Activity-driven fluctuations in living cells

Fodor, Étienne; Guo, Ming; Gov, Nir S.; Visco, Paolo; Weitz, David A.; Wijland, Frédéric van

doi:10.1209/0295-5075/110/48005

Cited by 123 publications

(163 citation statements)

References 34 publications

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“…Reduced equations for random motion of both kinds of p-1 particles are derived. As we find, the derived equation for deformation tracers coincides with the previously proposed phenomenological model [9]. On the other hand, relative random motion of flow tracers with respect to the elastic component is described by a Langevin equation with non-thermal metabolic noise.…”

supporting

confidence: 85%

“…The present analysis is however done entirely within the original description [10] in order to demonstrate what should be expected in its framework. Remarkably, we could then reproduce the phenomenological model [9] that shows good agreement with the experimental data for eukaryotic cells (see also the related publication [19]). Extensions and generalizations of our results to other models of gels can be performed, and this will be the task of additional work.…”

Section: P-2 Localization and Diffusion Of Tracer Particles In Viscoesupporting

confidence: 52%

“…In the experiments [2,9], it was moreover possible to chemically inhibit myosin activity while still having ATP inside a cell. Additionally, tracking experiments were also performed in the same cells under depletion of ATP.…”

Section: P-2 Localization and Diffusion Of Tracer Particles In Viscoementioning

confidence: 99%

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Localization and diffusion of tracer particles in viscoelastic media with active force dipoles

Yasuda

Okamoto

Komura

et al. 2017

EPL

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-Optical tracking in vivo experiments reveal that diffusion of particles in biological cells is strongly enhanced in the presence of ATP and the experimental data for animal cells could previously be reproduced within a phenomenological model of a gel with myosin motors acting within it [EPL 110, 48005 (2015)]. Here, the two-fluid model of a gel is considered where active macromolecules, described as force dipoles, cyclically operate both in the elastic and the fluid components. Through coarse-graining, effective equations of motions for idealized tracer particles displaying local deformations and local fluid flows are derived. The equation for deformation tracers coincides with the earlier phenomenological model and thus confirms it. For flow tracers, diffusion enhancement caused by active force dipoles in the fluid component, and thus due to metabolic activity, is found. The latter effect may explain why ATP-dependent diffusion enhancement could also be observed in bacteria that lack molecular motors in their skeleton or when the activity of myosin motors was chemically inhibited in eukaryotic cells.

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supporting

confidence: 85%

Section: P-2 Localization and Diffusion Of Tracer Particles In Viscoesupporting

confidence: 52%

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Localization and diffusion of tracer particles in viscoelastic media with active force dipoles

Yasuda

Okamoto

Komura

et al. 2017

EPL

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“…In soft-matter systems, examples include beads diffusing on lipid tubes (6), in actin and agarose networks (6)(7)(8)(9)(10), in concentrated colloidal suspensions (11,12), and in suspension with eukaryotic swimmers (13). For particles inside living cells, examples include RNA-protein particles and protein aggregates in Escherichia coli (14,15) and Saccharomyces cerevisiae (16) and submicron colloidal tracers in the cytoplasm of human cell lines (17,18). We suspect that there are many more examples to be found in biological systems, but studies involving single-particle tracking experiments in biological systems frequently do not report displacement distributions.…”

