1
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Deinum EE, Jacobs B. Rho of Plants patterning: linking mathematical models and molecular diversity. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1274-1288. [PMID: 37962515 PMCID: PMC10901209 DOI: 10.1093/jxb/erad447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/08/2023] [Indexed: 11/15/2023]
Abstract
ROPs (Rho of Plants) are plant specific small GTPases involved in many membrane patterning processes and play important roles in the establishment and communication of cell polarity. These small GTPases can produce a wide variety of patterns, ranging from a single cluster in tip-growing root hairs and pollen tubes to an oriented stripe pattern controlling protoxylem cell wall deposition. For an understanding of what controls these various patterns, models are indispensable. Consequently, many modelling studies on small GTPase patterning exist, often focusing on yeast or animal cells. Multiple patterns occurring in plants, however, require the stable co-existence of multiple active ROP clusters, which does not occur with the most common yeast/animal models. The possibility of such patterns critically depends on the precise model formulation. Additionally, different small GTPases are usually treated interchangeably in models, even though plants possess two types of ROPs with distinct molecular properties, one of which is unique to plants. Furthermore, the shape and even the type of ROP patterns may be affected by the cortical cytoskeleton, and cortex composition and anisotropy differ dramatically between plants and animals. Here, we review insights into ROP patterning from modelling efforts across kingdoms, as well as some outstanding questions arising from these models and recent experimental findings.
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Affiliation(s)
- Eva E Deinum
- Mathematical and Statistical Methods (Biometris), Plant Science Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Bas Jacobs
- Mathematical and Statistical Methods (Biometris), Plant Science Group, Wageningen University, 6708 PB Wageningen, The Netherlands
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2
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Beta C, Edelstein-Keshet L, Gov N, Yochelis A. From actin waves to mechanism and back: How theory aids biological understanding. eLife 2023; 12:e87181. [PMID: 37428017 DOI: 10.7554/elife.87181] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023] Open
Abstract
Actin dynamics in cell motility, division, and phagocytosis is regulated by complex factors with multiple feedback loops, often leading to emergent dynamic patterns in the form of propagating waves of actin polymerization activity that are poorly understood. Many in the actin wave community have attempted to discern the underlying mechanisms using experiments and/or mathematical models and theory. Here, we survey methods and hypotheses for actin waves based on signaling networks, mechano-chemical effects, and transport characteristics, with examples drawn from Dictyostelium discoideum, human neutrophils, Caenorhabditis elegans, and Xenopus laevis oocytes. While experimentalists focus on the details of molecular components, theorists pose a central question of universality: Are there generic, model-independent, underlying principles, or just boundless cell-specific details? We argue that mathematical methods are equally important for understanding the emergence, evolution, and persistence of actin waves and conclude with a few challenges for future studies.
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Affiliation(s)
- Carsten Beta
- Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany
| | | | - Nir Gov
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Arik Yochelis
- Swiss Institute for Dryland Environmental and Energy Research, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
- Department of Physics, Ben-Gurion University of the Negev, Be'er Sheva, Israel
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3
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Würthner L, Goychuk A, Frey E. Geometry-induced patterns through mechanochemical coupling. Phys Rev E 2023; 108:014404. [PMID: 37583206 DOI: 10.1103/physreve.108.014404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 05/15/2023] [Indexed: 08/17/2023]
Abstract
Intracellular protein patterns regulate a variety of vital cellular processes such as cell division and motility, which often involve dynamic cell-shape changes. These changes in cell shape may in turn affect the dynamics of pattern-forming proteins, hence leading to an intricate feedback loop between cell shape and chemical dynamics. While several computational studies have examined the rich resulting dynamics, the underlying mechanisms are not yet fully understood. To elucidate some of these mechanisms, we explore a conceptual model for cell polarity on a dynamic one-dimensional manifold. Using concepts from differential geometry, we derive the equations governing mass-conserving reaction-diffusion systems on time-evolving manifolds. Analyzing these equations mathematically, we show that dynamic shape changes of the membrane can induce pattern-forming instabilities in parts of the membrane, which we refer to as regional instabilities. Deformations of the local membrane geometry can also (regionally) suppress pattern formation and spatially shift already existing patterns. We explain our findings by applying and generalizing the local equilibria theory of mass-conserving reaction-diffusion systems. This allows us to determine a simple onset criterion for geometry-induced pattern-forming instabilities, which is linked to the phase-space structure of the reaction-diffusion system. The feedback loop between membrane shape deformations and reaction-diffusion dynamics then leads to a surprisingly rich phenomenology of patterns, including oscillations, traveling waves, and standing waves, even if these patterns do not occur in systems with a fixed membrane shape. Our paper reveals that the local conformation of the membrane geometry acts as an important dynamical control parameter for pattern formation in mass-conserving reaction-diffusion systems.
