Cells are the fundamental units of life. A cell’s ability to replicate, grow, divide, and interact with its environment lies at the heart of every organism. These basic biological processes are precisely regulated in space and time by a complex and dynamic network of interacting genes, RNAs, and proteins.
Our lab aims at providing a simpler view of this incredible biological complexity, primarily focusing on the regulation of cell division. We believe that understanding the system dynamics is essential to achieving this goal. The dynamical interaction of proteins can lead to robust systems-level behavior, for example, the irreversible cellular decision to divide. Different sets of proteins often interact in similar ways to generate the same function (e.g., an irreversible switch), underscoring the relevance of a generic dynamical view of biology.
In our studies we glean techniques from physics and mathematics, such as the theory of nonlinear dynamics and complex systems, which allows us to theoretically analyze the spatiotemporal dynamics of molecules inside cells. This approach is complemented by molecular and cellular experiments, in which we test our hypotheses by controllably perturbing biological processes in model organisms such as Xenopus frogs, zebrafish, and mammalian cells. This synergistic approach is geared toward understanding how cells are regulated in space and time. In the long-term we believe that a functional understanding of a cell’s most basic processes will contribute to developing new therapeutic strategies to combat diseases such as cancer.
Selected publications
1.
Ruiz-Reynés, D.; Mayol, E.; Sintes, T.; Hendriks, I. E; Hernández-García, E.; Duarte, C. M; Marbà, N.; Gomila, D.
Self-organized sulfide-driven traveling pulses shape seagrass meadows
In: Proceedings of the National Academy of Sciences, vol. 120, iss. 3, pp. e2216024120, 2023.
@article{nokey,
title = {Self-organized sulfide-driven traveling pulses shape seagrass meadows},
author = {D. Ruiz-Reynés and E. Mayol and T. Sintes and I. E Hendriks and E. Hernández-García and C. M Duarte and N. Marbà and D. Gomila},
doi = {https://doi.org/10.1073/pnas.2216024120},
year = {2023},
date = {2023-01-17},
urldate = {2023-01-17},
journal = {Proceedings of the National Academy of Sciences},
volume = {120},
issue = {3},
pages = {e2216024120},
abstract = {Seagrasses provide multiple ecosystem services and act as intense carbon sinks in coastal regions around the globe but are threatened by multiple anthropogenic pressures, leading to enhanced seagrass mortality that reflects in the spatial self-organization of the meadows. Spontaneous spatial vegetation patterns appear in such different ecosystems as drylands, peatlands, salt marshes, or seagrass meadows, and the mechanisms behind this phenomenon are still an open question in many cases. Here, we report on the formation of vegetation traveling pulses creating complex spatiotemporal patterns and rings in Mediterranean seagrass meadows. We show that these structures emerge due to an excitable behavior resulting from the coupled dynamics of vegetation and porewater hydrogen sulfide, toxic to seagrass, in the sediment. The resulting spatiotemporal patterns resemble those formed in other physical, chemical, and biological excitable media, but on a much larger scale. Based on theory, we derive a model that reproduces the observed seascapes and predicts the annihilation of these circular structures as they collide, a distinctive feature of excitable pulses. We show also that the patterns in field images and the empirically resolved radial profiles of vegetation density and sediment sulfide concentration across the structures are consistent with predictions from the theoretical model, which shows these structures to have diagnostic value, acting as a harbinger of the terminal state of the seagrass meadows prior to their collapse.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Seagrasses provide multiple ecosystem services and act as intense carbon sinks in coastal regions around the globe but are threatened by multiple anthropogenic pressures, leading to enhanced seagrass mortality that reflects in the spatial self-organization of the meadows. Spontaneous spatial vegetation patterns appear in such different ecosystems as drylands, peatlands, salt marshes, or seagrass meadows, and the mechanisms behind this phenomenon are still an open question in many cases. Here, we report on the formation of vegetation traveling pulses creating complex spatiotemporal patterns and rings in Mediterranean seagrass meadows. We show that these structures emerge due to an excitable behavior resulting from the coupled dynamics of vegetation and porewater hydrogen sulfide, toxic to seagrass, in the sediment. The resulting spatiotemporal patterns resemble those formed in other physical, chemical, and biological excitable media, but on a much larger scale. Based on theory, we derive a model that reproduces the observed seascapes and predicts the annihilation of these circular structures as they collide, a distinctive feature of excitable pulses. We show also that the patterns in field images and the empirically resolved radial profiles of vegetation density and sediment sulfide concentration across the structures are consistent with predictions from the theoretical model, which shows these structures to have diagnostic value, acting as a harbinger of the terminal state of the seagrass meadows prior to their collapse.
2.
Moreno-Spiegelberg, P.; Arinyo-i-Prats, A.; Ruiz-Reynés, D.; Matias, M. A.; Gomila, D.
Bifurcation structure of traveling pulses in type-I excitable media
In: Physical Review E, vol. 106, iss. 3, pp. 034206, 2022.
