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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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2
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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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3
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Lu D, Chen B. Coordinated motion of molecular motors on DNA chains with branch topology. ACTA MECHANICA SINICA = LI XUE XUE BAO 2022; 38:621225. [PMID: 35601132 PMCID: PMC9109741 DOI: 10.1007/s10409-021-09045-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/25/2021] [Indexed: 06/15/2023]
Abstract
To understand the macroscopic mechanical behaviors of responsive DNA hydrogels integrated with DNA motors, we constructed a state map for the translocation process of a single FtsKC on a single DNA chain at the molecular level and then investigated the movement of single or multiple FtsKC motors on DNA chains with varied branch topologies. Our studies indicate that multiple FtsKC motors can have coordinated motion, which is mainly due to the force-responsive behavior of individual FtsKC motors. We further suggest the potential application of motors of FtsKC, together with DNA chains of specific branch topology, to serve as strain sensors in hydrogels.
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Affiliation(s)
- Di Lu
- Department of Engineering Mechanics, Zhejiang University, Hangzhou, 310058 China
| | - Bin Chen
- Department of Engineering Mechanics, Zhejiang University, Hangzhou, 310058 China
- Key Laboratory of Soft Machines and Smart Devices of Zhejiang Province, Hangzhou, 310027 China
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4
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Affiliation(s)
- Dong Wang
- Department of Biological and Environmental Engineering Cornell University Ithaca New York 14853 USA
| | - Peifeng Liu
- State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200032 China
- Micro-Nano Research and Diagnosis Center Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Dan Luo
- Department of Biological and Environmental Engineering Cornell University Ithaca New York 14853 USA
- Kavli Institute at Cornell for Nanoscale Science Cornell University Ithaca New York 14853 USA
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5
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Senoussi A, Galas JC, Estevez-Torres A. Programmed mechano-chemical coupling in reaction-diffusion active matter. SCIENCE ADVANCES 2021; 7:eabi9865. [PMID: 34919433 PMCID: PMC8682988 DOI: 10.1126/sciadv.abi9865] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Embryo morphogenesis involves a complex combination of self-organization mechanisms that generate a great diversity of patterns. However, classical in vitro patterning experiments explore only one self-organization mechanism at a time, thus missing coupling effects. Here, we conjugate two major out-of-equilibrium patterning mechanisms—reaction-diffusion and active matter—by integrating dissipative DNA/enzyme reaction networks within an active gel composed of cytoskeletal motors and filaments. We show that the strength of the flow generated by the active gel controls the mechano-chemical coupling between the two subsystems. This property was used to engineer a synthetic material where contractions trigger chemical reaction networks both in time and space, thus mimicking key aspects of the polarization mechanism observed in C. elegans oocytes. We anticipate that reaction-diffusion active matter will promote the investigation of mechano-chemical transduction and the design of new materials with life-like properties.
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6
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Abstract
The eukaryotic cell's cytoskeleton is a prototypical example of an active material: objects embedded within it are driven by molecular motors acting on the cytoskeleton, leading to anomalous diffusive behavior. Experiments tracking the behavior of cell-attached objects have observed anomalous diffusion with a distribution of displacements that is non-Gaussian, with heavy tails. This has been attributed to "cytoquakes" or other spatially extended collective effects. We show, using simulations and analytical theory, that a simple continuum active gel model driven by fluctuating force dipoles naturally creates heavy power-law tails in cytoskeletal displacements. We predict that this power law exponent should depend on the geometry and dimensionality of where force dipoles are distributed through the cell; we find qualitatively different results for force dipoles in a 3D cytoskeleton and a quasi-two-dimensional cortex. We then discuss potential applications of this model both in cells and in synthetic active gels.
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Affiliation(s)
- Daniel W Swartz
- Department of Physics and Astronomy, Johns Hopkins University, USA
- Department of Physics, Massachusetts Institute of Technology, USA
| | - Brian A Camley
- Department of Physics and Astronomy, Johns Hopkins University, USA
- Department of Biophysics, Johns Hopkins University, USA
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7
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Gangrade A, Stephanopoulos N, Bhatia D. Programmable, self-assembled DNA nanodevices for cellular programming and tissue engineering. NANOSCALE 2021; 13:16834-16846. [PMID: 34622910 DOI: 10.1039/d1nr04475c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
DNA-based nanotechnology has evolved into an autonomous, highly innovative, and dynamic field of research at the nexus of supramolecular chemistry, nanotechnology, materials science, and biotechnology. DNA-based materials, including origami nanodevices, have started to emerge as an ideal scaffold for use in cellular programming, tissue engineering, and drug delivery applications. We cover herein the applications for DNA as a scaffold for interfacing with, and guiding, the activity of biological systems like cells and tissues. Although DNA is a highly programmable molecular building block, it suffers from a lack of functional capacity for guiding and modulating cells. Coupling DNA to biologically active molecules can bestow bioactivity to these nanodevices. The main goal of such nanodevices is to synthesize systems that can bind to cells and mimic the extracellular environment, and serve as a highly promising toolbox for multiple applications in cellular programming and tissue engineering. DNA-based programmable devices offer a highly promising approach for programming collections of cells, tissue engineering, and regenerative medicine applications.