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Affiliation(s)
- Laeschkir Würthner
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 Munich, Germany
| | - Andriy Goychuk
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 Munich, Germany
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 Munich, Germany
- Max Planck School Matter to Life, Hofgartenstraße 8, D-80539 Munich, Germany
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4
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Hladyshau S, Stoop JP, Kamada K, Nie S, Tsygankov D. Spatiotemporal Coordination of Rac1 and Cdc42 at the Whole Cell Level during Cell Ruffling. Cells 2023; 12:1638. [PMID: 37371108 DOI: 10.3390/cells12121638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Rho-GTPases are central regulators within a complex signaling network that controls cytoskeletal organization and cell movement. The network includes multiple GTPases, such as the most studied Rac1, Cdc42, and RhoA, along with their numerous effectors that provide mutual regulation through feedback loops. Here we investigate the temporal and spatial relationship between Rac1 and Cdc42 during membrane ruffling, using a simulation model that couples GTPase signaling with cell morphodynamics and captures the GTPase behavior observed with FRET-based biosensors. We show that membrane velocity is regulated by the kinetic rate of GTPase activation rather than the concentration of active GTPase. Our model captures both uniform and polarized ruffling. We also show that cell-type specific time delays between Rac1 and Cdc42 activation can be reproduced with a single signaling motif, in which the delay is controlled by feedback from Cdc42 to Rac1. The resolution of our simulation output matches those of time-lapsed recordings of cell dynamics and GTPase activity. Our data-driven modeling approach allows us to validate simulation results with quantitative precision using the same pipeline for the analysis of simulated and experimental data.
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Affiliation(s)
- Siarhei Hladyshau
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Jorik P Stoop
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Kosei Kamada
- Faculty of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Shuyi Nie
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Denis Tsygankov
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
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5
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Hladyshau S, Stoop JP, Kamada K, Nie S, Tsygankov DV. Spatiotemporal coordination of Rac1 and Cdc42 at the whole cell level during cell ruffling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.31.535147. [PMID: 37034645 PMCID: PMC10081307 DOI: 10.1101/2023.03.31.535147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Rho-GTPases are central regulators within a complex signaling network that controls the cytoskeletal organization and cell movement. This network includes multiple GTPases, such as the most studied Rac1, Cdc42, and RhoA, and their numerous effectors that provide mutual regulation and feedback loops. Here we investigate the temporal and spatial relationship between Rac1 and Cdc42 during membrane ruffling using a simulation model which couples GTPase signaling with cell morphodynamics to capture the GTPase behavior observed with FRET-based biosensors. We show that membrane velocity is regulated by the kinetic rate of GTPase activation rather than the concentration of active GTPase. Our model captures both uniform and polarized ruffling. We also show that cell-type specific time delays between Rac1 and Cdc42 activation can be reproduced with a single signaling motif, in which the delay is controlled by feedback from Cdc42 to Rac1. The resolution of our simulation output matches those of the time-lapsed recordings of cell dynamics and GTPase activity. This approach allows us to validate simulation results with quantitative precision using the same pipeline for the analysis of simulated and experimental data.
