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Zanotelli MR, Miller JP, Wang W, Ortiz I, Tahon E, Bordeleau F, Reinhart-King CA. Tension directs cancer cell migration over fiber alignment through energy minimization. Biomaterials 2024; 311:122682. [PMID: 38959532 DOI: 10.1016/j.biomaterials.2024.122682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 06/06/2024] [Accepted: 06/23/2024] [Indexed: 07/05/2024]
Abstract
Cell migration during many fundamental biological processes including metastasis requires cells to traverse tissue with heterogeneous mechanical cues that direct migration as well as determine force and energy requirements for motility. However, the influence of discrete structural and mechanical cues on migration remains challenging to determine as they are often coupled. Here, we decouple the pro-invasive cues of collagen fiber alignment and tension to study their individual impact on migration. When presented with both cues, cells preferentially travel in the axis of tension against fiber alignment. Computational and experimental data show applying tension perpendicular to alignment increases potential energy stored within collagen fibers, lowering requirements for cell-induced matrix deformation and energy usage during migration compared to motility in the direction of fiber alignment. Energy minimization directs migration trajectory, and tension can facilitate migration against fiber alignment. These findings provide a conceptual understanding of bioenergetics during migration through a fibrous matrix.
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Affiliation(s)
- Matthew R Zanotelli
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Joseph P Miller
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Wenjun Wang
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Ismael Ortiz
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Elise Tahon
- CHU de Québec-Université Laval Research Center (Oncology Division), Université Laval Cancer Research Center, Centre de Recherche en Organogénèse Expérimentale de l'Université Laval/LOEX, Québec, G1R 3S3, Canada
| | - Francois Bordeleau
- CHU de Québec-Université Laval Research Center (Oncology Division), Université Laval Cancer Research Center, Centre de Recherche en Organogénèse Expérimentale de l'Université Laval/LOEX, Québec, G1R 3S3, Canada; Département de Biologie Moléculaire, de Biochimie Médicale et de Pathologie, Université Laval, Québec, Canada, G1V 0A6.
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2
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Smith KC, Oglietti R, Moran SJ, Macosko JC, Lyles DS, Holzwarth G. Directional change during active diffusion of viral ribonucleoprotein particles through cytoplasm. Biophys J 2024; 123:2869-2876. [PMID: 38664967 PMCID: PMC11393665 DOI: 10.1016/j.bpj.2024.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/01/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
A mesh of cytoskeletal fibers, consisting of microtubules, intermediate filaments, and fibrous actin, prevents the Brownian diffusion of particles with a diameter larger than 0.10 μm, such as vesicular stomatitis virus ribonucleoprotein (RNP) particles, in mammalian cells. Nevertheless, RNP particles do move in random directions but at a lower rate than Brownian diffusion, which is thermally driven. This nonthermal biological transport process is called "active diffusion" because it is driven by ATP. The ATP powers motor proteins such as myosin II. The motor proteins bend and cross-link actin fibers, causing the mesh to jiggle. Until recently, little was known about how RNP particles get through the mesh. It has been customary to analyze the tracks of particles like RNPs by computing the slope of the ensemble-averaged mean-squared displacement of the particles as a signature of mechanism. Although widely used, this approach "loses information" about the timing of the switches between physical mechanisms. It has been recently shown that machine learning composed of variational Bayesian analysis, Gaussian mixture models, and hidden Markov models can use "all the information" in a single track to reveal that that the positions of RNP particles are spatially clustered. Machine learning assigns a number, called a state, to each cluster. RNP particles remain in one state for 0.2-1.0 s before switching (hopping) to a different state. This earlier work is here extended to analyze the movements of a particle within a state and to determine particle directionality within and between states.
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Affiliation(s)
- Kathleen C Smith
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina
| | - Ryan Oglietti
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina
| | - Steven J Moran
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Jed C Macosko
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina
| | - Douglas S Lyles
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina.
| | - George Holzwarth
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina
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3
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Muenker TM, Knotz G, Krüger M, Betz T. Accessing activity and viscoelastic properties of artificial and living systems from passive measurement. NATURE MATERIALS 2024; 23:1283-1291. [PMID: 39085417 DOI: 10.1038/s41563-024-01957-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 06/26/2024] [Indexed: 08/02/2024]
Abstract
Living systems are complex dynamic entities that operate far from thermodynamic equilibrium. Their active, non-equilibrium behaviour requires energy to drive cellular organization and dynamics. Unfortunately, most statistical mechanics approaches are not valid in non-equilibrium situations, forcing researchers to use intricate and often invasive methods to study living processes. Here we experimentally demonstrate that an observable termed mean back relaxation quantifies the active mechanics of living cells from passively observed particle trajectories. The mean back relaxation represents the average trajectory of a particle after a recent motion and is calculated from three-point probabilities. We show that this parameter allows the detection of broken detailed balance in confined systems. We experimentally observe that it provides access to the non-equilibrium generating energy and viscoelastic properties of artificial bulk materials and living cells. These findings suggest that the mean back relaxation can function as a marker of non-equilibrium dynamics and is a non-invasive avenue to determine viscoelastic material properties from passive measurements.
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Affiliation(s)
- Till M Muenker
- Third Institute of Physics, Georg August Universität Göttingen, Göttingen, Germany
| | - Gabriel Knotz
- Institute of Theoretical Physics, Georg August Universität Göttingen, Göttingen, Germany
| | - Matthias Krüger
- Institute of Theoretical Physics, Georg August Universität Göttingen, Göttingen, Germany.
| | - Timo Betz
- Third Institute of Physics, Georg August Universität Göttingen, Göttingen, Germany.
- Cluster of Excellence 'Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells' (MBExC), Georg August Universität Göttingen, Göttingen, Germany.
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4
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Chen YQ, Lee HC, Lee HH. Shp2 contributes to the regulation of nuclear shape and cellular viscoelasticity in response to substrate spatial cues. Biochem Biophys Res Commun 2024; 721:150144. [PMID: 38781661 DOI: 10.1016/j.bbrc.2024.150144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 04/19/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Cell polarization can be guided by substrate topology through space constraints and adhesion induction, which are part of cellular mechanosensing pathways. Here, we demonstrated that protein tyrosine phosphatase Shp2 plays a crucial role in mediating the response of cells to substrate spatial cues. When compared to cells spreading on surfaces coated uniformly with fibronectin (FN), cells attached to 10 μm-width FN-strip micropattern (MP), which provides spatial cues for uniaxial spreading, exhibited elongated focal adhesions (FAs) and aligned stress fibers in the direction of the MP. As a result of uniaxial cell spreading, nuclei became elongated, dependent on ROCK-mediated actomyosin contractility. Additionally, intracellular viscoelasticity also increased. Shp2-deficient cells did not display elongated FAs mediated by MP, well-aligned stress fibers, or changes in nuclear shape and intracellular viscoelasticity. Overall, our data suggest that Shp2 is involved in regulating FAs and the actin cytoskeleton to modulate nuclear shape and intracellular physical properties in response to substrate spatial cues.
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Affiliation(s)
- Yin-Quan Chen
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsin-Chang Lee
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsiao-Hui Lee
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan; Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Taipei, Taiwan.
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5
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Flormann DAD, Kainka L, Montalvo G, Anton C, Rheinlaender J, Thalla D, Vesperini D, Pohland MO, Kaub KH, Schu M, Pezzano F, Ruprecht V, Terriac E, Hawkins RJ, Lautenschläger F. The structure and mechanics of the cell cortex depend on the location and adhesion state. Proc Natl Acad Sci U S A 2024; 121:e2320372121. [PMID: 39042691 PMCID: PMC11295003 DOI: 10.1073/pnas.2320372121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/16/2024] [Indexed: 07/25/2024] Open
Abstract
Cells exist in different phenotypes and can transition between them. A phenotype may be characterized by many different aspects. Here, we focus on the example of whether the cell is adhered or suspended and choose particular parameters related to the structure and mechanics of the actin cortex. The cortex is essential to cell mechanics, morphology, and function, such as for adhesion, migration, and division of animal cells. To predict and control cellular functions and prevent malfunctioning, it is necessary to understand the actin cortex. The structure of the cortex governs cell mechanics; however, the relationship between the architecture and mechanics of the cortex is not yet well enough understood to be able to predict one from the other. Therefore, we quantitatively measured structural and mechanical cortex parameters, including cortical thickness, cortex mesh size, actin bundling, and cortex stiffness. These measurements required developing a combination of measurement techniques in scanning electron, expansion, confocal, and atomic force microscopy. We found that the structure and mechanics of the cortex of cells in interphase are different depending on whether the cell is suspended or adhered. We deduced general correlations between structural and mechanical properties and show how these findings can be explained within the framework of semiflexible polymer network theory. We tested the model predictions by perturbing the properties of the actin within the cortex using compounds. Our work provides an important step toward predictions of cell mechanics from cortical structures and suggests how cortex remodeling between different phenotypes impacts the mechanical properties of cells.