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Affiliation(s)
- Ankit Gangrade
- Biological Engineering, Indian Institute of Technology Gandhinagar, India.
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA
| | - Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, India.
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, India
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8
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Wang D, Liu P, Luo D. Putting DNA to Work as Generic Polymeric Materials. Angew Chem Int Ed Engl 2021; 61:e202110666. [PMID: 34545660 DOI: 10.1002/anie.202110666] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Indexed: 01/10/2023]
Abstract
DNA is a true polymer that stores the genetic information of an organism. With its amazing biological and polymeric characteristics, DNA has been regarded as a universal building block for the construction of diverse materials for real-world applications. Through various approaches including ligation, polymerization, chemical crosslinking, and physical crosslinking, both pure and hybrid DNA gels have been developed as generic materials. This Review discusses recent advances in the construction of DNA-based networks without considering any of DNA's genetic properties. In addition, we highlight the biomedical and non-biomedical applications of DNA as generic materials. Owing to the superb molecular recognition, self-assembly, and responsiveness of DNA, a mushrooming number of DNA materials with various properties have been developed for general utilization.
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Affiliation(s)
- Dong Wang
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, 14853, USA
| | - Peifeng Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, China.,Micro-Nano Research and Diagnosis Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Dan Luo
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, 14853, USA.,Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York, 14853, USA
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9
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Mizuno D, Tardin C, Schmidt CF. Rapid local compression in active gels is caused by nonlinear network response. SOFT MATTER 2020; 16:9369-9382. [PMID: 32945304 DOI: 10.1039/c9sm02362c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The actin cytoskeleton in living cells generates forces in conjunction with myosin motor proteins to directly and indirectly drive essential cellular processes. The semiflexible filaments of the cytoskeleton can respond nonlinearly to the collective action of motors. We here investigate mechanics and force generation in a model actin cytoskeleton, reconstituted in vitro, by observing the response and fluctuations of embedded micron-scale probe particles. Myosin mini-filaments can be modeled as force dipoles and give rise to deformations in the surrounding network of cross-linked actin. Anomalously correlated probe fluctuations indicate the presence of rapid local compression or draining of the network that emerges in addition to the ordinary linear shear elastic (incompressible) response to force dipoles. The anomalous propagation of compression can be attributed to the nonlinear response of actin filaments to the microscopic forces, and is quantitatively consistent with motor-generated large-scale stiffening of the gels.
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Affiliation(s)
- D Mizuno
- Department of Physics, Kyushu University, 819-0395 Fukuoka, Japan
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10
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Enzymatic degradation of liquid droplets of DNA is modulated near the phase boundary. Proc Natl Acad Sci U S A 2020; 117:16160-16166. [PMID: 32601183 DOI: 10.1073/pnas.2001654117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Biomolecules can undergo liquid-liquid phase separation (LLPS), forming dense droplets that are increasingly understood to be important for cellular function. Analogous systems are studied as early-life compartmentalization mechanisms, for applications as protocells, or as drug-delivery vehicles. In many of these situations, interactions between the droplet and enzymatic solutes are important to achieve certain functions. To explore this, we carried out experiments in which a model LLPS system, formed from DNA "nanostar" particles, interacted with a DNA-cleaving restriction enzyme, SmaI, whose activity degraded the droplets, causing them to shrink with time. By controlling adhesion of the DNA droplet to a glass surface, we were able to carry out time-resolved imaging of this "active dissolution" process. We found that the scaling properties of droplet shrinking were sensitive to the proximity to the dissolution ("boiling") temperature of the dense liquid: For systems far from the boiling point, enzymes acted only on the droplet surface, while systems poised near the boiling point permitted enzyme penetration. This was corroborated by the observation of enzyme-induced vacuole-formation ("bubbling") events, which can only occur through enzyme internalization, and which occurred only in systems poised near the boiling point. Overall, our results demonstrate a mechanism through which the phase stability of a liquid affects its enzymatic degradation through modulation of enzyme transport properties.
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11
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Mura F, Gradziuk G, Broedersz CP. Mesoscopic non-equilibrium measures can reveal intrinsic features of the active driving. SOFT MATTER 2019; 15:8067-8076. [PMID: 31576897 DOI: 10.1039/c9sm01169b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biological assemblies such as chromosomes, membranes, and the cytoskeleton are driven out of equilibrium at the nanoscale by enzymatic activity and molecular motors. Similar non-equilibrium dynamics can be realized in synthetic systems, such as chemically fueled colloidal particles. Characterizing the stochastic non-equilibrium dynamics of such active soft assemblies still remains a challenge. Recently, new non-invasive approaches have been proposed to determine the non-equilibrium behavior, which are based on detecting broken detailed balance in the stochastic trajectories of several coordinates of the system. Inspired by the method of two-point microrheology, in which the equilibrium fluctuations of a pair of probe particles reveal the viscoelastic response of an equilibrium system, here, we investigate whether we can extend such an approach to non-equilibrium assemblies: can one extract information on the nature of the active driving in a system from the analysis of a two-point non-equilibrium measure? We address this question theoretically in the context of a class of elastic systems, driven out of equilibrium by a spatially heterogeneous stochastic internal driving. We consider several scenarios for the spatial features of the internal driving that may be relevant in biological and synthetic systems, and investigate how such features of the active noise may be reflected in the long-range scaling behavior of two-point non-equilibrium measures.