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6
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Dynamic regulation of RAS and RAS signaling. Biochem J 2023; 480:1-23. [PMID: 36607281 PMCID: PMC9988006 DOI: 10.1042/bcj20220234] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 01/07/2023]
Abstract
RAS proteins regulate most aspects of cellular physiology. They are mutated in 30% of human cancers and 4% of developmental disorders termed Rasopathies. They cycle between active GTP-bound and inactive GDP-bound states. When active, they can interact with a wide range of effectors that control fundamental biochemical and biological processes. Emerging evidence suggests that RAS proteins are not simple on/off switches but sophisticated information processing devices that compute cell fate decisions by integrating external and internal cues. A critical component of this compute function is the dynamic regulation of RAS activation and downstream signaling that allows RAS to produce a rich and nuanced spectrum of biological outputs. We discuss recent findings how the dynamics of RAS and its downstream signaling is regulated. Starting from the structural and biochemical properties of wild-type and mutant RAS proteins and their activation cycle, we examine higher molecular assemblies, effector interactions and downstream signaling outputs, all under the aspect of dynamic regulation. We also consider how computational and mathematical modeling approaches contribute to analyze and understand the pleiotropic functions of RAS in health and disease.
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7
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Herron JC, Hu S, Liu B, Watanabe T, Hahn KM, Elston TC. Spatial models of pattern formation during phagocytosis. PLoS Comput Biol 2022; 18:e1010092. [PMID: 36190993 PMCID: PMC9560619 DOI: 10.1371/journal.pcbi.1010092] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/13/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
Phagocytosis, the biological process in which cells ingest large particles such as bacteria, is a key component of the innate immune response. Fcγ receptor (FcγR)-mediated phagocytosis is initiated when these receptors are activated after binding immunoglobulin G (IgG). Receptor activation initiates a signaling cascade that leads to the formation of the phagocytic cup and culminates with ingestion of the foreign particle. In the experimental system termed "frustrated phagocytosis", cells attempt to internalize micropatterned disks of IgG. Cells that engage in frustrated phagocytosis form "rosettes" of actin-enriched structures called podosomes around the IgG disk. The mechanism that generates the rosette pattern is unknown. We present data that supports the involvement of Cdc42, a member of the Rho family of GTPases, in pattern formation. Cdc42 acts downstream of receptor activation, upstream of actin polymerization, and is known to play a role in polarity establishment. Reaction-diffusion models for GTPase spatiotemporal dynamics exist. We demonstrate how the addition of negative feedback and minor changes to these models can generate the experimentally observed rosette pattern of podosomes. We show that this pattern formation can occur through two general mechanisms. In the first mechanism, an intermediate species forms a ring of high activity around the IgG disk, which then promotes rosette organization. The second mechanism does not require initial ring formation but relies on spatial gradients of intermediate chemical species that are selectively activated over the IgG patch. Finally, we analyze the models to suggest experiments to test their validity.
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Affiliation(s)
- John Cody Herron
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Shiqiong Hu
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Bei Liu
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Takashi Watanabe
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Klaus M. Hahn
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Timothy C. Elston
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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8
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Buttenschön A, Edelstein-Keshet L. Cell Repolarization: A Bifurcation Study of Spatio-Temporal Perturbations of Polar Cells. Bull Math Biol 2022; 84:114. [PMID: 36058957 DOI: 10.1007/s11538-022-01053-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 06/30/2022] [Indexed: 11/02/2022]
Abstract
The intrinsic polarity of migrating cells is regulated by spatial distributions of protein activity. Those proteins (Rho-family GTPases, such as Rac and Rho) redistribute in response to stimuli, determining the cell front and back. Reaction-diffusion equations with mass conservation and positive feedback have been used to explain initial polarization of a cell. However, the sensitivity of a polar cell to a reversal stimulus has not yet been fully understood. We carry out a PDE bifurcation analysis of two polarity models to investigate routes to repolarization: (1) a single-GTPase ("wave-pinning") model and (2) a mutually antagonistic Rac-Rho model. We find distinct routes to reversal in (1) vs. (2). We show numerical simulations of full PDE solutions for the RD equations, demonstrating agreement with predictions of the bifurcation results. Finally, we show that simulations of the polarity models in deforming 1D model cells are consistent with biological experiments.
