Dynamics in Biology

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

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.

Abstract | Links | BibTeX

@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}

}