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Affiliation(s)
- Federica Mura
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, D-80333 München, Germany.
| | - Grzegorz Gradziuk
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, D-80333 München, Germany.
| | - Chase P Broedersz
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, D-80333 München, Germany.
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12
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Gradziuk G, Mura F, Broedersz CP. Scaling behavior of nonequilibrium measures in internally driven elastic assemblies. Phys Rev E 2019; 99:052406. [PMID: 31212437 DOI: 10.1103/physreve.99.052406] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Indexed: 11/07/2022]
Abstract
Detecting and quantifying nonequilibrium activity is essential for studying internally driven assemblies, including synthetic active matter and complex living systems such as cells or tissue. We discuss a noninvasive approach of measuring nonequilibrium behavior based on the breaking of detailed balance. We focus on "cycling frequencies"-the average frequency with which the trajectories of pairs of degrees of freedom revolve in phase space-and explain their connection with other nonequilibrium measures, including the area enclosing rate and the entropy production rate. We test our approach on simple toy models composed of elastic networks immersed in a viscous fluid with site-dependent internal driving. We prove both numerically and analytically that the cycling frequencies obey a power law as a function of distance between the tracked degrees of freedom. Importantly, the behavior of the cycling frequencies contains information about the dimensionality of the system and the amplitude of active noise. The mapping we use in our analytical approach thus offers a convenient framework for predicting the behavior of two-point nonequilibrium measures for a given activity distribution in the network.
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Affiliation(s)
- Grzegorz Gradziuk
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, D-80333 München, Germany
| | - Federica Mura
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, D-80333 München, Germany
| | - Chase P Broedersz
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, D-80333 München, Germany
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13
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Witzel P, Götz M, Lanoiselée Y, Franosch T, Grebenkov DS, Heinrich D. Heterogeneities Shape Passive Intracellular Transport. Biophys J 2019; 117:203-213. [PMID: 31278001 DOI: 10.1016/j.bpj.2019.06.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/22/2019] [Accepted: 06/11/2019] [Indexed: 01/06/2023] Open
Abstract
A living cell's interior is one of the most complex and intrinsically dynamic systems, providing an elaborate interplay between cytosolic crowding and ATP-driven motion that controls cellular functionality. Here, we investigated two distinct fundamental features of the merely passive, non-biomotor-shuttled material transport within the cytoplasm of Dictyostelium discoideum cells: the anomalous non-linear scaling of the mean-squared displacement of a 150-nm-diameter particle and non-Gaussian distribution of increments. Relying on single-particle tracking data of 320,000 data points, we performed a systematic analysis of four possible origins for non-Gaussian transport: 1) sample-based variability, 2) rarely occurring strong motion events, 3) ergodicity breaking/aging, and 4) spatiotemporal heterogeneities of the intracellular medium. After excluding the first three reasons, we investigated the remaining hypothesis of a heterogeneous cytoplasm as cause for non-Gaussian transport. A, to our knowledge, novel fit model with randomly distributed diffusivities implementing medium heterogeneities suits the experimental data. Strikingly, the non-Gaussian feature is independent of the cytoskeleton condition and lag time. This reveals that efficiency and consistency of passive intracellular transport and the related anomalous scaling of the mean-squared displacement are regulated by cytoskeleton components, whereas cytoplasmic heterogeneities are responsible for the generic, non-Gaussian distribution of increments.
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Affiliation(s)
- Patrick Witzel
- Faculty for Chemistry and Pharmacy, Julius-Maximilians-Universität Würzburg, Würzburg, Germany; Fraunhofer Institute for Silicate Research ISC, Würzburg, Germany
| | - Maria Götz
- Faculty for Chemistry and Pharmacy, Julius-Maximilians-Universität Würzburg, Würzburg, Germany; Fraunhofer Institute for Silicate Research ISC, Würzburg, Germany
| | - Yann Lanoiselée
- Laboratoire de Physique de la Matière Condensée, CNRS-Ecole Polytechnique, Palaiseau, France
| | - Thomas Franosch
- Institut für Theoretische Physik, Universität Innsbruck, Innsbruck, Austria
| | - Denis S Grebenkov
- Laboratoire de Physique de la Matière Condensée, CNRS-Ecole Polytechnique, Palaiseau, France
| | - Doris Heinrich
- Fraunhofer Institute for Silicate Research ISC, Würzburg, Germany; Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, the Netherlands.
