Influence of circadian clocks on optimal regime of central C-N
metabolism of cyanobacteria

C 2018

Influence of circadian clocks on optimal regime of central C-N metabolism of cyanobacteria

ČERVENÝ, Jan, Jakub ŠALAGOVIČ, František MUZIKA, David ŠAFRÁNEK, Igor SCHREIBER et. al.

Basic information

Original name

Influence of circadian clocks on optimal regime of central C-N metabolism of cyanobacteria

Authors

ČERVENÝ, Jan (203 Czech Republic), Jakub ŠALAGOVIČ (703 Slovakia), František MUZIKA, David ŠAFRÁNEK (203 Czech Republic, guarantor, belonging to the institution) and Igor SCHREIBER

Edition

1st ed. Neuveden, Cyanobacteria: From Basic Science to Applications, p. 193-206, 14 pp. 2018

Publisher

Academic Press

Other information

Language

English

Type of outcome

Kapitola resp. kapitoly v odborné knize

Field of Study

20900 2.9 Industrial biotechnology

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

electronic version available online

References:

URL

RIV identification code

RIV/00216224:14330/18:00104828

Organization unit

Faculty of Informatics

ISBN

978-0-12-814667-5

DOI

http://dx.doi.org/10.1016/B978-0-12-814667-5.00009-X

UT WoS

000509547100010

Keywords in English

Computational modeling; Bioreactor; Formal methods; Industry 4.0; Microalgae; Network analysis; Optimization; Process control

Abstract

V originále

Mechanistic aspects of cyanobacteria clock and metabolism have been analyzed in considerable detail during recent decades, but only limited knowledge is available about particular link(s) between the clock and controlled metabolic processes. We describe a case study where we couple a mechanistic model of a circadian oscillator with a model of central carbon-nitrogen metabolism and apply formal methods based on temporal logic and bifurcation analysis to examine response of the metabolic part of the combined model to the autonomous clock oscillations. The analysis identified a set of parametric groups that, when applied to the in silico system, lead either to an optimal configuration of metabolic pathways for most efficient rhythmic function of the metabolism or to (oscillatory) system death. Under controlled conditions in monitored environments, such as cultivation in photobioreactors, the knowledge can be used for optimal regulation of production capacity that would reflect dynamic constraints of real world systems.

Links

LM2015055, research and development project

Name: Centrum pro systémovou biologii (Acronym: C4SYS)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

ČERVENÝ, Jan, Jakub ŠALAGOVIČ, František MUZIKA, David ŠAFRÁNEK and Igor SCHREIBER. Influence of circadian clocks on optimal regime of central C-N metabolism of cyanobacteria. Online. In Mishra, A. K.; Tiwari, D.; Rai, A. N. Cyanobacteria: From Basic Science to Applications. 1st ed. Neuveden: Academic Press, 2018, p. 193-206. ISBN 978-0-12-814667-5. Available from: https://dx.doi.org/10.1016/B978-0-12-814667-5.00009-X.

@inbook{1475736,
   author = {Červený, Jan and Šalagovič, Jakub and Muzika, František and Šafránek, David and Schreiber, Igor},
   address = {Neuveden},
   booktitle = {Cyanobacteria: From Basic Science to Applications},
   doi = {http://dx.doi.org/10.1016/B978-0-12-814667-5.00009-X},
   edition = {1st ed.},
   editor = {Mishra, A. K.; Tiwari, D.; Rai, A. N.},
   keywords = {Computational modeling; Bioreactor; Formal methods; Industry 4.0; Microalgae; Network analysis; Optimization; Process control},
   howpublished = {elektronická verze "online"},
   language = {eng},
   location = {Neuveden},
   isbn = {978-0-12-814667-5},
   pages = {193-206},
   publisher = {Academic Press},
   title = {Influence of circadian clocks on optimal regime of central C-N metabolism of cyanobacteria},
   url = {https://doi.org/10.1016/B978-0-12-814667-5.00009-X},
   year = {2018}
}

TY  - CHAP
ID  - 1475736
AU  - Červený, Jan - Šalagovič, Jakub - Muzika, František - Šafránek, David - Schreiber, Igor
PY  - 2018
TI  - Influence of circadian clocks on optimal regime of central C-N metabolism of cyanobacteria
VL  - Neuveden
PB  - Academic Press
CY  - Neuveden
SN  - 9780128146675
KW  - Computational modeling
KW  - Bioreactor
KW  - Formal methods
KW  - Industry 4.0
KW  - Microalgae
KW  - Network analysis
KW  - Optimization
KW  - Process control
UR  - https://doi.org/10.1016/B978-0-12-814667-5.00009-X
N2  - Mechanistic aspects of cyanobacteria clock and metabolism have been analyzed in considerable detail during recent decades, but only limited knowledge is available about particular link(s) between the clock and controlled metabolic processes. We describe a case study where we couple a mechanistic model of a circadian oscillator with a model of central carbon-nitrogen metabolism and apply formal methods based on temporal logic and bifurcation analysis to examine response of the metabolic part of the combined model to the autonomous clock oscillations. The analysis identified a set of parametric groups that, when applied to the in silico system, lead either to an optimal configuration of metabolic pathways for most efficient rhythmic function of the metabolism or to (oscillatory) system death. Under controlled conditions in monitored environments, such as cultivation in photobioreactors, the knowledge can be used for optimal regulation of production capacity that would reflect dynamic constraints of real world systems.
ER  -

ČERVENÝ, Jan, Jakub ŠALAGOVIČ, František MUZIKA, David ŠAFRÁNEK and Igor SCHREIBER. Influence of circadian clocks on optimal regime of central C-N metabolism of cyanobacteria. Online. In Mishra, A. K.; Tiwari, D.; Rai, A. N. \textit{Cyanobacteria: From Basic Science to Applications}. 1st ed. Neuveden: Academic Press, 2018, p.~193-206. ISBN~978-0-12-814667-5. Available from: https://dx.doi.org/10.1016/B978-0-12-814667-5.00009-X.

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