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Affiliation(s)
- Andreas Buttenschön
- Department of Mathematics, University of British Columbia, Vancouver, BC, V6T 1Z2, Canada.
| | - Leah Edelstein-Keshet
- Department of Mathematics, University of British Columbia, Vancouver, BC, V6T 1Z2, Canada
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9
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Yochelis A, Flemming S, Beta C. Versatile Patterns in the Actin Cortex of Motile Cells: Self-Organized Pulses Can Coexist with Macropinocytic Ring-Shaped Waves. PHYSICAL REVIEW LETTERS 2022; 129:088101. [PMID: 36053696 DOI: 10.1103/physrevlett.129.088101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Self-organized patterns in the actin cytoskeleton are essential for eukaryotic cellular life. They are the building blocks of many functional structures that often operate simultaneously to facilitate, for example, nutrient uptake and movement of cells. However, identifying how qualitatively distinct actin patterns can coexist remains a challenge. Using bifurcation theory of a mass conserved activator-inhibitor system, we uncover a generic mechanism of how different actin waves-traveling waves and excitable pulses-organize and simultaneously emerge. Live-cell imaging experiments indeed reveal that narrow, planar, and fast-moving excitable pulses may coexist with ring-shaped macropinocytic actin waves in the cortex of motile amoeboid cells.
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Affiliation(s)
- Arik Yochelis
- Department of Solar Energy and Environmental Physics, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion 8499000, Israel
- Department of Physics, Ben-Gurion University of the Negev, Be'er Sheva 8410501, Israel
| | - Sven Flemming
- Institute of Physics and Astronomy, University of Potsdam, Potsdam 14476, Germany
| | - Carsten Beta
- Institute of Physics and Astronomy, University of Potsdam, Potsdam 14476, Germany
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10
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Nordick B, Yu PY, Liao G, Hong T. Nonmodular oscillator and switch based on RNA decay drive regeneration of multimodal gene expression. Nucleic Acids Res 2022; 50:3693-3708. [PMID: 35380686 PMCID: PMC9023291 DOI: 10.1093/nar/gkac217] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/13/2022] [Accepted: 03/21/2022] [Indexed: 12/15/2022] Open
Abstract
Periodic gene expression dynamics are key to cell and organism physiology. Studies of oscillatory expression have focused on networks with intuitive regulatory negative feedback loops, leaving unknown whether other common biochemical reactions can produce oscillations. Oscillation and noise have been proposed to support mammalian progenitor cells’ capacity to restore heterogenous, multimodal expression from extreme subpopulations, but underlying networks and specific roles of noise remained elusive. We use mass-action-based models to show that regulated RNA degradation involving as few as two RNA species—applicable to nearly half of human protein-coding genes—can generate sustained oscillations without explicit feedback. Diverging oscillation periods synergize with noise to robustly restore cell populations’ bimodal expression on timescales of days. The global bifurcation organizing this divergence relies on an oscillator and bistable switch which cannot be decomposed into two structural modules. Our work reveals surprisingly rich dynamics of post-transcriptional reactions and a potentially widespread mechanism underlying development, tissue regeneration, and cancer cell heterogeneity.