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14
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Bacca M, Saleh OA, McMeeking RM. Contraction of polymer gels created by the activity of molecular motors. SOFT MATTER 2019; 15:4467-4475. [PMID: 31139780 DOI: 10.1039/c8sm02598c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We propose a theory based on non-equilibrium thermodynamics to describe the mechanical behavior of an active polymer gel created by the inclusion of molecular motors in its solvent. When activated, these motors attach to the chains of the polymer network and shorten them creating a global contraction of the gel, which mimics the active behavior of a cytoskeleton. The power generated by these motors is obtained by an ATP hydrolysis reaction, which transduces chemical energy into mechanical work. The latter is described by an increment of strain energy in the gel due to an increased stiffness. This effect is described with an increment of the cross-link density in the polymer network, which reduces its entropy. The theory then considers polymer network swelling and species diffusion to describe the transient passive behavior of the gel. We finally formulate the problem of uniaxial contraction of a slab of gel and compare the results with experiments, showing good agreement.
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Affiliation(s)
- Mattia Bacca
- Mechanical Engineering Department, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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15
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Gnesotto FS, Mura F, Gladrow J, Broedersz CP. Broken detailed balance and non-equilibrium dynamics in living systems: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:066601. [PMID: 29504517 DOI: 10.1088/1361-6633/aab3ed] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as high-fidelity transcription and translation, sensing, adaptation, biochemical patterning, and force generation. While biological systems such as motor enzymes violate detailed balance at the molecular scale, it remains unclear how non-equilibrium dynamics manifests at the mesoscale in systems that are driven through the collective activity of many motors. Indeed, in several cellular systems the presence of non-equilibrium dynamics is not always evident at large scales. For example, in the cytoskeleton or in chromosomes one can observe stationary stochastic processes that appear at first glance thermally driven. This raises the question how non-equilibrium fluctuations can be discerned from thermal noise. We discuss approaches that have recently been developed to address this question, including methods based on measuring the extent to which the system violates the fluctuation-dissipation theorem. We also review applications of this approach to reconstituted cytoskeletal networks, the cytoplasm of living cells, and cell membranes. Furthermore, we discuss a more recent approach to detect actively driven dynamics, which is based on inferring broken detailed balance. This constitutes a non-invasive method that uses time-lapse microscopy data, and can be applied to a broad range of systems in cells and tissue. We discuss the ideas underlying this method and its application to several examples including flagella, primary cilia, and cytoskeletal networks. Finally, we briefly discuss recent developments in stochastic thermodynamics and non-equilibrium statistical mechanics, which offer new perspectives to understand the physics of living systems.
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Affiliation(s)
- F S Gnesotto
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, D-80333 München, Germany
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16
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Schaffter SW, Green LN, Schneider J, Subramanian HKK, Schulman R, Franco E. T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures. Nucleic Acids Res 2018; 46:5332-5343. [PMID: 29718412 PMCID: PMC6007251 DOI: 10.1093/nar/gky283] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 12/18/2022] Open
Abstract
The use of proteins that bind and catalyze reactions with DNA alongside DNA nanostructures has broadened the functionality of DNA devices. DNA binding proteins have been used to specifically pattern and tune structural properties of DNA nanostructures and polymerases have been employed to directly and indirectly drive structural changes in DNA structures and devices. Despite these advances, undesired and poorly understood interactions between DNA nanostructures and proteins that bind DNA continue to negatively affect the performance and stability of DNA devices used in conjunction with enzymes. A better understanding of these undesired interactions will enable the construction of robust DNA nanostructure-enzyme hybrid systems. Here, we investigate the undesired disassembly of DNA nanotubes in the presence of viral RNA polymerases (RNAPs) under conditions used for in vitro transcription. We show that nanotubes and individual nanotube monomers (tiles) are non-specifically transcribed by T7 RNAP, and that RNA transcripts produced during non-specific transcription disassemble the nanotubes. Disassembly requires a single-stranded overhang on the nanotube tiles where transcripts can bind and initiate disassembly through strand displacement, suggesting that single-stranded domains on other DNA nanostructures could cause unexpected interactions in the presence of viral RNA polymerases.