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Affiliation(s)
- D. A. D. Flormann
- Department of Physics, Saarland University, Saarbrücken 66123, Germany
| | - L. Kainka
- Department of Physics, Saarland University, Saarbrücken 66123, Germany
| | - G. Montalvo
- Department of Physics, Saarland University, Saarbrücken 66123, Germany
| | - C. Anton
- Department of Physics, Saarland University, Saarbrücken 66123, Germany
| | - J. Rheinlaender
- Faculty of Science, Institute of Applied Physics, University of Tübingen, Tübingen72076, Germany
| | - D. Thalla
- Department of Physics, Saarland University, Saarbrücken 66123, Germany
| | - D. Vesperini
- Department of Physics, Saarland University, Saarbrücken 66123, Germany
| | - M. O. Pohland
- Department of Physics, Saarland University, Saarbrücken 66123, Germany
| | - K. H. Kaub
- Department of Physics, Saarland University, Saarbrücken 66123, Germany
- Department of Biophysical Chemistry, Georg-August-University, Göttingen37077, Germany
| | - M. Schu
- Department of Physics, Saarland University, Saarbrücken 66123, Germany
| | - F. Pezzano
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona08003, Spain
| | - V. Ruprecht
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona08003, Spain
- Universitat Pompeu Fabra, Barcelona08002, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona08010, Spain
| | - E. Terriac
- Department of Physics, Saarland University, Saarbrücken 66123, Germany
| | - R. J. Hawkins
- Department of Physics and Astronomy, University of Sheffield, SheffieldS3 7RH, United Kingdom
- African Institute for Mathematical Sciences, Accra20046, Ghana
| | - F. Lautenschläger
- Department of Physics, Saarland University, Saarbrücken 66123, Germany
- Center for Biophysics, Saarland University, Saarbrücken66123, Germany
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6
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Netz RR. Derivation of the nonequilibrium generalized Langevin equation from a time-dependent many-body Hamiltonian. Phys Rev E 2024; 110:014123. [PMID: 39160956 DOI: 10.1103/physreve.110.014123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 06/20/2024] [Indexed: 08/21/2024]
Abstract
It has become standard practice to describe systems that remain far from equilibrium even in their steady state by Langevin equations with colored noise which is chosen independently from the friction contribution. Since these Langevin equations are typically not derived from first-principle Hamiltonian dynamics, it is not clear whether they correspond to physically realizable scenarios. By exact Mori projection in phase space we derive the nonequilibrium generalized Langevin equation (GLE) for an arbitrary phase-space dependent observable A from a generic many-body Hamiltonian with a time-dependent external force h(t) acting on the same observable A. This is the same Hamiltonian from which the standard fluctuation-dissipation theorem is derived, which reflects the generality of our approach. The observable A could, for example, be the position of an atom, of a molecule or of a macroscopic object, the distance between two such entities or a more complex phase-space function such as the reaction coordinate of a chemical reaction or of the folding of a protein. The Hamiltonian could, for example, describe a fluid, a solid, a viscoelastic medium, or even a turbulent inhomogeneous environment. The GLE, which is a closed-form equation of motion for the observable A, is obtained in explicit form to all orders in h(t) and without restrictions on the type of many-body Hamiltonian or the observable A. If the dynamics of the observable A corresponds to a Gaussian process, the resultant GLE has a similar form as the equilibrium Mori GLE, and in particular the friction memory kernel is given by the two-point autocorrelation function of the sum of the complementary and the external force h(t). This is a nontrivial and useful result, as many observables that characterize nonequilibrium systems display Gaussian statistics. For non-Gaussian nonequilibrium observables correction terms appear in the GLE and in the relation between the force autocorrelation and the friction memory kernel, which are explicitly given in terms of cubic correlation functions of A. Interpreting the external force h(t) as a stochastic process, we derive nonequilibrium corrections to the fluctuation-dissipation theorem and present methods to extract all GLE parameters from experimental or simulation time-series data, thus making our nonequilibrium GLE a practical tool to study and model general nonequilibrium systems.
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7
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Martinez-Corral R, Nam KM, DePace AH, Gunawardena J. The Hill function is the universal Hopfield barrier for sharpness of input-output responses. Proc Natl Acad Sci U S A 2024; 121:e2318329121. [PMID: 38787881 PMCID: PMC11145184 DOI: 10.1073/pnas.2318329121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
The Hill functions, [Formula: see text], have been widely used in biology for over a century but, with the exception of [Formula: see text], they have had no justification other than as a convenient fit to empirical data. Here, we show that they are the universal limit for the sharpness of any input-output response arising from a Markov process model at thermodynamic equilibrium. Models may represent arbitrary molecular complexity, with multiple ligands, internal states, conformations, coregulators, etc, under core assumptions that are detailed in the paper. The model output may be any linear combination of steady-state probabilities, with components other than the chosen input ligand held constant. This formulation generalizes most of the responses in the literature. We use a coarse-graining method in the graph-theoretic linear framework to show that two sharpness measures for input-output responses fall within an effectively bounded region of the positive quadrant, [Formula: see text], for any equilibrium model with [Formula: see text] input binding sites. [Formula: see text] exhibits a cusp which approaches, but never exceeds, the sharpness of [Formula: see text], but the region and the cusp can be exceeded when models are taken away from thermodynamic equilibrium. Such fundamental thermodynamic limits are called Hopfield barriers, and our results provide a biophysical justification for the Hill functions as the universal Hopfield barriers for sharpness. Our results also introduce an object, [Formula: see text], whose structure may be of mathematical interest, and suggest the importance of characterizing Hopfield barriers for other forms of cellular information processing.
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Affiliation(s)
| | - Kee-Myoung Nam
- Department of Systems Biology, Harvard Medical School, Boston, MA02115
| | - Angela H. DePace
- Department of Systems Biology, Harvard Medical School, Boston, MA02115
- HHMI, Boston, MA02115
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8
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Klimek A, Mondal D, Block S, Sharma P, Netz RR. Data-driven classification of individual cells by their non-Markovian motion. Biophys J 2024; 123:1173-1183. [PMID: 38515300 PMCID: PMC11140416 DOI: 10.1016/j.bpj.2024.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024] Open
Abstract
We present a method to differentiate organisms solely by their motion based on the generalized Langevin equation (GLE) and use it to distinguish two different swimming modes of strongly confined unicellular microalgae Chlamydomonas reinhardtii. The GLE is a general model for active or passive motion of organisms and particles that can be derived from a time-dependent general many-body Hamiltonian and in particular includes non-Markovian effects (i.e., the trajectory memory of its past). We extract all GLE parameters from individual cell trajectories and perform an unbiased cluster analysis to group them into different classes. For the specific cell population employed in the experiments, the GLE-based assignment into the two different swimming modes works perfectly, as checked by control experiments. The classification and sorting of single cells and organisms is important in different areas; our method, which is based on motion trajectories, offers wide-ranging applications in biology and medicine.
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Affiliation(s)
- Anton Klimek
- Fachbereich Physik, Freie Universität Berlin, Berlin, Germany
| | - Debasmita Mondal
- Department of Physics, Indian Institute of Science, Bangalore, India; James Franck Institute, University of Chicago, Chicago, Illinois
| | - Stephan Block
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Prerna Sharma
- Department of Physics, Indian Institute of Science, Bangalore, India; Department of Bioengineering, Indian Institute of Science, Bangalore, India
| | - Roland R Netz
- Fachbereich Physik, Freie Universität Berlin, Berlin, Germany.
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9
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Gironella-Torrent M, Bergamaschi G, Sorkin R, Wuite GJL, Ritort F. Viscoelastic phenotyping of red blood cells. Biophys J 2024; 123:770-781. [PMID: 38268191 PMCID: PMC10995428 DOI: 10.1016/j.bpj.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/21/2023] [Accepted: 01/18/2024] [Indexed: 01/26/2024] Open
Abstract
Red blood cells (RBCs) are the simplest cell types with complex dynamical and viscoelastic phenomenology. While the mechanical rigidity and the flickering noise of RBCs have been extensively investigated, an accurate determination of the constitutive equations of the relaxational kinetics is lacking. Here we measure the force relaxation of RBCs under different types of tensional and compressive extension-jump protocols by attaching an optically trapped bead to the RBC membrane. Relaxational kinetics follows linear response from 60 pN (tensional) to -20 pN (compressive) applied forces, exhibiting a triple exponential function with three well-separated timescales over four decades (0.01-100 s). While the fast timescale (τF∼0.02(1)s) corresponds to the relaxation of the membrane, the intermediate and slow timescales (τI=4(1)s; τS=70(8)s) likely arise from the cortex dynamics and the cytosol viscosity. Relaxation is highly heterogeneous across the RBC population, yet the three relaxation times are correlated, showing dynamical scaling. Finally, we find that glucose depletion and laser illumination of RBCs lead to faster triple exponential kinetics and RBC rigidification. Viscoelastic phenotyping is a promising dynamical biomarker applicable to other cell types and active systems.
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Affiliation(s)
- Marta Gironella-Torrent
- Small Biosystems Lab, Condensed Matter Physics Department, University of Barcelona, Barcelona, Spain; Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Giulia Bergamaschi
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Raya Sorkin
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, Israel
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Felix Ritort
- Small Biosystems Lab, Condensed Matter Physics Department, University of Barcelona, Barcelona, Spain; Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, Barcelona, Spain
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10
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Farago O, Smith NR. Confined run-and-tumble particles with non-Markovian tumbling statistics. Phys Rev E 2024; 109:044121. [PMID: 38755884 DOI: 10.1103/physreve.109.044121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/20/2024] [Indexed: 05/18/2024]
Abstract
Confined active particles constitute simple, yet realistic, examples of systems that converge into a nonequilibrium steady state. We investigate a run-and-tumble particle in one spatial dimension, trapped by an external potential, with a given distribution g(t) of waiting times between tumbling events whose mean value is equal to τ. Unless g(t) is an exponential distribution (corresponding to a constant tumbling rate), the process is non-Markovian, which makes the analysis of the model particularly challenging. We use an analytical framework involving effective position-dependent tumbling rates to develop a numerical method that yields the full steady-state distribution (SSD) of the particle's position. The method is very efficient and requires modest computing resources, including in the large-deviation and/or small-τ regime, where the SSD can be related to the the large-deviation function, s(x), via the scaling relation P_{st}(x)∼e^{-s(x)/τ}.
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Affiliation(s)
- Oded Farago
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, Marcus Family Campus, Be'er Sheva 8410501, Israel
| | - Naftali R Smith
- Department of Environmental Physics, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Be'er Sheva 8499000, Israel
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11
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Martinez-Corral R, Nam KM, DePace AH, Gunawardena J. The Hill function is the universal Hopfield barrier for sharpness of input-output responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587054. [PMID: 38585761 PMCID: PMC10996692 DOI: 10.1101/2024.03.27.587054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The Hill functions, ℋ h ( x ) = x h / 1 + x h , have been widely used in biology for over a century but, with the exception of ℋ 1 , they have had no justification other than as a convenient fit to empirical data. Here, we show that they are the universal limit for the sharpness of any input-output response arising from a Markov process model at thermodynamic equilibrium. Models may represent arbitrary molecular complexity, with multiple ligands, internal states, conformations, co-regulators, etc, under core assumptions that are detailed in the paper. The model output may be any linear combination of steady-state probabilities, with components other than the chosen input ligand held constant. This formulation generalises most of the responses in the literature. We use a coarse-graining method in the graph-theoretic linear framework to show that two sharpness measures for input-output responses fall within an effectively bounded region of the positive quadrant, Ω m ⊂ ℝ + 2 , for any equilibrium model with m input binding sites. Ω m exhibits a cusp which approaches, but never exceeds, the sharpness of ℋ m but the region and the cusp can be exceeded when models are taken away from thermodynamic equilibrium. Such fundamental thermodynamic limits are called Hopfield barriers and our results provide a biophysical justification for the Hill functions as the universal Hopfield barriers for sharpness. Our results also introduce an object, Ω m , whose structure may be of mathematical interest, and suggest the importance of characterising Hopfield barriers for other forms of cellular information processing.
