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4. Mathematical modeling of nitrogen regulated biological systems

Author

Casanova Ferrer, Pau, Muñoz-García, Javier, Ares García, Saúl, UC3M. Departamento de Matemáticas, and Ministerio de Ciencia e Innovación (España)

Subjects
Mathematical models, Nitrogen fixation, Biological systems, Matemáticas, Cyanobacteria, Biología y Biomedicina, Gene regulatory networks
Abstract

Mención Internacional en el título de doctor This doctoral thesis was supported through the FPI contract BES-2017-079755 associated to the grant FIS2016-78313-P from Ministerio de Ciencia e Innovación (MCIN)/Agencia Estatal de Investigación (AEI)/ 10.13039/501100011033/ and FEDER Una manera de hacer Europa. Additionally the author also acknowledge finantial support from MCIN/AEI/10.13039/501100011033 through grant BADS, no. PID2019-109320GB-100 Programa de Doctorado en Ingeniería Matemática por la Universidad Carlos III de Madrid Presidente: Luis Guillermo Morelli.- Secretaria: María Pilar Guerrero Contreras.- Vocal: Vicente Mariscal Romero

Published
2023

7. Additional file 3 of A coarse-grained approach to model the dynamics of the actomyosin cortex [Dataset]

Author

Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., Míguez, David G., Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., and Míguez, David G.

Published
2022

8. Additional file 5 of A coarse-grained approach to model the dynamics of the actomyosin cortex [Dataset]

Author

Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., Míguez, David G., Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., and Míguez, David G.

Published
2022

9. Additional file 4 of A coarse-grained approach to model the dynamics of the actomyosin cortex [Dataset]

Author

Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., Míguez, David G., Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., and Míguez, David G.

Published
2022

10. Additional file 11 of A coarse-grained approach to model the dynamics of the actomyosin cortex [Dataset]

Author

Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., Míguez, David G., Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., and Míguez, David G.

Published
2022

11. Additional file 7 of A coarse-grained approach to model the dynamics of the actomyosin cortex [Dataset]

Author

Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., Míguez, David G., Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., and Míguez, David G.

Published
2022

12. Additional file 8 of A coarse-grained approach to model the dynamics of the actomyosin cortex [Dataset]

Author

Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., Míguez, David G., Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., and Míguez, David G.

Published
2022

13. Additional file 2 of A coarse-grained approach to model the dynamics of the actomyosin cortex [Dataset]

Author

Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., Míguez, David G., Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., and Míguez, David G.

Published
2022

14. Additional file 9 of A coarse-grained approach to model the dynamics of the actomyosin cortex [Dataset]

Author

Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., Míguez, David G., Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., and Míguez, David G.

Published
2022

15. Additional file 6 of A coarse-grained approach to model the dynamics of the actomyosin cortex [Dataset]

Author

Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., Míguez, David G., Ministerio de Ciencia, Innovación y Universidades (España), Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., and Míguez, David G.

Published
2022

16. A coarse-grained approach to model the dynamics of the actomyosin cortex

Author

Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Comunidad de Madrid, Fundación Ramón Areces, Banco Santander, Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., Míguez, David G., Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Comunidad de Madrid, Fundación Ramón Areces, Banco Santander, Hernández del Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, María D., and Míguez, David G.

Abstract

[Background]: The dynamics of the actomyosin machinery is at the core of many important biological processes. Several relevant cellular responses such as the rhythmic compression of the cell cortex are governed, at a mesoscopic level, by the nonlinear interaction between actin monomers, actin crosslinkers, and myosin motors. Coarse-grained models are an optimal tool to study actomyosin systems, since they can include processes that occur at long time and space scales, while maintaining the most relevant features of the molecular interactions. [Results]: Here, we present a coarse-grained model of a two-dimensional actomyosin cortex, adjacent to a three-dimensional cytoplasm. Our simplified model incorporates only well-characterized interactions between actin monomers, actin crosslinkers and myosin, and it is able to reproduce many of the most important aspects of actin filament and actomyosin network formation, such as dynamics of polymerization and depolymerization, treadmilling, network formation, and the autonomous oscillatory dynamics of actomyosin. [Conclusions]: We believe that the present model can be used to study the in vivo response of actomyosin networks to changes in key parameters of the system, such as alterations in the attachment of actin filaments to the cell cortex.