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Affiliation(s)
- Samuel W Schaffter
- Department of Chemical and Biomolecular Engineering – Johns Hopkins University
| | - Leopold N Green
- Department of Mechanical Engineering – University of California - Riverside
| | - Joanna Schneider
- Department of Chemical and Biomolecular Engineering – Johns Hopkins University
| | | | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering – Johns Hopkins University
- Department of Computer Science – Johns Hopkins University
| | - Elisa Franco
- Department of Mechanical Engineering – University of California - Riverside
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17
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Córdoba A. The Effects of the Interplay between Motor and Brownian Forces on the Rheology of Active Gels. J Phys Chem B 2018; 122:4267-4277. [PMID: 29578713 DOI: 10.1021/acs.jpcb.8b00238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Active gels perform key mechanical roles inside the cell, such as cell division, motion, and force sensing. The unique mechanical properties required to perform such functions arise from the interactions between molecular motors and semiflexible polymeric filaments. Molecular motors can convert the energy released in the hydrolysis of ATP into forces of up to piconewton magnitudes. Moreover, the polymeric filaments that form active gels are flexible enough to respond to Brownian forces but also stiff enough to support the large tensions induced by the motor-generated forces. Brownian forces are expected to have a significant effect especially at motor activities at which stable noncontractile in vitro active gels are prepared for rheological measurements. Here, a microscopic mean-field theory of active gels originally formulated in the limit of motor-dominated dynamics is extended to include Brownian forces. In the model presented here, Brownian forces are included accurately, at real room temperature, even in systems with high motor activity. It is shown that a subtle interplay, or competition, between motor-generated forces and Brownian forces has an important impact on the mass transport and rheological properties of active gels. The model predictions show that at low frequencies the dynamic modulus of active gels is determined mostly by motor protein dynamics. However, Brownian forces significantly increase the breadth of the relaxation spectrum and can affect the shape of the dynamic modulus over a wide frequency range even for ratios of motor to Brownian forces of more than a hundred. Since the ratio between motor and Brownian forces is sensitive to ATP concentration, the results presented here shed some light on how the transient mechanical response of active gels changes with varying ATP concentration.
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Affiliation(s)
- Andrés Córdoba
- Department of Chemical Engineering , Universidad de Concepción , Concepción , Chile
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18
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Tom AM, Rajesh R, Vemparala S. Aggregation of flexible polyelectrolytes: Phase diagram and dynamics. J Chem Phys 2017; 147:144903. [DOI: 10.1063/1.4993684] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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19
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Alvarado J, Sheinman M, Sharma A, MacKintosh FC, Koenderink GH. Force percolation of contractile active gels. SOFT MATTER 2017; 13:5624-5644. [PMID: 28812094 DOI: 10.1039/c7sm00834a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Living systems provide a paradigmatic example of active soft matter. Cells and tissues comprise viscoelastic materials that exert forces and can actively change shape. This strikingly autonomous behavior is powered by the cytoskeleton, an active gel of semiflexible filaments, crosslinks, and molecular motors inside cells. Although individual motors are only a few nm in size and exert minute forces of a few pN, cells spatially integrate the activity of an ensemble of motors to produce larger contractile forces (∼nN and greater) on cellular, tissue, and organismal length scales. Here we review experimental and theoretical studies on contractile active gels composed of actin filaments and myosin motors. Unlike other active soft matter systems, which tend to form ordered patterns, actin-myosin systems exhibit a generic tendency to contract. Experimental studies of reconstituted actin-myosin model systems have long suggested that a mechanical interplay between motor activity and the network's connectivity governs this contractile behavior. Recent theoretical models indicate that this interplay can be understood in terms of percolation models, extended to include effects of motor activity on the network connectivity. Based on concepts from percolation theory, we propose a state diagram that unites a large body of experimental observations. This framework provides valuable insights into the mechanisms that drive cellular shape changes and also provides design principles for synthetic active materials.
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Affiliation(s)
- José Alvarado
- Systems Biophysics Department, AMOLF, 1098 XG Amsterdam, The Netherlands.
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20
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Merindol R, Walther A. Materials learning from life: concepts for active, adaptive and autonomous molecular systems. Chem Soc Rev 2017; 46:5588-5619. [DOI: 10.1039/c6cs00738d] [Citation(s) in RCA: 288] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A broad overview of functional aspects in biological and synthetic out-of-equilibrium systems.
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Affiliation(s)
- Rémi Merindol
- Institute for Macromolecular Chemistry
- Albert-Ludwigs-University Freiburg
- 79106 Freiburg
- Germany
| | - Andreas Walther
- Institute for Macromolecular Chemistry
- Albert-Ludwigs-University Freiburg
- 79106 Freiburg
- Germany
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21
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Taylor N, Elbaum-Garfinkle S, Vaidya N, Zhang H, Stone HA, Brangwynne CP. Biophysical characterization of organelle-based RNA/protein liquid phases using microfluidics. SOFT MATTER 2016; 12:9142-9150. [PMID: 27791212 PMCID: PMC6724727 DOI: 10.1039/c6sm01087c] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Living cells contain numerous membrane-less RNA/protein (RNP) bodies that assemble by intracellular liquid-liquid phase separation. The properties of these condensed phase droplets are increasingly recognized as important in their physiological function within living cells, and also through the link to protein aggregation pathologies. However, techniques such as droplet coalescence analysis or standard microrheology do not always enable robust property measurements of model RNA/protein droplets in vitro. Here, we introduce a microfluidic platform that drives protein droplets into a single large phase, which facilitates viscosity measurements using passive microrheology and/or active two-phase flow analysis. We use this technique to study various phase separating proteins from structures including P granules, nucleoli, and Whi3 droplets. In each case, droplets exhibit simple liquid behavior, with shear rate-independent viscosities, over observed timescales. Interestingly, we find that a reported order of magnitude difference between the timescale of Whi3 and LAF-1 droplet coalescence is driven by large differences in surface tension rather than viscosity, with implications for droplet assembly and function. The ability to simultaneously perform active and passive microrheological measurements enables studying the impact of ATP-dependent biological activity on RNP droplets, which is a key area for future research.