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Affiliation(s)
| | - Kee-Myoung Nam
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Angela H. DePace
- Howard Hughes Medical Institute, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jeremy Gunawardena
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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12
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Ye Y, Homer HA. A surge in cytoplasmic viscosity triggers nuclear remodeling required for Dux silencing and pre-implantation embryo development. Cell Rep 2024; 43:113917. [PMID: 38446665 DOI: 10.1016/j.celrep.2024.113917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/17/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Embryonic genome activation (EGA) marks the transition from dependence on maternal transcripts to an embryonic transcriptional program. The precise temporal regulation of gene expression, specifically the silencing of the Dux/murine endogenous retrovirus type L (MERVL) program during late 2-cell interphase, is crucial for developmental progression in mouse embryos. How this finely tuned regulation is achieved within this specific window is poorly understood. Here, using particle-tracking microrheology throughout the mouse oocyte-to-embryo transition, we identify a surge in cytoplasmic viscosity specific to late 2-cell interphase brought about by high microtubule and endomembrane density. Importantly, preventing the rise in 2-cell viscosity severely impairs nuclear reorganization, resulting in a persistently open chromatin configuration and failure to silence Dux/MERVL. This, in turn, derails embryo development beyond the 2- and 4-cell stages. Our findings reveal a mechanical role of the cytoplasm in regulating Dux/MERVL repression via nuclear remodeling during a temporally confined period in late 2-cell interphase.
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Affiliation(s)
- Yunan Ye
- The Christopher Chen Oocyte Biology Research Laboratory, Centre for Clinical Research, The University of Queensland, Herston, QLD 4029, Australia
| | - Hayden Anthony Homer
- The Christopher Chen Oocyte Biology Research Laboratory, Centre for Clinical Research, The University of Queensland, Herston, QLD 4029, Australia.
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13
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Moran SJ, Oglietti R, Smith KC, Macosko JC, Holzwarth G, Lyles DS. Mechanisms of active diffusion of vesicular stomatitis virus inclusion bodies and cellular early endosomes in the cytoplasm of mammalian cells. PLoS One 2024; 19:e0290672. [PMID: 38483897 PMCID: PMC10939199 DOI: 10.1371/journal.pone.0290672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
Viral and cellular particles too large to freely diffuse have two different types of mobility in the eukaryotic cell cytoplasm: directed motion mediated by motor proteins moving along cytoskeletal elements with the particle as its load, and motion in random directions mediated by motor proteins interconnecting cytoskeletal elements. The latter motion is referred to as "active diffusion." Mechanisms of directed motion have been extensively studied compared to mechanisms of active diffusion, despite the observation that active diffusion is more common for many viral and cellular particles. Our previous research showed that active diffusion of vesicular stomatitis virus (VSV) ribonucleoproteins (RNPs) in the cytoplasm consists of hopping between traps and that actin filaments and myosin II motors are components of the hop-trap mechanism. This raises the question whether similar mechanisms mediate random motion of larger particles with different physical and biological properties. Live-cell fluorescence imaging and a variational Bayesian analysis used in pattern recognition and machine learning were used to determine the molecular mechanisms of random motion of VSV inclusion bodies and cellular early endosomes. VSV inclusion bodies are membraneless cellular compartments that are the major sites of viral RNA synthesis, and early endosomes are representative of cellular membrane-bound organelles. Like VSV RNPs, inclusion bodies and early endosomes moved from one trapped state to another, but the distance between states was inconsistent with hopping between traps, indicating that the apparent state-to-state movement is mediated by trap movement. Like VSV RNPs, treatment with the actin filament depolymerizing inhibitor latrunculin A increased VSV inclusion body mobility by increasing the size of the traps. In contrast neither treatment with latrunculin A nor depolymerization of microtubules by nocodazole treatment affected the size of traps that confine early endosome mobility, indicating that intermediate filaments are likely major trap components for these cellular organelles.
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Affiliation(s)
- Steven J. Moran
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Ryan Oglietti
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Kathleen C. Smith
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Jed C. Macosko
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - George Holzwarth
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Douglas S. Lyles
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
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14
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Kwon T, Kwon S, Sung BJ. The effects of asymmetry in active noises on the efficiency of single colloidal Stirling engines with active noises. SOFT MATTER 2024; 20:2600-2609. [PMID: 38426540 DOI: 10.1039/d3sm01386c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Molecular machines, which operate in highly fluctuating environments far from equilibrium, may benefit from their non-equilibrium environments. It is, however, a topic of controversy how the efficiency of the microscopic engines can be enhanced. Recent experiments showed that microscopic Stirling engines in bacterial reservoirs could show high performance beyond the equilibrium thermodynamics. In this work, we perform overdamped Langevin dynamics simulations for microscopic Stirling heat engines in bacterial reservoirs and show that the temperature dependence of the magnitude of active noises should be responsible for such high efficiency. Only when we introduce temperature-dependent active noises, the efficiency of the microscopic Stirling engines is enhanced significantly as in experiments.
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Affiliation(s)
- Taejin Kwon
- Department of Chemistry and Cosmetics, Jeju National University, Jeju 63243, Republic of Korea
| | - Seulki Kwon
- The Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bong June Sung
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea.
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15
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Nolte DD. Coherent light scattering from cellular dynamics in living tissues. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024; 87:036601. [PMID: 38433567 DOI: 10.1088/1361-6633/ad2229] [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: 11/01/2022] [Accepted: 01/24/2024] [Indexed: 03/05/2024]
Abstract
This review examines the biological physics of intracellular transport probed by the coherent optics of dynamic light scattering from optically thick living tissues. Cells and their constituents are in constant motion, composed of a broad range of speeds spanning many orders of magnitude that reflect the wide array of functions and mechanisms that maintain cellular health. From the organelle scale of tens of nanometers and upward in size, the motion inside living tissue is actively driven rather than thermal, propelled by the hydrolysis of bioenergetic molecules and the forces of molecular motors. Active transport can mimic the random walks of thermal Brownian motion, but mean-squared displacements are far from thermal equilibrium and can display anomalous diffusion through Lévy or fractional Brownian walks. Despite the average isotropic three-dimensional environment of cells and tissues, active cellular or intracellular transport of single light-scattering objects is often pseudo-one-dimensional, for instance as organelle displacement persists along cytoskeletal tracks or as membranes displace along the normal to cell surfaces, albeit isotropically oriented in three dimensions. Coherent light scattering is a natural tool to characterize such tissue dynamics because persistent directed transport induces Doppler shifts in the scattered light. The many frequency-shifted partial waves from the complex and dynamic media interfere to produce dynamic speckle that reveals tissue-scale processes through speckle contrast imaging and fluctuation spectroscopy. Low-coherence interferometry, dynamic optical coherence tomography, diffusing-wave spectroscopy, diffuse-correlation spectroscopy, differential dynamic microscopy and digital holography offer coherent detection methods that shed light on intracellular processes. In health-care applications, altered states of cellular health and disease display altered cellular motions that imprint on the statistical fluctuations of the scattered light. For instance, the efficacy of medical therapeutics can be monitored by measuring the changes they induce in the Doppler spectra of livingex vivocancer biopsies.
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Affiliation(s)
- David D Nolte
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, United States of America
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16
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Lazzarino M, Zanetti M, Chen SN, Gao S, Peña B, Lam CK, Wu JC, Taylor MRG, Mestroni L, Sbaizero O. Defective Biomechanics and Pharmacological Rescue of Human Cardiomyocytes with Filamin C Truncations. Int J Mol Sci 2024; 25:2942. [PMID: 38474188 PMCID: PMC10932268 DOI: 10.3390/ijms25052942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Actin-binding filamin C (FLNC) is expressed in cardiomyocytes, where it localizes to Z-discs, sarcolemma, and intercalated discs. Although FLNC truncation variants (FLNCtv) are an established cause of arrhythmias and heart failure, changes in biomechanical properties of cardiomyocytes are mostly unknown. Thus, we investigated the mechanical properties of human-induced pluripotent stem cells-derived cardiomyocytes (hiPSC-CMs) carrying FLNCtv. CRISPR/Cas9 genome-edited homozygous FLNCKO-/- hiPSC-CMs and heterozygous knock-out FLNCKO+/- hiPSC-CMs were analyzed and compared to wild-type FLNC (FLNCWT) hiPSC-CMs. Atomic force microscopy (AFM) was used to perform micro-indentation to evaluate passive and dynamic mechanical properties. A qualitative analysis of the beating traces showed gene dosage-dependent-manner "irregular" peak profiles in FLNCKO+/- and FLNCKO-/- hiPSC-CMs. Two Young's moduli were calculated: E1, reflecting the compression of the plasma membrane and actin cortex, and E2, including the whole cell with a cytoskeleton and nucleus. Both E1 and E2 showed decreased stiffness in mutant FLNCKO+/- and FLNCKO-/- iPSC-CMs compared to that in FLNCWT. The cell adhesion force and work of adhesion were assessed using the retraction curve of the SCFS. Mutant FLNC iPSC-CMs showed gene dosage-dependent decreases in the work of adhesion and adhesion forces from the heterozygous FLNCKO+/- to the FLNCKO-/- model compared to FLNCWT, suggesting damaged cytoskeleton and membrane structures. Finally, we investigated the effect of crenolanib on the mechanical properties of hiPSC-CMs. Crenolanib is an inhibitor of the Platelet-Derived Growth Factor Receptor α (PDGFRA) pathway which is upregulated in FLNCtv hiPSC-CMs. Crenolanib was able to partially rescue the stiffness of FLNCKO-/- hiPSC-CMs compared to control, supporting its potential therapeutic role.
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Affiliation(s)
- Marco Lazzarino
- CNR-IOM, Area Science Park, 34149 Trieste, Italy; (M.L.); (M.Z.)
- Cardiovascular Institute, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (S.N.C.); (S.G.); (B.P.); (M.R.G.T.); (L.M.)
| | - Michele Zanetti
- CNR-IOM, Area Science Park, 34149 Trieste, Italy; (M.L.); (M.Z.)
- Cardiovascular Institute, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (S.N.C.); (S.G.); (B.P.); (M.R.G.T.); (L.M.)
| | - Suet Nee Chen
- Cardiovascular Institute, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (S.N.C.); (S.G.); (B.P.); (M.R.G.T.); (L.M.)
| | - Shanshan Gao
- Cardiovascular Institute, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (S.N.C.); (S.G.); (B.P.); (M.R.G.T.); (L.M.)
| | - Brisa Peña
- Cardiovascular Institute, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (S.N.C.); (S.G.); (B.P.); (M.R.G.T.); (L.M.)