Section: Introductionmentioning

confidence: 99%

Cytoplasmic RNA-Protein Particles Exhibit Non-Gaussian Subdiffusive Behavior

Lampo

Stylianidou²,

Backlund

et al. 2017

Biophysical Journal

188

261

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The cellular cytoplasm is a complex, heterogeneous environment (both spatially and temporally) that exhibits viscoelastic behavior. To further develop our quantitative insight into cellular transport, we analyze data sets of mRNA molecules fluorescently labeled with MS2-GFP tracked in real time in live Escherichia coli and Saccharomyces cerevisiae cells. As shown previously, these RNA-protein particles exhibit subdiffusive behavior that is viscoelastic in its origin. Examining the ensemble of particle displacements reveals a Laplace distribution at all observed timescales rather than the Gaussian distribution predicted by the central limit theorem. This ensemble non-Gaussian behavior is caused by a combination of an exponential distribution in the time-averaged diffusivities and non-Gaussian behavior of individual trajectories. We show that the non-Gaussian behavior is a consequence of significant heterogeneity between trajectories and dynamic heterogeneity along single trajectories. Informed by theory and simulation, our work provides an in-depth analysis of the complex diffusive behavior of RNA-protein particles in live cells.

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“…Caging model.-We propose a model for the vesicle dynamics and the effect of the surrounding fluctuating actin mesh that takes the observed power law behavior of G * into account. The model has itself been previously introduced in [30], but it is generalized here to encompass strong memory effects [31]. The underlying physical picture is that the vesicle is caged in the cytoskeleton [ Fig.…”

mentioning

confidence: 99%

Nonequilibrium Dissipation in Living Oocytes

Ahmed

2018

Biophysical Journal

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-Living organisms are inherently out-of-equilibrium systems. We employ recent developments in stochastic energetics and rely on a minimal microscopic model to predict the amount of mechanical energy dissipated by such dynamics. Our model includes complex rheological effects and nonequilibrium stochastic forces. By performing active microrheology and tracking micronsized vesicles in the cytoplasm of living oocytes, we provide unprecedented measurements of the spectrum of dissipated energy. We show that our model is fully consistent with the experimental data, and we use it to offer predictions for the injection and dissipation energy scales involved in active fluctuations.Perrin's century old picture [1] where the Brownian motion of a colloid results from the many collisions exerted by the solvent's molecules is a cornerstone of soft-matter physics. Langevin [2] modeled the ensuing energy exchanges between the solvent and the colloidal particle in terms of a dissipation channel and energy injection kicks. The key ingredient in the success of that theory was to completely integrate out the "uninteresting" degrees of freedom of the solvent whose properties are gathered in a friction constant and a temperature. In this work we take exactly the reverse stance and ask how, by observing the motion of a tracer embedded in a living medium, one can infer the amount of energy exchange and dissipation with the surrounding medium. The main goal is to quantify the energetic properties of the medium, both injection and dissipation-wise. This is a stimulating question because there are of course striking differences between a living cell and its equilibrium polymer gel counterpart, to which newly developed [3, 4] methods of nonequilibrium statistical mechanics apply. Beyond thermal exchanges that fall within the scope of a Langevin approach, ATP consumption fuels molecular motor activity and drives relentless rearrangement of the cytoskeleton. This chemically driven continuous injection and dissipation of energy adds a nonequilibrium channel that eludes straightforward quantitative analysis. In short, a living cell is not only a fertile playground for testing new ideas from nonequilibrium physics, but also one in which these ideas can lead to a quantitative evaluation of an otherwise ill-understood activity which is of intrinsic biophysical interest. Our work addresses both aspects by a combination of active microrheology, tracking experiments, and theoretical modeling.One experimental way to access nonequilibrium physics in the intracellular medium is to focus on the deviation from thermal equilibrium behavior of the tracer's position statistics: forming the ratio of the response of the tracer's position to an infinitesimal external perturbation to its unperturbed mean-square displacement leads to a quantity that only reduces to the inverse temperature when in p-1 arXiv:1511.00921v2 [q-bio.SC]

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Activity-driven fluctuations in living cells

Cited by 123 publications

References 34 publications

Localization and diffusion of tracer particles in viscoelastic media with active force dipoles

Localization and diffusion of tracer particles in viscoelastic media with active force dipoles

Cytoplasmic RNA-Protein Particles Exhibit Non-Gaussian Subdiffusive Behavior

Nonequilibrium Dissipation in Living Oocytes

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