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Affiliation(s)
- Nicole Taylor
- Department of Chemical and Biological Engineering, Princeton University, USA.
| | | | - Nilesh Vaidya
- Department of Chemical and Biological Engineering, Princeton University, USA.
| | - Huaiying Zhang
- Department of Chemical and Biological Engineering, Princeton University, USA.
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, USA
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22
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Park CY, Fygenson DK, Saleh OA. Electrostatics and depletion determine competition between 2D nematic and 3D bundled phases of rod-like DNA nanotubes. SOFT MATTER 2016; 12:5089-5095. [PMID: 27126684 DOI: 10.1039/c6sm00222f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Rod-like particles form solutions of technological and biological importance. In particular, biofilaments such as actin and microtubules are known to form a variety of phases, both in vivo and in vitro, whose appearance can be controlled by depletion, confinement, and electrostatic interactions. Here, we utilize DNA nanotubes to undertake a comprehensive study of the effects of those interactions on two particular rod-like phases: a 2D nematic phase consisting of aligned rods pressed against a glass surface, and a 3D bundled network phase. We experimentally measure the stability of these two phases over a range of depletant concentrations and ionic strengths, finding that the 2D phase is slightly more stable than the 3D phase. We formulate a quantitative model of phase stability based on consideration of pairwise rod-rod and rod-surface interactions; notably, we include a careful accounting of solution electrostatics interactions using an effective-charge strategy. The model is relatively simple and contains no free parameters, yet predicts phase boundaries in good agreement with the experiment. Our results indicate that electrostatic interactions, rather than depletion, are largely responsible for the enhanced stability of the 2D phase. This work provides insight into the polymorphism of rod-like solutions, indicating why certain phases appear, and providing a means (and a predictive model) for controlling those phases.
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Affiliation(s)
- Chang-Young Park
- Material Research Laboratory, University of California, Santa Barbara, CA 93106, USA
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23
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Tom AM, Rajesh R, Vemparala S. Aggregation dynamics of rigid polyelectrolytes. J Chem Phys 2016; 144:034904. [DOI: 10.1063/1.4939870] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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24
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Ben-Isaac E, Fodor É, Visco P, van Wijland F, Gov NS. Modeling the dynamics of a tracer particle in an elastic active gel. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:012716. [PMID: 26274211 DOI: 10.1103/physreve.92.012716] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Indexed: 06/04/2023]
Abstract
The internal dynamics of active gels both in artificial (in vitro) model systems and inside the cytoskeleton of living cells has been extensively studied with experiments of recent years. These dynamics are probed using tracer particles embedded in the network of biopolymers together with molecular motors, and distinct nonthermal behavior is observed. We present a theoretical model of the dynamics of a trapped active particle, which allows us to quantify the deviations from equilibrium behavior, using both analytic and numerical calculations. We map the different regimes of dynamics in this system and highlight the different manifestations of activity: breakdown of the virial theorem and equipartition, different elasticity-dependent "effective temperatures," and distinct non-Gaussian distributions. Our results shed light on puzzling observations in active gel experiments and provide physical interpretation of existing observations, as well as predictions for future studies.
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Affiliation(s)
- E Ben-Isaac
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - É Fodor
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS/P7, Université Paris Diderot, 10 rue Alice Domon et Léonie Duquet, 75205 Paris cedex 13, France
| | - P Visco
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS/P7, Université Paris Diderot, 10 rue Alice Domon et Léonie Duquet, 75205 Paris cedex 13, France
| | - F van Wijland
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS/P7, Université Paris Diderot, 10 rue Alice Domon et Léonie Duquet, 75205 Paris cedex 13, France
| | - Nir S Gov
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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25
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Sheinman M, Sharma A, Alvarado J, Koenderink GH, MacKintosh FC. Inherently unstable networks collapse to a critical point. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:012710. [PMID: 26274206 DOI: 10.1103/physreve.92.012710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 06/04/2023]
Abstract
Nonequilibrium systems that are driven or drive themselves towards a critical point have been studied for almost three decades. Here we present a minimalist example of such a system, motivated by experiments on collapsing active elastic networks. Our model of an unstable elastic network exhibits a collapse towards a critical point from any macroscopically connected initial configuration. Taking into account steric interactions within the network, the model qualitatively and quantitatively reproduces results of the experiments on collapsing active gels.