- Bioengineering Department, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Chi Keung Lam
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; (C.K.L.); (J.C.W.)
| | - Joseph C. Wu
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; (C.K.L.); (J.C.W.)
| | - Matthew R. G. Taylor
- Cardiovascular Institute, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (S.N.C.); (S.G.); (B.P.); (M.R.G.T.); (L.M.)
| | - Luisa Mestroni
- Cardiovascular Institute, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (S.N.C.); (S.G.); (B.P.); (M.R.G.T.); (L.M.)
| | - Orfeo Sbaizero
- Cardiovascular Institute, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (S.N.C.); (S.G.); (B.P.); (M.R.G.T.); (L.M.)
- Engineering and Architecture Department, University of Trieste, 34127 Trieste, Italy
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17
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Grelier M, Sivak DA, Ehrich J. Unlocking the potential of information flow: Maximizing free-energy transduction in a model of an autonomous rotary molecular motor. Phys Rev E 2024; 109:034115. [PMID: 38632770 DOI: 10.1103/physreve.109.034115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 01/30/2024] [Indexed: 04/19/2024]
Abstract
Molecular motors fulfill critical functions within all living beings. Understanding their underlying working principles is therefore of great interest. Here we develop a simple model inspired by the two-component biomolecular motor F_{o}-F_{1} ATP synthase. We analyze its energetics and characterize information flows between the machine's components. At maximum output power we find that information transduction plays a minor role for free-energy transduction. However, when the two components are coupled to different environments (e.g., when in contact with heat baths at different temperatures), we show that information flow becomes a resource worth exploiting to maximize free-energy transduction. Our findings suggest that real-world powerful and efficient information engines could be found in machines whose components are subjected to fluctuations of different strength, since in this situation the benefit gained from using information for work extraction can outweigh the costs of information generation.
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Affiliation(s)
- Mathis Grelier
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6 Canada
- PULS Group, Department of Physics, FAU Erlangen-Nürnberg, IZNF, 91058 Erlangen, Germany
| | - David A Sivak
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6 Canada
| | - Jannik Ehrich
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6 Canada
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18
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Das R, Sakaue T, Shivashankar GV, Prost J, Hiraiwa T. Chromatin Remodeling Due to Transient-Link-and-Pass Activity Enhances Subnuclear Dynamics. PHYSICAL REVIEW LETTERS 2024; 132:058401. [PMID: 38364140 DOI: 10.1103/physrevlett.132.058401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/02/2024] [Indexed: 02/18/2024]
Abstract
Spatiotemporal coordination of chromatin and subnuclear compartments is crucial for cells. Numerous enzymes act inside nucleus-some of those transiently link and pass two chromatin segments. Here, we study how such an active perturbation affects fluctuating dynamics of an inclusion in the chromatic medium. Using numerical simulations and a versatile effective model, we categorize inclusion dynamics into three distinct modes. The transient-link-and-pass activity speeds up inclusion dynamics by affecting a slow mode related to chromatin remodeling, viz., size and shape of the chromatin meshes.
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Affiliation(s)
- Rakesh Das
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, Kanagawa 252-5258, Japan
| | - G V Shivashankar
- Department of Health Sciences and Technology (D-HEST), ETH Zurich, Villigen 8092, Switzerland
- Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Jacques Prost
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
- Laboratoire Physico Chimie Curie, Institut Curie, Paris Science et Lettres Research University, 75005 Paris, France
| | - Tetsuya Hiraiwa
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
- Institute of Physics, Academia Sinica, Taipei City 115201, Taiwan
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19
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Kwon E, Baek Y. α-divergence improves the entropy production estimation via machine learning. Phys Rev E 2024; 109:014143. [PMID: 38366477 DOI: 10.1103/physreve.109.014143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 01/05/2024] [Indexed: 02/18/2024]
Abstract
Recent years have seen a surge of interest in the algorithmic estimation of stochastic entropy production (EP) from trajectory data via machine learning. A crucial element of such algorithms is the identification of a loss function whose minimization guarantees the accurate EP estimation. In this study we show that there exists a host of loss functions, namely, those implementing a variational representation of the α-divergence, which can be used for the EP estimation. By fixing α to a value between -1 and 0, the α-NEEP (Neural Estimator for Entropy Production) exhibits a much more robust performance against strong nonequilibrium driving or slow dynamics, which adversely affects the existing method based on the Kullback-Leibler divergence (α=0). In particular, the choice of α=-0.5 tends to yield the optimal results. To corroborate our findings, we present an exactly solvable simplification of the EP estimation problem, whose loss function landscape and stochastic properties give deeper intuition into the robustness of the α-NEEP.
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Affiliation(s)
- Euijoon Kwon
- Department of Physics and Astronomy & Center for Theoretical Physics, Seoul National University, Seoul 08826, Republic of Korea
| | - Yongjoo Baek
- Department of Physics and Astronomy & Center for Theoretical Physics, Seoul National University, Seoul 08826, Republic of Korea
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20
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Leighton MP, Sivak DA. Jensen bound for the entropy production rate in stochastic thermodynamics. Phys Rev E 2024; 109:L012101. [PMID: 38366465 DOI: 10.1103/physreve.109.l012101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/30/2023] [Indexed: 02/18/2024]
Abstract
Bounding and estimating entropy production has long been an important goal of nonequilibrium thermodynamics. We recently derived a lower bound on the total and subsystem entropy production rates of continuous stochastic systems. This "Jensen bound" has led to fundamental limits on the performance of collective transport systems and permitted thermodynamic inference of free-energy transduction between components of bipartite molecular machines. Our original derivation relied on a number of assumptions, which restricted the bound's regime of applicability. Here we derive the Jensen bound far more generally for multipartite overdamped Langevin dynamics. We then consider several extensions, allowing for position-dependent diffusion coefficients, underdamped dynamics, and non-multipartite overdamped dynamics. Our results extend the Jensen bound to a far broader class of systems.
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Affiliation(s)
- Matthew P Leighton
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - David A Sivak
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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21
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Abbasi A, Netz RR, Naji A. Non-Markovian Modeling of Nonequilibrium Fluctuations and Dissipation in Active Viscoelastic Biomatter. PHYSICAL REVIEW LETTERS 2023; 131:228202. [PMID: 38101355 DOI: 10.1103/physrevlett.131.228202] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/19/2023] [Indexed: 12/17/2023]
Abstract
Based on a Hamiltonian that incorporates the elastic coupling between a tracer particle and the embedding active viscoelastic biomatter, we derive a generalized non-Markovian Langevin model for the nonequilibrium mechanical tracer response. Our analytical expressions for the frequency-dependent tracer response function and the tracer positional autocorrelation function agree quantitatively with experimental data for red blood cells and actomyosin networks with and without adenosine triphosphate over the entire frequency range and in particular reproduce the low-frequency violation of the fluctuation-dissipation theorem. The viscoelastic power laws, the elastic constants and effective friction coefficients extracted from the experimental data allow straightforward physical interpretation.
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Affiliation(s)
- Amir Abbasi
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Roland R Netz
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Ali Naji
- School of Nano Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19538-33511, Iran
- Department of Physics, College of Science, Sultan Qaboos University, Muscat 123, Oman
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22
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Goswami K, Metzler R. Trapped tracer in a non-equilibrium bath: dynamics and energetics. SOFT MATTER 2023; 19:8802-8819. [PMID: 37946588 DOI: 10.1039/d3sm01177a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
We study the dynamics of a tracer that is elastically coupled to active particles being kept at two different temperatures, as a prototype of tracer dynamics in a non-equilibrium bath. Employing analytical techniques, we find the exact solution of the probability density function for the effective motion of the tracer. The analytical results are supported by numerical simulations. By combining the experimentally accessible quantities such as the response function and the power spectrum, we measure the non-equilibrium fluctuations in terms of the effective temperature. In addition, we compute the energy dissipation rate to find the precise effects of activity. Our study is relevant in understanding athermal fluctuations arising in cytoskeletal networks or inside a chromosome.
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Affiliation(s)
- Koushik Goswami
- Institute of Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany.
| | - Ralf Metzler
- Institute of Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany.
- Asia Pacific Centre for Theoretical Physics, Pohang 37673, Republic of Korea.
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23
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Umeda K, Nishizawa K, Nagao W, Inokuchi S, Sugino Y, Ebata H, Mizuno D. Activity-dependent glassy cell mechanics II: Nonthermal fluctuations under metabolic activity. Biophys J 2023; 122:4395-4413. [PMID: 37865819 PMCID: PMC10698330 DOI: 10.1016/j.bpj.2023.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/28/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023] Open
Abstract
The glassy cytoplasm, crowded with bio-macromolecules, is fluidized in living cells by mechanical energy derived from metabolism. Characterizing the living cytoplasm as a nonequilibrium system is crucial in elucidating the intricate mechanism that relates cell mechanics to metabolic activities. In this study, we conducted active and passive microrheology in eukaryotic cells, and quantified nonthermal fluctuations by examining the violation of the fluctuation-dissipation theorem. The power spectral density of active force generation was estimated following the Langevin theory extended to nonequilibrium systems. However, experiments performed while regulating cellular metabolic activity showed that the nonthermal displacement fluctuation, rather than the active nonthermal force, is linked to metabolism. We discuss that mechano-enzymes in living cells do not act as microscopic objects. Instead, they generate meso-scale collective fluctuations with displacements controlled by enzymatic activity. The activity induces structural relaxations in glassy cytoplasm. Even though the autocorrelation of nonthermal fluctuations is lost at long timescales due to the structural relaxations, the nonthermal displacement fluctuation remains regulated by metabolic reactions. Our results therefore demonstrate that nonthermal fluctuations serve as a valuable indicator of a cell's metabolic activities, regardless of the presence or absence of structural relaxations.
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Affiliation(s)
| | | | - Wataru Nagao
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Shono Inokuchi
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Yujiro Sugino
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Ebata
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Daisuke Mizuno
- Department of Physics, Kyushu University, Fukuoka, Japan.
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24
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Arzash S, Gannavarapu A, MacKintosh FC. Mechanical criticality of fiber networks at a finite temperature. Phys Rev E 2023; 108:054403. [PMID: 38115508 DOI: 10.1103/physreve.108.054403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 10/05/2023] [Indexed: 12/21/2023]
Abstract
At zero temperature, spring networks with connectivity below Maxwell's isostatic threshold undergo a mechanical phase transition from a floppy state at small strains to a rigid state for applied shear strain above a critical strain threshold. Disordered networks in the floppy mechanical regime can be stabilized by entropic effects at finite temperature. We develop a scaling theory for this mechanical phase transition at finite temperature, yielding relationships between various scaling exponents. Using Monte Carlo simulations, we verify these scaling relations and identify anomalous entropic elasticity with sublinear T dependence in the linear elastic regime. While our results are consistent with prior studies of phase behavior near the isostatic point, the present work also makes predictions relevant to the broad class of disordered thermal semiflexible polymer networks for which the connectivity generally lies far below the isostatic threshold.
