (), 1985
A mathematical model of electron transport Thermodynamic necessity for photosystem II regulation : light stom - ata
Laisk, Proc Soc Lond B Biol Sci 44(), 1989
Laisk, Proc Soc Lond B Biol Sci 44(), 1989
Improved photobiological H production in engineered green algal cells
Kruse, J Biol Chem 7(), 2005
Kruse, J Biol Chem 7(), 2005
Mammalian TOR : a homeostatic ATP sensor
Dennis, Science 5(), 2001
Dennis, Science 5(), 2001
Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets.
Singh VK, Ghosh I., Theor Biol Med Model 3(), 2006
PMID: 16887020
Singh VK, Ghosh I., Theor Biol Med Model 3(), 2006
PMID: 16887020
The redox state of free nicotinamide adenine dinucleotide phosphate in the cytoplasm of rat liver
Veech, Biochem J (), 1969
Veech, Biochem J (), 1969
VANESA - a software application for the visualization and analysis of networks in system biology applications.
Brinkrolf C, Janowski SJ, Kormeier B, Lewinski M, Hippe K, Borck D, Hofestadt R., J Integr Bioinform 11(2), 2014
PMID: 24953454
Brinkrolf C, Janowski SJ, Kormeier B, Lewinski M, Hippe K, Borck D, Hofestadt R., J Integr Bioinform 11(2), 2014
PMID: 24953454
Glucose-stimulated oscillations in free cytosolic ATP concentration imaged in single islet beta-cells: evidence for a Ca2+-dependent mechanism.
Ainscow EK, Rutter GA., Diabetes 51 Suppl 1(), 2002
PMID: 11815476
Ainscow EK, Rutter GA., Diabetes 51 Suppl 1(), 2002
PMID: 11815476
Evaluation of the participation of ferredoxin in oxygen reduction in the photosynthetic electron transport chain of isolated pea thylakoids.
Kozuleva MA, Ivanov BN., Photosyn. Res. 105(1), 2010
PMID: 20532996
Kozuleva MA, Ivanov BN., Photosyn. Res. 105(1), 2010
PMID: 20532996
Metabolic flux analysis of Escherichia coli creB and arcA mutants reveals shared control of carbon catabolism under microaerobic growth conditions
Nikel, J Bacteriol 48(), 2009
Nikel, J Bacteriol 48(), 2009
Sustained photobiological hydrogen gas production upon reversible inactivation of oxygen evolution in the green AlgaChlamydomonas reinhardtii
Melis, Plant Physiol (), 2000
Melis, Plant Physiol (), 2000
BRENDA , the enzyme information system in Nucleic Acids
Scheer, Res 39(), 2011
Scheer, Res 39(), 2011
Cyanobacterial metabolic engineering for biofuel and chemical production.
Oliver NJ, Rabinovitch-Deere CA, Carroll AL, Nozzi NE, Case AE, Atsumi S., Curr Opin Chem Biol 35(), 2016
PMID: 27614173
Oliver NJ, Rabinovitch-Deere CA, Carroll AL, Nozzi NE, Case AE, Atsumi S., Curr Opin Chem Biol 35(), 2016
PMID: 27614173
Levels of nicotinamide adenine dinucleotide and reduced nicotinamide adenine dinucleotide in facultative bac - teria and the effect of oxygen
Wimpenny, J Bacteriol (), 1972
Wimpenny, J Bacteriol (), 1972
Adaptive and bio - semantics of continuous petri nets : choosing the appropriate interpretation
Herajy, Fundam Inform (), 2018
Herajy, Fundam Inform (), 2018
A novel method for measurement of submembrane ATP concen - tration
Gribble, J Biol Chem 9(), 2000
Gribble, J Biol Chem 9(), 2000
The IntAct molecular interaction database in Nucleic Acids Au to m at ica lly ge ne ra te d ro ug h PD Fb yP ro of Ch ec kf ro m Ri ve rV al le yT ec hn ol og ie sL td DE GRUYTER Brinkrolf et al
Kerrien, Res 40(), 2012
Kerrien, Res 40(), 2012
Silane modified upconversion nanoparticles with multifunctions: imaging, therapy and hypoxia detection.
Xu S, Zhang X, Xu H, Dong B, Qu X, Chen B, Zhang S, Zhang T, Cheng Y, Xu S, Song H., Sci Rep 6(), 2016
PMID: 26924009
Xu S, Zhang X, Xu H, Dong B, Qu X, Chen B, Zhang S, Zhang T, Cheng Y, Xu S, Song H., Sci Rep 6(), 2016
PMID: 26924009
Evidence for rapid consumption of millimolar concentrations of cytoplasmic ATP during rigor - contracture of metabolically compromised single cardiomyocytes
Allue, Biochem J (), 1996
Allue, Biochem J (), 1996
Kinetic models in industrial biotechnology - Improving cell factory performance.
Almquist J, Cvijovic M, Hatzimanikatis V, Nielsen J, Jirstrand M., Metab. Eng. 24(), 2014
PMID: 24747045
Almquist J, Cvijovic M, Hatzimanikatis V, Nielsen J, Jirstrand M., Metab. Eng. 24(), 2014
PMID: 24747045
Concentrations of nicotinamide nucleotide coenzymes in micro-organisms.
London J, Knight M., J. Gen. Microbiol. 44(2), 1966
PMID: 4381873
London J, Knight M., J. Gen. Microbiol. 44(2), 1966
PMID: 4381873
Updates on industrial production of amino acids using Corynebacterium glutamicum.
Wendisch VF, Jorge JMP, Perez-Garcia F, Sgobba E., World J. Microbiol. Biotechnol. 32(6), 2016
PMID: 27116971
Wendisch VF, Jorge JMP, Perez-Garcia F, Sgobba E., World J. Microbiol. Biotechnol. 32(6), 2016
PMID: 27116971
Export
Markieren/ Markierung löschen
Markierte Publikationen
Web of Science
Dieser Datensatz im Web of Science®Quellen
PMID: 30218605
PubMed | Europe PMC
Suchen in
Google Scholar