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Affiliation(s)
- M Sheinman
- Department of Physics and Astronomy, VU University, Amsterdam, The Netherlands
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - A Sharma
- Department of Physics and Astronomy, VU University, Amsterdam, The Netherlands
- Drittes Physikalisches Institut, Georg-August-Universitat Göttingen, Göttingen, Germany
| | - J Alvarado
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
- Department of Mechanical Engineering, Hatsopoulos Microfluids Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - G H Koenderink
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - F C MacKintosh
- Department of Physics and Astronomy, VU University, Amsterdam, The Netherlands
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26
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Vaca C, Shlomovitz R, Yang Y, Valentine MT, Levine AJ. Bond breaking dynamics in semiflexible networks under load. SOFT MATTER 2015; 11:4899-4911. [PMID: 26012737 DOI: 10.1039/c5sm00262a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We examine the bond-breaking dynamics of transiently cross-linked semiflexible networks using a single filament model in which that filament is peeled from an array of cross-linkers. We examine the effect of quenched disorder in the placement of the linkers along the filament and the effect of stochastic bond-breaking (assuming Bell model unbinding kinetics) on the dynamics of filament cross-linker dissociation and the statistics of ripping events. We find that bond forces decay exponentially away from the point of loading and that bond breaking proceeds sequentially down the linker array from the point of loading in a series of stochastic ripping events. We compare these theoretical predictions to the observed trajectories of large beads in a cross-linked microtubule network and identify the observed jumps of the bead with the linker rupture events predicted by the single filament model.
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Affiliation(s)
- Christian Vaca
- Department of Physics & Astronomy, UCLA, Los Angeles, CA 90005, USA.
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27
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Al-Kaidy H, Duwe A, Huster M, Muffler K, Schlegel C, Sieker T, Stadtmüller R, Tippkötter N, Ulber R. Biotechnology and Bioprocess Engineering - From the First Ullmann's Article to Recent Trends. CHEMBIOENG REVIEWS 2015. [DOI: 10.1002/cben.201500008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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28
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Ahmed WW, Fodor É, Betz T. Active cell mechanics: Measurement and theory. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:3083-94. [PMID: 26025677 DOI: 10.1016/j.bbamcr.2015.05.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/16/2015] [Accepted: 05/21/2015] [Indexed: 10/25/2022]
Abstract
Living cells are active mechanical systems that are able to generate forces. Their structure and shape are primarily determined by biopolymer filaments and molecular motors that form the cytoskeleton. Active force generation requires constant consumption of energy to maintain the nonequilibrium activity to drive organization and transport processes necessary for their function. To understand this activity it is necessary to develop new approaches to probe the underlying physical processes. Active cell mechanics incorporates active molecular-scale force generation into the traditional framework of mechanics of materials. This review highlights recent experimental and theoretical developments towards understanding active cell mechanics. We focus primarily on intracellular mechanical measurements and theoretical advances utilizing the Langevin framework. These developing approaches allow a quantitative understanding of nonequilibrium mechanical activity in living cells. This article is part of a Special Issue entitled: Mechanobiology.
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Affiliation(s)
- Wylie W Ahmed
- Institut Curie, Centre de recherche, 11, rue Pierre et Marie Curie, 75005 Paris, France; Sorbonne Universités, Université Pierre et Marie Curie, Paris, France; Centre National de la Recherche Scientifique, UMR168, Paris, France.
| | - Étienne Fodor
- Laboratoire Matière et Systèmes Complexes, UMR7057, Université Paris Diderot, 75013 Paris, France
| | - Timo Betz
- Institut Curie, Centre de recherche, 11, rue Pierre et Marie Curie, 75005 Paris, France; Sorbonne Universités, Université Pierre et Marie Curie, Paris, France; Centre National de la Recherche Scientifique, UMR168, Paris, France
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29
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Córdoba A, Schieber JD, Indei T. The role of filament length, finite-extensibility and motor force dispersity in stress relaxation and buckling mechanisms in non-sarcomeric active gels. SOFT MATTER 2015; 11:38-57. [PMID: 25375087 DOI: 10.1039/c4sm01944j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
After relaxing some assumptions we apply a single-chain mean-field mathematical model recently introduced [RSC Adv. (2014)] to describe the role of molecular motors in the mechanical properties of active gels. The model allows physics that are not available in models postulated on coarser levels of description. Moreover it proposes a level of description that allows the prediction of observables at time scales too difficult to achieve in multi-chain simulations for realistic filament lengths and densities. We model the semiflexible filaments that compose the active gel as bead-spring chains; molecular motors are accounted for by using a mean-field approach, in which filaments undergo transitions of one motor attachment state depending on the state of the probe filament. The level of description includes the end-to-end distance and attachment state of the filaments, and the motor-generated forces, as stochastic state variables which evolve according to a proposed differential Chapman-Kolmogorov equation. The motor-generated forces are drawn from a stationary distribution of motor stall forces. We consider bead-spring chains with multiple beads, explore the effect of finite-extensibility of the strands and incorporate into the model motor force distributions that have been measured experimentally. The model can no longer be solved analytically but is amenable to numerical simulation. This version of the model allows a more quantitative description of buckling dynamics [Lenz et. al. PRL, 2012, 108, 238107] and the dynamic modulus of active gels. The effect of finite extensibility of the filament strands on the dynamic modulus was also found to be in agreement with the microrheology experiments of Mizuno et. al., [Science, 2007, 315, 370-373].