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Affiliation(s)
- Sadjad Arzash
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77030, USA
| | - Anupama Gannavarapu
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77030, USA
| | - Fred C MacKintosh
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77030, USA
- Department of Chemistry and Department of Physics and Astronomy, Rice University, Houston, Texas 77005, USA
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25
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Gu Q, Shanahan L, Hart JW, Belser S, Shofer N, Atatüre M, Knowles HS. Simultaneous Nanorheometry and Nanothermometry Using Intracellular Diamond Quantum Sensors. ACS NANO 2023; 17:20034-20042. [PMID: 37791968 PMCID: PMC10604098 DOI: 10.1021/acsnano.3c05285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023]
Abstract
The viscoelasticity of the cytoplasm plays a critical role in cell morphology, cell division, and intracellular transport. Viscoelasticity is also interconnected with other biophysical properties, such as temperature, which is known to influence cellular bioenergetics. Probing the connections between intracellular temperature and cytoplasmic viscoelasticity provides an exciting opportunity for the study of biological phenomena, such as metabolism and disease progression. The small length scales and transient nature of changes in these parameters combined with their complex interdependencies pose a challenge for biosensing tools, which are often limited to a single readout modality. Here, we present a dual-mode quantum sensor capable of performing simultaneous nanoscale thermometry and rheometry in dynamic cellular environments. We use nitrogen-vacancy centers in diamond nanocrystals as biocompatible sensors for in vitro measurements. We combine subdiffraction resolution single-particle tracking in a fluidic environment with optically detected magnetic resonance spectroscopy to perform simultaneous sensing of viscoelasticity and temperature. We use our sensor to demonstrate probing of the temperature-dependent viscoelasticity in complex media at the nanoscale. We then investigate the interplay between intracellular forces and the cytoplasmic rheology in live cells. Finally, we identify different rheological regimes and reveal evidence of active trafficking and details of the nanoscale viscoelasticity of the cytoplasm.
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Affiliation(s)
| | | | | | - Sophia Belser
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United
Kingdom
| | - Noah Shofer
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United
Kingdom
| | - Mete Atatüre
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United
Kingdom
| | - Helena S. Knowles
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United
Kingdom
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26
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Fernandes Martins G, Horowitz JM. Topologically constrained fluctuations and thermodynamics regulate nonequilibrium response. Phys Rev E 2023; 108:044113. [PMID: 37978593 DOI: 10.1103/physreve.108.044113] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/07/2023] [Indexed: 11/19/2023]
Abstract
The limits on a system's response to external perturbations inform our understanding of how physical properties can be shaped by microscopic characteristics. Here, we derive constraints on the steady-state nonequilibrium response of physical observables in terms of the topology of the microscopic state space and the strength of thermodynamic driving. Notably, evaluation of these limits requires no kinetic information beyond the state-space structure. When applied to models of receptor binding, we find that sensitivity is bounded by the steepness of a Hill function with a Hill coefficient enhanced by the chemical driving beyond the structural equilibrium limit.
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Affiliation(s)
| | - Jordan M Horowitz
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Center for the Study of Complex Systems, University of Michigan, Ann Arbor, Michigan 48104, USA
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27
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Démery V, Gambassi A. Non-Gaussian fluctuations of a probe coupled to a Gaussian field. Phys Rev E 2023; 108:044604. [PMID: 37978697 DOI: 10.1103/physreve.108.044604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/02/2023] [Indexed: 11/19/2023]
Abstract
The motion of a colloidal probe in a complex fluid, such as a micellar solution, is usually described by the generalized Langevin equation, which is linear. However, recent numerical simulations and experiments have shown that this linear model fails when the probe is confined and that the intrinsic dynamics of the probe is actually nonlinear. Noting that the kurtosis of the displacement of the probe may reveal the nonlinearity of its dynamics also in the absence confinement, we compute it for a probe coupled to a Gaussian field and possibly trapped by a harmonic potential. We show that the excess kurtosis increases from zero at short times, reaches a maximum, and then decays algebraically at long times, with an exponent which depends on the spatial dimensionality and on the features and correlations of the dynamics of the field. Our analytical predictions are confirmed by numerical simulations of the stochastic dynamics of the probe and the field where the latter is represented by a finite number of modes.
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Affiliation(s)
- Vincent Démery
- Gulliver, CNRS, ESPCI Paris PSL, 75005 Paris, France and Univ Lyon, ENS de Lyon, CNRS, Laboratoire de Physique, F-69342 Lyon, France
| | - Andrea Gambassi
- SISSA-International School for Advanced Studies and INFN, 34136 Trieste, Italy
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28
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Chen S, Markovich T, MacKintosh FC. Motor-free contractility of active biopolymer networks. Phys Rev E 2023; 108:044405. [PMID: 37978629 DOI: 10.1103/physreve.108.044405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/19/2023] [Indexed: 11/19/2023]
Abstract
Contractility in animal cells is often generated by molecular motors such as myosin, which require polar substrates for their function. Motivated by recent experimental evidence of motor-independent contractility, we propose a robust motor-free mechanism that can generate contraction in biopolymer networks without the need for substrate polarity. We show that contractility is a natural consequence of active binding-unbinding of crosslinkers that breaks the principle of detailed balance, together with the asymmetric force-extension response of semiflexible biopolymers. We have extended our earlier work to discuss the motor-free contraction of viscoelastic biopolymer networks. We calculate the resulting contractile velocity using a microscopic model and show that it can be reduced to a simple coarse-grained model under certain limits. Our model may provide an explanation of recent reports of motor-independent contractility in cells. Our results also suggest a mechanism for generating contractile forces in synthetic active materials.
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Affiliation(s)
- Sihan Chen
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Tomer Markovich
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
- School of Mechanical Engineering, Tel Aviv University, Tel Aviv 69978, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 69978, Israel
| | - Fred C MacKintosh
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
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29
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Nakul U, Roy S, Nalupurackal G, Chakraborty S, Siwach P, Goswami J, Edwina P, Bajpai SK, Singh R, Roy B. Studying fluctuating trajectories of optically confined passive tracers inside cells provides familiar active forces. BIOMEDICAL OPTICS EXPRESS 2023; 14:5440. [PMID: 37810271 PMCID: PMC7615170 DOI: 10.1364/boe.499990] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/14/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023]
Abstract
In recent years, there has been a growing interest in studying the trajectories of microparticles inside living cells. Among other things, such studies are useful in understanding the spatio-temporal properties of a cell. In this work, we study the stochastic trajectories of a passive microparticle inside a cell using experiments and theory. Our theory is based on modeling the microparticle inside a cell as an active particle in a viscoelastic medium. The activity is included in our model from an additional stochastic term with non-zero persistence in the Langevin equation describing the dynamics of the microparticle. Using this model, we are able to predict the power spectral density (PSD) measured in the experiment and compute active forces. This caters to the situation where a tracer particle is optically confined and then yields a PSD for positional fluctuations. The low frequency part of the PSD yields information about the active forces that the particle feels. The fit to the model extracts such active force. Thus, we can conclude that trapping the particle does not affect the values of the forces extracted from the active fits if accounted for appropriately by proper theoretical models. In addition, the fit also provides system properties and optical tweezers trap stiffness.
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Affiliation(s)
- Urvashi Nakul
- Department of Physics, Quantum Centre of Excellence for Diamond and Emergent Materials (QuCenDiEM), IIT Madras, Chennai 600036, India
| | - Srestha Roy
- Department of Physics, Quantum Centre of Excellence for Diamond and Emergent Materials (QuCenDiEM), IIT Madras, Chennai 600036, India
| | - Gokul Nalupurackal
- Department of Physics, Quantum Centre of Excellence for Diamond and Emergent Materials (QuCenDiEM), IIT Madras, Chennai 600036, India
| | - Snigdhadev Chakraborty
- Department of Physics, Quantum Centre of Excellence for Diamond and Emergent Materials (QuCenDiEM), IIT Madras, Chennai 600036, India
| | - Priyanka Siwach
- Department of Physics, Quantum Centre of Excellence for Diamond and Emergent Materials (QuCenDiEM), IIT Madras, Chennai 600036, India
| | - Jayesh Goswami
- Department of Physics, Quantum Centre of Excellence for Diamond and Emergent Materials (QuCenDiEM), IIT Madras, Chennai 600036, India
| | - Privita Edwina
- Department of Physics, Quantum Centre of Excellence for Diamond and Emergent Materials (QuCenDiEM), IIT Madras, Chennai 600036, India
- Department of Applied Mechanics, IIT Madras, Chennai 600036, India
| | | | - Rajesh Singh
- Department of Physics, IIT Madras, Chennai 600036, India
| | - Basudev Roy
- Department of Physics, Quantum Centre of Excellence for Diamond and Emergent Materials (QuCenDiEM), IIT Madras, Chennai 600036, India
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30
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Gautam D, Srivastava A, Chowdhury R, Laskar IR, Rao VKP, Mukherjee S. Mechanical microscopy of cancer cells: TGF-β induced epithelial to mesenchymal transition corresponds to low intracellular viscosity in cancer cells. THE JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 2023; 154:1787-1799. [PMID: 37725520 DOI: 10.1121/10.0020848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 08/21/2023] [Indexed: 09/21/2023]
Abstract
Viscosity is an essential parameter that regulates bio-molecular reaction rates of diffusion-driven cellular processes. Hence, abnormal viscosity levels are often associated with various diseases and malfunctions like cancer. For this reason, monitoring intracellular viscosity becomes vital. While several approaches have been developed for in vitro and in vivo measurement of viscosity, analysis of intracellular viscosity in live cells has not yet been well realized. Our research introduces a novel, natural frequency-based, non-invasive method to determine the intracellular viscosity in cells. This method can not only efficiently analyze the differences in intracellular viscosity post modulation with molecules like PEG or glucose but is sensitive enough to distinguish the difference in intra-cellular viscosity among various cancer cell lines such as Huh-7, MCF-7, and MDAMB-231. Interestingly, TGF-β a cytokine reported to induce epithelial to mesenchymal transition (EMT), a feature associated with cancer invasiveness resulted in reduced viscosity of cancer cells, as captured through our method. To corroborate our findings with existing methods of analysis, we analyzed intra-cellular viscosity with a previously described viscosity-sensitive molecular rotor-based fluorophore-TPSII. In parity with our position sensing device (PSD)-based approach, an increase in fluorescence intensity was observed with viscosity enhancers, while, TGF-β exposure resulted in its reduction in the cells studied. This is the first study of its kind that attempts to characterize differences in intracellular viscosity using a novel, non-invasive PSD-based method.