Published
2022

17. Additional file 7 of A coarse-grained approach to model the dynamics of the actomyosin cortex

Author

Hernández-del-Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, Maria D., and Míguez, David G.

Subjects
macromolecular substances
Abstract

Additional file 7 Figure S4. Oscillations for different levels of Myosin. Oscillations in the number of G-actin in the cortex for conditions of (A) low and (B) high concentration of Myosin in the system. The corresponding Fourier transform for each oscillation is also shown.

Published
2022
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18. Additional file 2 of A coarse-grained approach to model the dynamics of the actomyosin cortex

Author

Hernández-del-Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, Maria D., and Míguez, David G.

Subjects
macromolecular substances
Abstract

Additional file 2 Figure S1. Percentage of G-Actin in filaments. Percentage of G-Actin in filaments of different size for the three characteristic regimes.

Published
2022
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19. Additional file 3 of A coarse-grained approach to model the dynamics of the actomyosin cortex

Author

Hernández-del-Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, Maria D., and Míguez, David G.

Subjects
macromolecular substances
Abstract

Additional file 3 Figure S2. Dependence of speed of treadmiling with F-actin length. Plot of the dependence of the instantaneous speed on the filament size. Short filaments move faster than average. Long filaments move at the same speed in average.

Published
2022
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20. Additional file 12 of A coarse-grained approach to model the dynamics of the actomyosin cortex

Author

Hernández-del-Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, Maria D., and Míguez, David G.

Subjects
macromolecular substances
Abstract

Additional file 12 Figure S7. Scheme of the effect of Myosin over F-actin. (1), Myosin movement in parallel f-Actin. (2) F-actin sliding. (3) Tension building in the filaments. (4) Release from cortex after threshold tension is reached. After release, tension (illustrated in red) is redistributed to other F-actin in the network.

Published
2022
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21. Additional file 5 of A coarse-grained approach to model the dynamics of the actomyosin cortex

Author

Hernández-del-Valle, Miguel, Valencia-Expósito, Andrea, López-Izquierdo, Antonio, Casanova-Ferrer, Pau, Tarazona, Pedro, Martín-Bermudo, Maria D., and Míguez, David G.

Subjects
macromolecular substances
Abstract

Additional file 5 Figure S3. G-Actin, F-actin after incorporation of ACs. Number of G-Actin in the grid (green), G-actin as part of networks (orange) and ACs (blue) after incorporation of ACs into the system at t=5E6 iterations. The formation of networks is initial very fast, followed by a regime where incorporation of molecules into networks is gradually slowing down until equilibrium is reached.

Published
2022
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24. Modelling of patA and hetF gene function in Anabaena heterocyst formation

Author

Casanova Ferrer, Pau, Ares García, Saúl, and Muñoz-García, Javier

Subjects
Matemáticas, Pattern formation, Heterocyst differentiation, Cyanobacteria
Abstract

[Póster presentado a]: XXII Congreso de Física Estadística (FisEs'18), Madrid, 18-20 de octubre de 2018. Differentiated cell types can form patterns in filamentous cyanobacteria. Specifically the genus Anabaena has received special interest because under nitrogen-limiting conditions some of the vegetative cells differentiate into a nitrogen-fixing form called heterocyst [1]. These heterocysts cannot undergo cell division or have photosynthetic activity, but share fixed nitrogen products with the whole filament. In order to efficiently distribute the fixed nitrogen, heterocysts are arranged forming quasiregular patterns in the filament...

Published
2018

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