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Affiliation(s)
- Andrés Córdoba
- Department of Chemical and Biological Engineering and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, 3440 S. Dearborn St, Chicago, Illinois 60616, USA.
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30
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Al-Kaidy H, Duwe A, Huster M, Muffler K, Schlegel C, Sieker T, Stadtmüller R, Tippkötter N, Ulber R. Biotechnologie und Bioverfahrenstechnik - Vom ersten Ullmanns Artikel bis hin zu aktuellen Forschungsthemen. CHEM-ING-TECH 2014. [DOI: 10.1002/cite.201400083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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31
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Kim J, Khetarpal I, Sen S, Murray RM. Synthetic circuit for exact adaptation and fold-change detection. Nucleic Acids Res 2014; 42:6078-89. [PMID: 24728988 PMCID: PMC4027175 DOI: 10.1093/nar/gku233] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Biological organisms use their sensory systems to detect changes in their environment. The ability of sensory systems to adapt to static inputs allows wide dynamic range as well as sensitivity to input changes including fold-change detection, a response that depends only on fold changes in input, and not on absolute changes. This input scale invariance underlies an important strategy for search that depends solely on the spatial profile of the input. Synthetic efforts to reproduce the architecture and response of cellular circuits provide an important step to foster understanding at the molecular level. We report the bottom-up assembly of biochemical systems that show exact adaptation and fold-change detection. Using a malachite green aptamer as the output, a synthetic transcriptional circuit with the connectivity of an incoherent feed-forward loop motif exhibits pulse generation and exact adaptation. A simple mathematical model was used to assess the amplitude and duration of pulse response as well as the parameter regimes required for fold-change detection. Upon parameter tuning, this synthetic circuit exhibits fold-change detection for four successive rounds of two-fold input changes. The experimental realization of fold-change detection circuit highlights the programmability of transcriptional switches and the ability to obtain predictive dynamical systems in a cell-free environment for technological applications.
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Affiliation(s)
- Jongmin Kim
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ishan Khetarpal
- Department of Computer Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Shaunak Sen
- Department of Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA
| | - Richard M Murray
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA Department of Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA
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32
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Córdoba A, Schieber JD, Indei T. A single-chain model for active gels I: active dumbbell model. RSC Adv 2014. [DOI: 10.1039/c4ra02262a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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33
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Sharma A, Sheinman M, Heidemann KM, MacKintosh FC. Elastic response of filamentous networks with compliant crosslinks. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:052705. [PMID: 24329294 DOI: 10.1103/physreve.88.052705] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Indexed: 06/03/2023]
Abstract
Experiments have shown that elasticity of disordered filamentous networks with compliant crosslinks is very different from networks with rigid crosslinks. Here, we model and analyze filamentous networks as a collection of randomly oriented rigid filaments connected to each other by flexible crosslinks that are modeled as wormlike chains. For relatively large extensions we allow for enthalpic stretching of crosslink backbones. We show that for sufficiently high crosslink density, the network linear elastic response is affine on the scale of the filaments' length. The nonlinear regime can become highly nonaffine and is characterized by a divergence of the elastic modulus at finite strain. In contrast to the prior predictions, we do not find an asymptotic regime in which the differential elastic modulus scales linearly with the stress, although an approximate linear dependence can be seen in a transition from entropic to enthalpic regimes. We discuss our results in light of recent experiments.
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Affiliation(s)
- A Sharma
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands
| | - M Sheinman
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands
| | - K M Heidemann
- Institute for Numerical and Applied Mathematics, Göttingen University, Germany
| | - F C MacKintosh
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands
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34
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Padirac A, Fujii T, Estévez-Torres A, Rondelez Y. Spatial waves in synthetic biochemical networks. J Am Chem Soc 2013; 135:14586-92. [PMID: 23731347 DOI: 10.1021/ja403584p] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We report the experimental observation of traveling concentration waves and spirals in a chemical reaction network built from the bottom up. The mechanism of the network is an oscillator of the predator-prey type, and this is the first time that predator-prey waves have been observed in the laboratory. The molecular encoding of the nonequilibrium behavior relies on small DNA oligonucleotides that enforce the network connectivity and three purified enzymes that control the reactivity. Wave velocities in the range 80-400 μm min(-1) were measured. A reaction-diffusion model in quantitative agreement with the experiments is proposed. Three fundamental parameters are easy to tune in nucleic acid reaction networks: the topology of the network, the rate constants of the individual reactions, and the diffusion coefficients of the individual species. For this reason, we expect such networks to bring unprecedented opportunities for assaying the principles of spatiotemporal order formation in chemistry.
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Affiliation(s)
- Adrien Padirac
- LIMMS/CNRS-IIS, The University of Tokyo , Komaba 4-6-2, Meguro-ku, Tokyo 153-8505, Japan
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