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Affiliation(s)
- Diplesh Gautam
- Department of Mechanical Engineering, Birla Institute of Technology and Science, Pilani, Rajasthan 333 031, India
| | - Abhilasha Srivastava
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan 333 031, India
| | - Rajdeep Chowdhury
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan 333 031, India
| | - Inamur R Laskar
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, Rajasthan 333 031, India
| | - Venkatesh K P Rao
- Department of Mechanical Engineering, Birla Institute of Technology and Science, Pilani, Rajasthan 333 031, India
| | - Sudeshna Mukherjee
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan 333 031, India
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31
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Nishizawa K, Honda N, Inokuchi S, Ebata H, Ariga T, Mizuno D. Measuring fluctuating dynamics of sparsely crosslinked actin gels with dual-feedback nonlinear microrheology. Phys Rev E 2023; 108:034601. [PMID: 37849150 DOI: 10.1103/physreve.108.034601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 08/06/2023] [Indexed: 10/19/2023]
Abstract
We investigate the fluctuating dynamics of colloidal particles in weakly crosslinked F-actin networks with optical-trap-based microrheology. Using the dual-feedback technology, embedded colloidal particles were stably forced beyond the linear regime in a manner that does not suppress spontaneous fluctuations of particles. Upon forcing, a particle that was stably confined in a cage made of the network's crosslinks started to intermittently jump to the next caging microenvironments. By investigating the statistics of the jump dynamics, we discuss how heterogeneous relaxations observed in equilibrium systems became homogeneous when similar jumps were activated under constant forcing beyond the linear regime.
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Affiliation(s)
- Kenji Nishizawa
- Department of Physics, The University of Tokyo, Tokyo 113-8654, Japan
| | - Natsuki Honda
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan
| | - Shono Inokuchi
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan
| | - Hiroyuki Ebata
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan
| | - Takayuki Ariga
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Daisuke Mizuno
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan
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32
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Saha TK, Ehrich J, Gavrilov M, Still S, Sivak DA, Bechhoefer J. Information Engine in a Nonequilibrium Bath. PHYSICAL REVIEW LETTERS 2023; 131:057101. [PMID: 37595211 DOI: 10.1103/physrevlett.131.057101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 06/29/2023] [Indexed: 08/20/2023]
Abstract
Information engines can convert thermal fluctuations of a bath at temperature T into work at rates of order k_{B}T per relaxation time of the system. We show experimentally that such engines, when in contact with a bath that is out of equilibrium, can extract much more work. We place a heavy, micron-scale bead in a harmonic potential that ratchets up to capture favorable fluctuations. Adding a fluctuating electric field increases work extraction up to ten times, limited only by the strength of the applied field. Our results connect Maxwell's demon with energy harvesting and demonstrate that information engines in nonequilibrium baths can greatly outperform conventional engines.
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Affiliation(s)
- Tushar K Saha
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada
| | - Jannik Ehrich
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada
- Department of Physics and Astronomy, University of Hawaii at Mānoa, Honolulu, Hawaii 96822, USA
| | - Momčilo Gavrilov
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada
| | - Susanne Still
- Department of Physics and Astronomy, University of Hawaii at Mānoa, Honolulu, Hawaii 96822, USA
| | - David A Sivak
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada
| | - John Bechhoefer
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada
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33
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Smith NR. Nonequilibrium steady state of trapped active particles. Phys Rev E 2023; 108:L022602. [PMID: 37723780 DOI: 10.1103/physreve.108.l022602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/26/2023] [Indexed: 09/20/2023]
Abstract
We consider an overdamped particle with a general physical mechanism that creates noisy active movement (e.g., a run-and-tumble particle or active Brownian particle, etc.), that is confined by an external potential. Focusing on the limit in which the correlation time τ of the active noise is small, we find the nonequilibrium steady-state distribution P_{st}(X) of the particle's position X. While typical fluctuations of X follow a Boltzmann distribution with an effective temperature that is not difficult to find, the tails of P_{st}(X) deviate from a Boltzmann behavior: In the limit τ→0, they scale as P_{st}(X)∼e^{-s(X)/τ}. We calculate the large-deviation function s(X) exactly for arbitrary trapping potential and active noise in dimension d=1, by relating it to the rate function that describes large deviations of the position of the same active particle in absence of an external potential at long times. We then extend our results to d>1 assuming rotational symmetry.
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Affiliation(s)
- Naftali R Smith
- Department of Environmental Physics, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
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34
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Oses C, De Rossi MC, Bruno L, Verneri P, Diaz MC, Benítez B, Guberman A, Levi V. From the membrane to the nucleus: mechanical signals and transcription regulation. Biophys Rev 2023; 15:671-683. [PMID: 37681098 PMCID: PMC10480138 DOI: 10.1007/s12551-023-01103-3] [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: 04/06/2023] [Accepted: 07/20/2023] [Indexed: 09/09/2023] Open
Abstract
Mechanical forces drive and modulate a wide variety of processes in eukaryotic cells including those occurring in the nucleus. Relevantly, forces are fundamental during development since they guide lineage specifications of embryonic stem cells. A sophisticated macromolecular machinery transduces mechanical stimuli received at the cell surface into a biochemical output; a key component in this mechanical communication is the cytoskeleton, a complex network of biofilaments in constant remodeling that links the cell membrane to the nuclear envelope. Recent evidence highlights that forces transmitted through the cytoskeleton directly affect the organization of chromatin and the accessibility of transcription-related molecules to their targets in the DNA. Consequently, mechanical forces can directly modulate transcription and change gene expression programs. Here, we will revise the biophysical toolbox involved in the mechanical communication with the cell nucleus and discuss how mechanical forces impact on the organization of this organelle and more specifically, on transcription. We will also discuss how live-cell fluorescence imaging is producing exquisite information to understand the mechanical response of cells and to quantify the landscape of interactions of transcription factors with chromatin in embryonic stem cells. These studies are building new biophysical insights that could be fundamental to achieve the goal of manipulating forces to guide cell differentiation in culture systems.
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Affiliation(s)
- Camila Oses
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - María Cecilia De Rossi
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - Luciana Bruno
- Facultad de Ciencias Exactas Y Naturales, Instituto de Cálculo (IC), CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - Paula Verneri
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - María Candelaria Diaz
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - Belén Benítez
- Instituto de Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - Alejandra Guberman
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
- Facultad de Ciencias Exactas Y Naturales, Departamento de Fisiología, Universidad de Buenos Aires, Biología Molecular Y Celular, C1428EGA Buenos Aires, Argentina
| | - Valeria Levi
- Instituto de Química Biológica de La Facultad de Ciencias Exactas Y Naturales (IQUIBICEN), Facultad de Ciencias Exactas Y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
- Facultad de Ciencias Exactas Y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
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35
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Bacanu A, Pelletier JF, Jung Y, Fakhri N. Inferring scale-dependent non-equilibrium activity using carbon nanotubes. NATURE NANOTECHNOLOGY 2023; 18:905-911. [PMID: 37157022 DOI: 10.1038/s41565-023-01395-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 04/04/2023] [Indexed: 05/10/2023]
Abstract
In living systems, irreversible, yet stochastic, molecular interactions form multiscale structures (such as cytoskeletal networks), which mediate processes (such as cytokinesis and cellular motility) in a close relationship between the structure and function. However, owing to a lack of methods to quantify non-equilibrium activity, their dynamics remain poorly characterized. Here, by measuring the time-reversal asymmetry encoded in the conformational dynamics of filamentous single-walled carbon nanotubes embedded in the actomyosin network of Xenopus egg extract, we characterize the multiscale dynamics of non-equilibrium activity encoded in bending-mode amplitudes. Our method is sensitive to distinct perturbations to the actomyosin network and the concentration ratio of adenosine triphosphate to adenosine diphosphate. Thus, our method can dissect the functional coupling of microscopic dynamics to the emergence of larger scale non-equilibrium activity. We relate the spatiotemporal scales of non-equilibrium activity to the key physical parameters of a semiflexible filament embedded in a non-equilibrium viscoelastic environment. Our analysis provides a general tool to characterize steady-state non-equilibrium activity in high-dimensional spaces.
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Affiliation(s)
- Alexandru Bacanu
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - James F Pelletier
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
| | - Yoon Jung
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nikta Fakhri
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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36
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Wei M, Ben Zion MY, Dauchot O. Reconfiguration, Interrupted Aging, and Enhanced Dynamics of a Colloidal Gel Using Photoswitchable Active Doping. PHYSICAL REVIEW LETTERS 2023; 131:018301. [PMID: 37478452 DOI: 10.1103/physrevlett.131.018301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/06/2023] [Accepted: 06/01/2023] [Indexed: 07/23/2023]
Abstract
We study quasi-2D gels made of a colloidal network doped with Janus particles activated by light. Following the gel formation, we monitor both the structure and dynamics before, during, and after the activation period. Before activity is switched on, the gel is slowly aging. During the activation, the mobility of the passive particles exhibits a characteristic scale-dependent response, while the colloidal network remains connected, and the gel maintains its structural integrity. Once activity is switched off, the gel stops aging and keeps the memory of the structure inherited from the active phase. Remarkably, the motility remains larger than that of the gel, before the active period. The system has turned into a genuinely softer gel, with frozen dynamics, but with more space for thermal fluctuations. The above conclusions remain valid long after the activity period.