@article{nokey,
title = {Bifurcation structure of traveling pulses in type-I excitable media},
author = {P. Moreno-Spiegelberg and A. Arinyo-i-Prats and D. Ruiz-Reynés and M. A. Matias and D. Gomila},
doi = {https://doi.org/10.1103/PhysRevE.106.034206},
year = {2022},
date = {2022-09-15},
urldate = {2022-09-15},
journal = {Physical Review E},
volume = {106},
issue = {3},
pages = {034206},
abstract = {We study the scenario in which traveling pulses emerge in a prototypical type-I one-dimensional excitable medium, which exhibits two different routes to excitable behavior, mediated by a homoclinic (saddle-loop) and a saddle-node on the invariant cycle bifurcations. We characterize the region in parameter space in which traveling pulses are stable together with the different bifurcations behind either their destruction or loss of stability. In particular, some of the bifurcations delimiting the stability region have been connected, using singular limits, with the two different scenarios that mediated type-I local excitability. Finally, the existence of traveling pulses has been linked to a drift pitchfork instability of localized steady structures.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We study the scenario in which traveling pulses emerge in a prototypical type-I one-dimensional excitable medium, which exhibits two different routes to excitable behavior, mediated by a homoclinic (saddle-loop) and a saddle-node on the invariant cycle bifurcations. We characterize the region in parameter space in which traveling pulses are stable together with the different bifurcations behind either their destruction or loss of stability. In particular, some of the bifurcations delimiting the stability region have been connected, using singular limits, with the two different scenarios that mediated type-I local excitability. Finally, the existence of traveling pulses has been linked to a drift pitchfork instability of localized steady structures.
3.
Nolet, F. E. *; Vandervelde, A. *; Vanderbeke, A. *; Pineros, L. *; Chang, J. B.; Gelens, L.
Nuclei determine the spatial origin of mitotic waves
In: eLife, vol. 9, pp. e52868, 2020, ISSN: 2050-084X.
@article{nolet_nuclei_2020,
title = {Nuclei determine the spatial origin of mitotic waves},
author = {F. E. * Nolet and A. * Vandervelde and A. * Vanderbeke and L. * Pineros and J. B. Chang and L. Gelens},
url = {https://elifesciences.org/articles/52868},
doi = {10.7554/eLife.52868},
issn = {2050-084X},
year = {2020},
date = {2020-05-26},
urldate = {2020-05-26},
journal = {eLife},
volume = {9},
pages = {e52868},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
4.
Gelens, L.; Qian, J.; Bollen, M.; Saurin, A. T.
The Importance of Kinase–Phosphatase Integration: Lessons from Mitosis
In: Trends in Cell Biology, vol. 28, iss. 1, pp. 6-21, 2017, ISSN: 0962-8924.
@article{gelens_importance_2017,
title = {The Importance of Kinase–Phosphatase Integration: Lessons from Mitosis},
author = {L. Gelens and J. Qian and M. Bollen and A. T. Saurin},
url = {http://www.sciencedirect.com/science/article/pii/S0962892417301782},
doi = {https://doi.org/10.1016/j.tcb.2017.09.005},
issn = {0962-8924},
year = {2017},
date = {2017-11-01},
urldate = {2017-11-01},
journal = {Trends in Cell Biology},
volume = {28},
issue = {1},
pages = {6-21},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
5.
Anderson*, G. A.; Gelens*, L.; Baker, J.; Ferrell, J. E. Jr.
Desynchronizing Embryonic Cell Division Waves Reveals the Robustness of Xenopus laevis Development
In: Cell Reports, vol. 21, iss. 1, pp. 37–46, 2017, (featured on the cover).
@article{anderson_desynchronizing_2017,
title = {Desynchronizing Embryonic Cell Division Waves Reveals the Robustness of \textit{Xenopus laevis} Development},
author = {G. A. Anderson* and L. Gelens* and J. Baker and J. E. Jr. Ferrell},
url = {http://www.cell.com/cell-reports/fulltext/S2211-1247(17)31278-0},
doi = {10.1016/j.celrep.2017.09.017},
year = {2017},
date = {2017-09-01},
urldate = {2017-09-01},
journal = {Cell Reports},
volume = {21},
issue = {1},
pages = {37--46},
note = {featured on the cover},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
6.
Gelens, L.; Anderson, G. A.; Jr., J. E. Ferrell
Spatial trigger waves: positive feedback gets you a long way
In: Molecular Biology of the Cell, vol. 25, no. 22, pp. 3486–3493, 2014, ISSN: 1059-1524, 1939-4586.
@article{gelens_spatial_2014,
title = {Spatial trigger waves: positive feedback gets you a long way},
author = {L. Gelens and G. A. Anderson and J. E. Ferrell Jr.},
url = {http://www.molbiolcell.org/content/25/22/3486},
doi = {10.1091/mbc.E14-08-1306},
issn = {1059-1524, 1939-4586},
year = {2014},
date = {2014-11-01},
urldate = {2014-11-01},
journal = {Molecular Biology of the Cell},
volume = {25},
number = {22},
pages = {3486--3493},
abstract = {Trigger waves are a recurring biological phenomenon involved in transmitting information quickly and reliably over large distances. Well-characterized examples include action potentials propagating along the axon of a neuron, calcium waves in various tissues, and mitotic waves in Xenopus eggs. Here we use the FitzHugh-Nagumo model, a simple model inspired by the action potential that is widely used in physics and theoretical biology, to examine different types of trigger waves—spatial switches, pulses, and oscillations—and to show how they arise.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Trigger waves are a recurring biological phenomenon involved in transmitting information quickly and reliably over large distances. Well-characterized examples include action potentials propagating along the axon of a neuron, calcium waves in various tissues, and mitotic waves in Xenopus eggs. Here we use the FitzHugh-Nagumo model, a simple model inspired by the action potential that is widely used in physics and theoretical biology, to examine different types of trigger waves—spatial switches, pulses, and oscillations—and to show how they arise.