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Affiliation(s)
- Benjamin Nordick
- School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee 37916, USA
| | - Polly Y Yu
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Guangyuan Liao
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee 37916, USA
| | - Tian Hong
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee 37916, USA.,National Institute for Mathematical and Biological Synthesis, Knoxville, Tennessee 37916, USA
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11
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Krause AL, Gaffney EA, Maini PK, Klika V. Modern perspectives on near-equilibrium analysis of Turing systems. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200268. [PMID: 34743603 PMCID: PMC8580451 DOI: 10.1098/rsta.2020.0268] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/18/2021] [Indexed: 05/02/2023]
Abstract
In the nearly seven decades since the publication of Alan Turing's work on morphogenesis, enormous progress has been made in understanding both the mathematical and biological aspects of his proposed reaction-diffusion theory. Some of these developments were nascent in Turing's paper, and others have been due to new insights from modern mathematical techniques, advances in numerical simulations and extensive biological experiments. Despite such progress, there are still important gaps between theory and experiment, with many examples of biological patterning where the underlying mechanisms are still unclear. Here, we review modern developments in the mathematical theory pioneered by Turing, showing how his approach has been generalized to a range of settings beyond the classical two-species reaction-diffusion framework, including evolving and complex manifolds, systems heterogeneous in space and time, and more general reaction-transport equations. While substantial progress has been made in understanding these more complicated models, there are many remaining challenges that we highlight throughout. We focus on the mathematical theory, and in particular linear stability analysis of 'trivial' base states. We emphasize important open questions in developing this theory further, and discuss obstacles in using these techniques to understand biological reality. This article is part of the theme issue 'Recent progress and open frontiers in Turing's theory of morphogenesis'.
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Affiliation(s)
- Andrew L. Krause
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
- Department of Mathematical Sciences, Durham University, Upper Mountjoy Campus, Stockton Rd, Durham DH1 3LE, UK
| | - Eamonn A. Gaffney
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
| | - Philip K. Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
| | - Václav Klika
- Department of Mathematics, FNSPE, Czech Technical University in Prague, Trojanova, 13, 12000 Praha, Czech Republic
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12
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Hladyshau S, Kho M, Nie S, Tsygankov D. Spatiotemporal development of coexisting wave domains of Rho activity in the cell cortex. Sci Rep 2021; 11:19512. [PMID: 34593939 PMCID: PMC8484676 DOI: 10.1038/s41598-021-99029-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/14/2021] [Indexed: 11/26/2022] Open
Abstract
The Rho family GTPases are molecular switches that regulate cytoskeletal dynamics and cell movement through a complex spatiotemporal organization of their activity. In Patiria miniata (starfish) oocytes under in vitro experimental conditions (with overexpressed Ect2, induced expression of Δ90 cyclin B, and roscovitine treatment), such activity generates multiple co-existing regions of coherent propagation of actin waves. Here we use computational modeling to investigate the development and properties of such wave domains. The model reveals that the formation of wave domains requires a balance between the activation and inhibition in the Rho signaling motif. Intriguingly, the development of the wave domains is preceded by a stage of low-activity quasi-static patterns, which may not be readily observed in experiments. Spatiotemporal patterns of this stage and the different paths of their destabilization define the behavior of the system in the later high-activity (observable) stage. Accounting for a strong intrinsic noise allowed us to achieve good quantitative agreement between simulated dynamics in different parameter regimes of the model and different wave dynamics in Patiria miniata and wild type Xenopus laevis (frog) data. For quantitative comparison of simulated and experimental results, we developed an automated method of wave domain detection, which revealed a sharp reversal in the process of pattern formation in starfish oocytes. Overall, our findings provide an insight into spatiotemporal regulation of complex and diverse but still computationally reproducible cell-level actin dynamics.