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Affiliation(s)
- Mengshi Wei
- Gulliver UMR CNRS 7083, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
| | - Matan Yah Ben Zion
- School of Physics and Astronomy, and the Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Olivier Dauchot
- Gulliver UMR CNRS 7083, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
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37
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Jain I, Rao M, Tran PT. Reliable and robust control of nucleus centering is contingent on nonequilibrium force patterns. iScience 2023; 26:106665. [PMID: 37182105 PMCID: PMC10173738 DOI: 10.1016/j.isci.2023.106665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/23/2023] [Accepted: 04/09/2023] [Indexed: 05/16/2023] Open
Abstract
Cell centers their division apparatus to ensure symmetric cell division, a challenging task when the governing dynamics is stochastic. Using fission yeast, we show that the patterning of nonequilibrium polymerization forces of microtubule (MT) bundles controls the precise localization of spindle pole body (SPB), and hence the division septum, at the onset of mitosis. We define two cellular objectives, reliability, the mean SPB position relative to the geometric center, and robustness, the variance of the SPB position, which are sensitive to genetic perturbations that change cell length, MT bundle number/orientation, and MT dynamics. We show that simultaneous control of reliability and robustness is required to minimize septum positioning error achieved by the wild type (WT). A stochastic model for the MT-based nucleus centering, with parameters measured directly or estimated using Bayesian inference, recapitulates the maximum fidelity of WT. Using this, we perform a sensitivity analysis of the parameters that control nuclear centering.
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Affiliation(s)
- Ishutesh Jain
- Institut Curie, PSL Universite, Sorbonne Universite, CNRS UMR 144, 75005 Paris, France
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences - TIFR, Bangalore 560065, India
| | - Madan Rao
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences - TIFR, Bangalore 560065, India
- Corresponding author
| | - Phong T. Tran
- Institut Curie, PSL Universite, Sorbonne Universite, CNRS UMR 144, 75005 Paris, France
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corresponding author
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38
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Ebata H, Umeda K, Nishizawa K, Nagao W, Inokuchi S, Sugino Y, Miyamoto T, Mizuno D. Activity-dependent glassy cell mechanics Ⅰ: Mechanical properties measured with active microrheology. Biophys J 2023; 122:1781-1793. [PMID: 37050875 PMCID: PMC10209042 DOI: 10.1016/j.bpj.2023.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 01/27/2023] [Accepted: 04/07/2023] [Indexed: 04/14/2023] Open
Abstract
Active microrheology was conducted in living cells by applying an optical-trapping force to vigorously fluctuating tracer beads with feedback-tracking technology. The complex shear modulus G(ω)=G'(ω)-iG″(ω) was measured in HeLa cells in an epithelial-like confluent monolayer. We found that G(ω)∝(-iω)1/2 over a wide range of frequencies (1 Hz < ω/2π < 10 kHz). Actin disruption and cell-cycle progression from G1 to S and G2 phases only had a limited effect on G(ω) in living cells. On the other hand, G(ω) was found to be dependent on cell metabolism; ATP-depleted cells showed an increased elastic modulus G'(ω) at low frequencies, giving rise to a constant plateau such that G(ω)=G0+A(-iω)1/2. Both the plateau and the additional frequency dependency ∝(-iω)1/2 of ATP-depleted cells are consistent with a rheological response typical of colloidal jamming. On the other hand, the plateau G0 disappeared in ordinary metabolically active cells, implying that living cells fluidize their internal states such that they approach the critical jamming point.
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Affiliation(s)
- Hiroyuki Ebata
- Department of Physics, Kyushu University, Fukuoka, Japan
| | | | - Kenji Nishizawa
- Institute of Developmental Biology of Marseille, Marseille, France
| | - Wataru Nagao
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Shono Inokuchi
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Yujiro Sugino
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Takafumi Miyamoto
- Department of Endocrinology and Metabolism, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan; Transborder Medical Research Center, University of Tsukuba, Ibaraki, Japan
| | - Daisuke Mizuno
- Department of Physics, Kyushu University, Fukuoka, Japan.
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39
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Lemma LM, Varghese M, Ross TD, Thomson M, Baskaran A, Dogic Z. Spatio-temporal patterning of extensile active stresses in microtubule-based active fluids. PNAS NEXUS 2023; 2:pgad130. [PMID: 37168671 PMCID: PMC10165807 DOI: 10.1093/pnasnexus/pgad130] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 02/27/2023] [Accepted: 04/03/2023] [Indexed: 05/13/2023]
Abstract
Microtubule-based active fluids exhibit turbulent-like autonomous flows, which are driven by the molecular motor powered motion of filamentous constituents. Controlling active stresses in space and time is an essential prerequisite for controlling the intrinsically chaotic dynamics of extensile active fluids. We design single-headed kinesin molecular motors that exhibit optically enhanced clustering and thus enable precise and repeatable spatial and temporal control of extensile active stresses. Such motors enable rapid, reversible switching between flowing and quiescent states. In turn, spatio-temporal patterning of the active stress controls the evolution of the ubiquitous bend instability of extensile active fluids and determines its critical length dependence. Combining optically controlled clusters with conventional kinesin motors enables one-time switching from contractile to extensile active stresses. These results open a path towards real-time control of the autonomous flows generated by active fluids.
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Affiliation(s)
- Linnea M Lemma
- Department of Physics, Brandeis University, 415 South St., Waltham, 02453 MA, USA
- Department of Physics, University of California, Santa Barbara, 93106 CA, USA
| | - Minu Varghese
- Department of Physics, Brandeis University, 415 South St., Waltham, 02453 MA, USA
| | - Tyler D Ross
- Department of Computing and Mathematical Sciences, California Institute of Technology, 1200 E California Blvd. Pasadena, 91125 CA, USA
| | - Matt Thomson
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd., Pasadena, 91125 CA, USA
| | - Aparna Baskaran
- Department of Physics, Brandeis University, 415 South St., Waltham, 02453 MA, USA
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40
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Fernández Casafuz AB, De Rossi MC, Bruno L. Mitochondrial cellular organization and shape fluctuations are differentially modulated by cytoskeletal networks. Sci Rep 2023; 13:4065. [PMID: 36906690 PMCID: PMC10008531 DOI: 10.1038/s41598-023-31121-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/07/2023] [Indexed: 03/13/2023] Open
Abstract
The interactions between mitochondria and the cytoskeleton have been found to alter mitochondrial function; however, the mechanisms underlying this phenomenon are largely unknown. Here, we explored how the integrity of the cytoskeleton affects the cellular organization, morphology and mobility of mitochondria in Xenopus laevis melanocytes. Cells were imaged in control condition and after different treatments that selectively affect specific cytoskeletal networks (microtubules, F-actin and vimentin filaments). We observed that mitochondria cellular distribution and local orientation rely mostly on microtubules, positioning these filaments as the main scaffolding of mitochondrial organization. We also found that cytoskeletal networks mold mitochondria shapes in distinct ways: while microtubules favor more elongated organelles, vimentin and actin filaments increase mitochondrial bending, suggesting the presence of mechanical interactions between these filaments and mitochondria. Finally, we identified that microtubule and F-actin networks play opposite roles in mitochondria shape fluctuations and mobility, with microtubules transmitting their jittering to the organelles and F-actin restricting the organelles motion. All our results support that cytoskeleton filaments interact mechanically with mitochondria and transmit forces to these organelles molding their movements and shapes.
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Affiliation(s)
- Agustina Belén Fernández Casafuz
- CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo (IC), Buenos Aires, 1428, Argentina
| | - María Cecilia De Rossi
- CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica (IQUIBICEN), Buenos Aires, 1428, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.
| | - Luciana Bruno
- CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo (IC), Buenos Aires, 1428, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.
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41
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Lee M, Hugonnet H, Lee MJ, Cho Y, Park Y. Optical trapping with holographically structured light for single-cell studies. BIOPHYSICS REVIEWS 2023; 4:011302. [PMID: 38505814 PMCID: PMC10903426 DOI: 10.1063/5.0111104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/25/2022] [Indexed: 03/21/2024]
Abstract
A groundbreaking work in 1970 by Arthur Ashkin paved the way for developing various optical trapping techniques. Optical tweezers have become an established method for the manipulation of biological objects, due to their noninvasiveness and precise controllability. Recent innovations are accelerating and now enable single-cell manipulation through holographic light structuring. In this review, we provide an overview of recent advances in optical tweezer techniques for studies at the individual cell level. Our review focuses on holographic optical tweezers that utilize active spatial light modulators to noninvasively manipulate live cells. The versatility of the technology has led to valuable integrations with microscopy, microfluidics, and biotechnological techniques for various single-cell studies. We aim to recapitulate the basic principles of holographic optical tweezers, highlight trends in their biophysical applications, and discuss challenges and future prospects.
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42
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Chen S, Markovich T, MacKintosh FC. Nonaffine Deformation of Semiflexible Polymer and Fiber Networks. PHYSICAL REVIEW LETTERS 2023; 130:088101. [PMID: 36898114 DOI: 10.1103/physrevlett.130.088101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Networks of semiflexible or stiff polymers such as most biopolymers are known to deform inhomogeneously when sheared. The effects of such nonaffine deformation have been shown to be much stronger than for flexible polymers. To date, our understanding of nonaffinity in such systems is limited to simulations or specific 2D models of athermal fibers. Here, we present an effective medium theory for nonaffine deformation of semiflexible polymer and fiber networks, which is general to both 2D and 3D and in both thermal and athermal limits. The predictions of this model are in good agreement with both prior computational and experimental results for linear elasticity. Moreover, the framework we introduce can be extended to address nonlinear elasticity and network dynamics.
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Affiliation(s)
- Sihan Chen
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Tomer Markovich
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
- School of Mechanical Engineering, Tel Aviv University, Tel Aviv 69978, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 69978, Israel
| | - Fred C MacKintosh
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
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43
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Paneru G, Tlusty T, Pak HK. Bona fide stochastic resonance under nonGaussian active fluctuations. SOFT MATTER 2023; 19:1356-1362. [PMID: 36723030 DOI: 10.1039/d2sm01449a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We report on the experimental observation of stochastic resonance (SR) in a nonGaussian active bath without any periodic modulation. A Brownian particle hopping in a nanoscale double-well potential under the influence of nonGaussian correlated noise, with mean interval τP and correlation time τc, shows a series of equally-spaced peaks in the residence time distribution at integral multiples of τP. The strength of the first peak is found to be maximum when the mean residence time d matches the double condition, 4τc ≈ τP ≈ d/2, demonstrating a new type of bona fide SR. The experimental findings agree with a simple model that explains the emergence of SR without periodic modulation of the double-well potential. Additionally, we show that generic SR under periodic modulation, known to degrade in strongly correlated continuous noise, is recovered by the discrete nonGaussian kicks.
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Affiliation(s)
- Govind Paneru
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea.
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Tsvi Tlusty
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea.
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Hyuk Kyu Pak
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea.
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
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44
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Kumar P, Chakrabarti R. Dynamics of self-propelled tracer particles inside a polymer network. Phys Chem Chem Phys 2023; 25:1937-1946. [PMID: 36541408 DOI: 10.1039/d2cp04253c] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The transport of tracer particles through mesh-like environments such as biological hydrogels and polymer matrices is ubiquitous in nature. These tracers can be passive, such as colloids, or active (self-propelled), for example, synthetic nanomotors or bacteria. Computer simulations in principle could be extremely useful in exploring the mechanism of the active transport of tracer particles through mesh-like environments. Therefore, we construct a polymer network on a diamond lattice and use computer simulations to investigate the dynamics of spherical self-propelled particles inside the network. Our main objective is to elucidate the effect of the self-propulsion on the tracer particle dynamics as a function of the tracer size and the stiffness of the polymer network. We compute the time-averaged mean-squared displacement (MSD) and the van-Hove correlations of the tracer. On the one hand, in the case of a bigger sticky particle, the caging caused by the network particles wins over the escape assisted by the self-propulsion. This results an intermediate-time subdiffusion. On the other hand, smaller tracers or tracers with high self-propulsion velocities can easily escape from the cages and show intermediate-time superdiffusion. The stiffer the network, the slower the dynamics of the tracer, and bigger tracers exhibit longer lived intermediate time superdiffusion, since the persistence time scales as ∼σ3, where σ is the diameter of the tracer. At the intermediate time, non-Gaussianity is more pronounced for active tracers. At the long time, the dynamics of the tracer, if passive or weakly active, becomes Gaussian and diffusive, but remains flat for tracers with high self-propulsion, accounting for their seemingly unrestricted motion inside the network.
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Affiliation(s)
- Praveen Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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Godec A, Makarov DE. Challenges in Inferring the Directionality of Active Molecular Processes from Single-Molecule Fluorescence Resonance Energy Transfer Trajectories. J Phys Chem Lett 2023; 14:49-56. [PMID: 36566432 DOI: 10.1021/acs.jpclett.2c03244] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We discuss some of the practical challenges that one faces in using stochastic thermodynamics to infer directionality of molecular machines from experimental single-molecule trajectories. Because of the limited spatiotemporal resolution of single-molecule experiments and because both forward and backward transitions between the same pairs of states cannot always be detected, differentiating between the forward and backward directions of, e.g., an ATP-consuming molecular machine that operates periodically, turns out to be a nontrivial task. Using a simple extension of a Markov-state model that is commonly employed to analyze single-molecule transition-path measurements, we illustrate how irreversibility can be hidden from such measurements but in some cases can be uncovered when non-Markov effects in low-dimensional single-molecule trajectories are considered.
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Affiliation(s)
- Aljaž Godec
- Mathematical bioPhysics Group, Max Planck Institute for Multidisciplinary Sciences, 37077Göttingen, Germany
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Guo T, Jiang CS, Yang SZ, Zhu Y, He C, Carter AB, Antony VB, Peng H, Zhou Y. Mitochondrial fission and bioenergetics mediate human lung fibroblast durotaxis. JCI Insight 2023; 8:e157348. [PMID: 36422990 PMCID: PMC9870082 DOI: 10.1172/jci.insight.157348] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Pulmonary fibrosis is characterized by stiffening of the extracellular matrix. Fibroblasts migrate in the direction of greater stiffness, a phenomenon termed durotaxis. The mechanically guided fibroblast migration could be a crucial step in the progression of lung fibrosis. In this study, we found primary human lung fibroblasts sense increasing matrix stiffness with a change of mitochondrial dynamics in favor of mitochondrial fission and increased production of ATP. Mitochondria polarize in the direction of a physiologically relevant stiffness gradient, with conspicuous localization to the leading edge, primarily lamellipodia and filopodia, of migrating lung fibroblasts. Matrix stiffness-regulated mitochondrial fission and durotactic lung fibroblast migration are mediated by a dynamin-related protein 1/mitochondrial fission factor-dependent (DRP1/MFF-dependent) pathway. Importantly, we found that the DRP1/MFF pathway is activated in fibrotic lung myofibroblasts in both human IPF and bleomycin-induced mouse lung fibrosis. These findings suggest that energy-producing mitochondria need to be sectioned via fission and repositioned in durotactic lung fibroblasts to meet the higher energy demand. This represents a potentially new mechanism through which mitochondria may contribute to the progression of fibrotic lung diseases. Inhibition of durotactic migration of lung fibroblasts may play an important role in preventing the progression of human idiopathic pulmonary fibrosis.
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Affiliation(s)
- Ting Guo
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Respiratory Medicine, the Second Xiangya Hospital, Central-South University, Changsha, China
| | - Chun-sun Jiang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Shan-Zhong Yang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yi Zhu
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Chao He
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - A. Brent Carter
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Birmingham Veterans Administration Medical Center, Birmingham, Alabama, USA
| | - Veena B. Antony
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Hong Peng
- Department of Respiratory Medicine, the Second Xiangya Hospital, Central-South University, Changsha, China
| | - Yong Zhou
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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47
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Tejedor AR, Carracedo R, Ramírez J. Molecular dynamics simulations of active entangled polymers reptating through a passive mesh. POLYMER 2023. [DOI: 10.1016/j.polymer.2023.125677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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48
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Rosenhouse-Dantsker A, Gazgalis D, Logothetis DE. PI(4,5)P 2 and Cholesterol: Synthesis, Regulation, and Functions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1422:3-59. [PMID: 36988876 DOI: 10.1007/978-3-031-21547-6_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is the most abundant membrane phosphoinositide and cholesterol is an essential component of the plasma membrane (PM). Both lipids play key roles in a variety of cellular functions including as signaling molecules and major regulators of protein function. This chapter provides an overview of these two important lipids. Starting from a brief description of their structure, synthesis, and regulation, the chapter continues to describe the primary functions and signaling processes in which PI(4,5)P2 and cholesterol are involved. While PI(4,5)P2 and cholesterol can act independently, they often act in concert or affect each other's impact. The chapters in this volume on "Cholesterol and PI(4,5)P2 in Vital Biological Functions: From Coexistence to Crosstalk" focus on the emerging relationship between cholesterol and PI(4,5)P2 in a variety of biological systems and processes. In this chapter, the next section provides examples from the ion channel field demonstrating that PI(4,5)P2 and cholesterol can act via common mechanisms. The chapter ends with a discussion of future directions.
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Affiliation(s)
| | - Dimitris Gazgalis
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, MA, USA
| | - Diomedes E Logothetis
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, MA, USA
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49
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Blache U, Ford EM, Ha B, Rijns L, Chaudhuri O, Dankers PY, Kloxin AM, Snedeker JG, Gentleman E. Engineered hydrogels for mechanobiology. NATURE REVIEWS. METHODS PRIMERS 2022; 2:98. [PMID: 37461429 PMCID: PMC7614763 DOI: 10.1038/s43586-022-00179-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 07/20/2023]
Abstract
Cells' local mechanical environment can be as important in guiding cellular responses as many well-characterized biochemical cues. Hydrogels that mimic the native extracellular matrix can provide these mechanical cues to encapsulated cells, allowing for the study of their impact on cellular behaviours. Moreover, by harnessing cellular responses to mechanical cues, hydrogels can be used to create tissues in vitro for regenerative medicine applications and for disease modelling. This Primer outlines the importance and challenges of creating hydrogels that mimic the mechanical and biological properties of the native extracellular matrix. The design of hydrogels for mechanobiology studies is discussed, including appropriate choice of cross-linking chemistry and strategies to tailor hydrogel mechanical cues. Techniques for characterizing hydrogels are explained, highlighting methods used to analyze cell behaviour. Example applications for studying fundamental mechanobiological processes and regenerative therapies are provided, along with a discussion of the limitations of hydrogels as mimetics of the native extracellular matrix. The article ends with an outlook for the field, focusing on emerging technologies that will enable new insights into mechanobiology and its role in tissue homeostasis and disease.
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Affiliation(s)
- Ulrich Blache
- Fraunhofer Institute for Cell Therapy and Immunology and Fraunhofer Cluster of Excellence for Immune-Mediated Disease, Leipzig, Germany
| | - Eden M. Ford
- Department of Chemical and Biomolecular Engineering, University of Delaware, DE, USA
| | - Byunghang Ha
- Department of Mechanical Engineering, Stanford University, CA, USA
| | - Laura Rijns
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Laboratory of Chemical Biology, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Ovijit Chaudhuri
- Department of Mechanical Engineering, Stanford University, CA, USA
| | - Patricia Y.W. Dankers
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Laboratory of Chemical Biology, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - April M. Kloxin
- Department of Chemical and Biomolecular Engineering, University of Delaware, DE, USA
- Department of Material Science and Engineering, University of Delaware, DE, USA
| | - Jess G. Snedeker
- University Hospital Balgrist and ETH Zurich, Zurich, Switzerland
| | - Eileen Gentleman
- Centre for Craniofacial and Regenerative Biology, King’s College London, London SE1 9RT, UK
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50
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Erlich A, Étienne J, Fouchard J, Wyatt T. How dynamic prestress governs the shape of living systems, from the subcellular to tissue scale. Interface Focus 2022; 12:20220038. [PMID: 36330322 PMCID: PMC9560792 DOI: 10.1098/rsfs.2022.0038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/08/2022] [Indexed: 10/16/2023] Open
Abstract
Cells and tissues change shape both to carry out their function and during pathology. In most cases, these deformations are driven from within the systems themselves. This is permitted by a range of molecular actors, such as active crosslinkers and ion pumps, whose activity is biologically controlled in space and time. The resulting stresses are propagated within complex and dynamical architectures like networks or cell aggregates. From a mechanical point of view, these effects can be seen as the generation of prestress or prestrain, resulting from either a contractile or growth activity. In this review, we present this concept of prestress and the theoretical tools available to conceptualize the statics and dynamics of living systems. We then describe a range of phenomena where prestress controls shape changes in biopolymer networks (especially the actomyosin cytoskeleton and fibrous tissues) and cellularized tissues. Despite the diversity of scale and organization, we demonstrate that these phenomena stem from a limited number of spatial distributions of prestress, which can be categorized as heterogeneous, anisotropic or differential. We suggest that in addition to growth and contraction, a third type of prestress-topological prestress-can result from active processes altering the microstructure of tissue.
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Affiliation(s)
| | - Jocelyn Étienne
- Université Grenoble Alpes, CNRS, LIPHY, 38000 Grenoble, France
| | - Jonathan Fouchard
- Laboratoire de Biologie du Développement, Institut de Biologie Paris Seine (IBPS), Sorbonne Université, CNRS (UMR 7622), INSERM (URL 1156), 7 quai Saint Bernard, 75005 Paris, France
| | - Tom Wyatt
- Wellcome Trust–Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
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