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Affiliation(s)
- Siarhei Hladyshau
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Mary Kho
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shuyi Nie
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Denis Tsygankov
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
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13
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Dieterle MP, Husari A, Steinberg T, Wang X, Ramminger I, Tomakidi P. From the Matrix to the Nucleus and Back: Mechanobiology in the Light of Health, Pathologies, and Regeneration of Oral Periodontal Tissues. Biomolecules 2021; 11:824. [PMID: 34073044 PMCID: PMC8228498 DOI: 10.3390/biom11060824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023] Open
Abstract
Among oral tissues, the periodontium is permanently subjected to mechanical forces resulting from chewing, mastication, or orthodontic appliances. Molecularly, these movements induce a series of subsequent signaling processes, which are embedded in the biological concept of cellular mechanotransduction (MT). Cell and tissue structures, ranging from the extracellular matrix (ECM) to the plasma membrane, the cytosol and the nucleus, are involved in MT. Dysregulation of the diverse, fine-tuned interaction of molecular players responsible for transmitting biophysical environmental information into the cell's inner milieu can lead to and promote serious diseases, such as periodontitis or oral squamous cell carcinoma (OSCC). Therefore, periodontal integrity and regeneration is highly dependent on the proper integration and regulation of mechanobiological signals in the context of cell behavior. Recent experimental findings have increased the understanding of classical cellular mechanosensing mechanisms by both integrating exogenic factors such as bacterial gingipain proteases and newly discovered cell-inherent functions of mechanoresponsive co-transcriptional regulators such as the Yes-associated protein 1 (YAP1) or the nuclear cytoskeleton. Regarding periodontal MT research, this review offers insights into the current trends and open aspects. Concerning oral regenerative medicine or weakening of periodontal tissue diseases, perspectives on future applications of mechanobiological principles are discussed.
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Affiliation(s)
- Martin Philipp Dieterle
- Center for Dental Medicine, Division of Oral Biotechnology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany; (M.P.D.); (X.W.); (I.R.); (P.T.)
| | - Ayman Husari
- Center for Dental Medicine, Department of Orthodontics, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany;
- Faculty of Engineering, University of Freiburg, Georges-Köhler-Allee 101, 79110 Freiburg, Germany
| | - Thorsten Steinberg
- Center for Dental Medicine, Division of Oral Biotechnology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany; (M.P.D.); (X.W.); (I.R.); (P.T.)
| | - Xiaoling Wang
- Center for Dental Medicine, Division of Oral Biotechnology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany; (M.P.D.); (X.W.); (I.R.); (P.T.)
| | - Imke Ramminger
- Center for Dental Medicine, Division of Oral Biotechnology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany; (M.P.D.); (X.W.); (I.R.); (P.T.)
| | - Pascal Tomakidi
- Center for Dental Medicine, Division of Oral Biotechnology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany; (M.P.D.); (X.W.); (I.R.); (P.T.)
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14
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On the influence of cell shape on dynamic reaction-diffusion polarization patterns. PLoS One 2021; 16:e0248293. [PMID: 33735291 PMCID: PMC7971540 DOI: 10.1371/journal.pone.0248293] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
The distribution of signaling molecules following mechanical or chemical stimulation of a cell defines cell polarization, with regions of high active Cdc42 at the front and low active Cdc42 at the rear. As reaction-diffusion phenomena between signaling molecules, such as Rho GTPases, define the gradient dynamics, we hypothesize that the cell shape influences the maintenance of the “front-to-back” cell polarization patterns. We investigated the influence of cell shape on the Cdc42 patterns using an established computational polarization model. Our simulation results showed that not only cell shape but also Cdc42 and Rho-related (in)activation parameter values affected the distribution of active Cdc42. Despite an initial Cdc42 gradient, the in silico results showed that the maximal Cdc42 concentration shifts in the opposite direction, a phenomenon we propose to call “reverse polarization”. Additional in silico analyses indicated that “reverse polarization” only occurred in a particular parameter value space that resulted in a balance between inactivation and activation of Rho GTPases. Future work should focus on a mathematical description of the underpinnings of reverse polarization, in combination with experimental validation using, for example, dedicated FRET-probes to spatiotemporally track Rho GTPase patterns in migrating cells. In summary, the findings of this study enhance our understanding of the role of cell shape in intracellular signaling.
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