1
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Goychuk A, Kannan D, Kardar M. Delayed Excitations Induce Polymer Looping and Coherent Motion. PHYSICAL REVIEW LETTERS 2024; 133:078101. [PMID: 39213554 DOI: 10.1103/physrevlett.133.078101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/25/2024] [Accepted: 07/12/2024] [Indexed: 09/04/2024]
Abstract
We consider inhomogeneous polymers driven by energy-consuming active processes which encode temporal patterns of athermal kicks. We find that such temporal excitation programs, propagated by tension along the polymer, can effectively couple distinct polymer loci. Consequently, distant loci exhibit correlated motions that fold the polymer into specific conformations, as set by the local actions of the active processes and their distribution along the polymer. Interestingly, active kicks that are canceled out by a time-delayed echo can induce strong compaction of the active polymer.
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2
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Joshi K, York HM, Wright CS, Biswas RR, Arumugam S, Iyer-Biswas S. Emergent Spatiotemporal Organization in Stochastic Intracellular Transport Dynamics. Annu Rev Biophys 2024; 53:193-220. [PMID: 38346244 DOI: 10.1146/annurev-biophys-030422-044448] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The interior of a living cell is an active, fluctuating, and crowded environment, yet it maintains a high level of coherent organization. This dichotomy is readily apparent in the intracellular transport system of the cell. Membrane-bound compartments called endosomes play a key role in carrying cargo, in conjunction with myriad components including cargo adaptor proteins, membrane sculptors, motor proteins, and the cytoskeleton. These components coordinate to effectively navigate the crowded cell interior and transport cargo to specific intracellular locations, even though the underlying protein interactions and enzymatic reactions exhibit stochastic behavior. A major challenge is to measure, analyze, and understand how, despite the inherent stochasticity of the constituent processes, the collective outcomes show an emergent spatiotemporal order that is precise and robust. This review focuses on this intriguing dichotomy, providing insights into the known mechanisms of noise suppression and noise utilization in intracellular transport processes, and also identifies opportunities for future inquiry.
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Affiliation(s)
- Kunaal Joshi
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana, USA;
| | - Harrison M York
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia;
| | - Charles S Wright
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana, USA;
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia;
| | - Rudro R Biswas
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana, USA;
| | - Senthil Arumugam
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
- Single Molecule Science, University of New South Wales, Sydney, New South Wales, Australia
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia;
- European Molecular Biological Laboratory Australia (EMBL Australia), Monash University, Melbourne, Victoria, Australia
| | - Srividya Iyer-Biswas
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana, USA;
- Santa Fe Institute, Santa Fe, New Mexico, USA
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3
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Vos BE, Muenker TM, Betz T. Characterizing intracellular mechanics via optical tweezers-based microrheology. Curr Opin Cell Biol 2024; 88:102374. [PMID: 38824902 DOI: 10.1016/j.ceb.2024.102374] [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: 11/30/2023] [Revised: 04/24/2024] [Accepted: 05/03/2024] [Indexed: 06/04/2024]
Abstract
Intracellular organization is a highly regulated homeostatic state maintained to ensure eukaryotic cells' correct and efficient functioning. Thanks to decades of research, vast knowledge of the proteins involved in intracellular transport and organization has been acquired. However, how these influence and potentially regulate the intracellular mechanical properties of the cell is largely unknown. There is a deep knowledge gap between the understanding of cortical mechanics, which is accessible by a series of experimental tools, and the intracellular situation that has been largely neglected due to the difficulty of performing intracellular mechanics measurements. Recently, tools required for such quantitative and localized analysis of intracellular mechanics have been introduced. Here, we review how these approaches and the resulting viscoelastic models lead the way to a full mechanical description of the cytoplasm, which is instrumental for a quantitative characterization of the intracellular life of cells.
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Affiliation(s)
- Bart E Vos
- Third Institute of Physics, Georg August University, Göttingen, Germany
| | - Till M Muenker
- Third Institute of Physics, Georg August University, Göttingen, Germany
| | - Timo Betz
- Third Institute of Physics, Georg August University, Göttingen, Germany; Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), Georg August University, Göttingen, Germany.
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4
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Tan J, Zhu C, Li L, Wang J, Xia XH, Wang C. Engineering Cell Membranes: From Extraction Strategies to Emerging Biosensing Applications. Anal Chem 2024; 96:7880-7894. [PMID: 38272835 DOI: 10.1021/acs.analchem.3c01746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Affiliation(s)
- Jing Tan
- College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P.R. China
| | - Chengcheng Zhu
- College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P.R. China
| | - Lulu Li
- College of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212000, P.R. China
| | - Jin Wang
- College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P.R. China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, P.R. China
| | - Chen Wang
- College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P.R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, P.R. China
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5
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Zhang M, Zhang Z, Niu X, Ti H, Zhou Y, Gao B, Li Y, Liu J, Chen X, Li H. Interplay Between Intracellular Transport Dynamics and Liquid‒Liquid Phase Separation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308338. [PMID: 38447188 PMCID: PMC11109639 DOI: 10.1002/advs.202308338] [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: 11/02/2023] [Revised: 01/22/2024] [Indexed: 03/08/2024]
Abstract
Liquid‒liquid phase separation (LLPS) is a ubiquitous process in which proteins, RNA, and biomolecules assemble into membrane-less compartments, playing important roles in many biological functions and diseases. The current knowledge on the biophysical and biochemical principles of LLPS is largely from in vitro studies; however, the physiological environment in living cells is complex and not at equilibrium. The characteristics of intracellular dynamics and their roles in physiological LLPS remain to be resolved. Here, by using single-particle tracking of quantum dots and dynamic monitoring of the formation of stress granules (SGs) in single cells, the spatiotemporal dynamics of intracellular transport in cells undergoing LLPS are quantified. It is shown that intracellular diffusion and active transport are both reduced. Furthermore, the formation of SG droplets contributes to increased spatial heterogeneity within the cell. More importantly, the study demonstrated that the LLPS of SGs can be regulated by intracellular dynamics in two stages: the reduced intracellular diffusion promotes SG assembly and the microtubule-associated transport facilitates SG coalescences. The work on intracellular dynamics not only improves the understanding of the mechanism of physiology phase separations occurring in nonequilibrium environments but also reveals an interplay between intracellular dynamics and LLPS.
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Affiliation(s)
- Ming‐Li Zhang
- School of Systems Science and Institute of Nonequilibrium SystemsBeijing Normal UniversityBeijing100875China
| | - Ziheng Zhang
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Xue‐Zhi Niu
- School of Systems Science and Institute of Nonequilibrium SystemsBeijing Normal UniversityBeijing100875China
| | - Hui‐Ying Ti
- School of Systems Science and Institute of Nonequilibrium SystemsBeijing Normal UniversityBeijing100875China
| | - Yu‐Xuan Zhou
- School of Systems Science and Institute of Nonequilibrium SystemsBeijing Normal UniversityBeijing100875China
| | - Bo Gao
- School of Systems Science and Institute of Nonequilibrium SystemsBeijing Normal UniversityBeijing100875China
| | - Yiwei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics and Molecular Imaging Key LaboratoryDepartment of Biomedical EngineeringCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
| | - Ji‐Long Liu
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Xiaosong Chen
- School of Systems Science and Institute of Nonequilibrium SystemsBeijing Normal UniversityBeijing100875China
| | - Hui Li
- School of Systems Science and Institute of Nonequilibrium SystemsBeijing Normal UniversityBeijing100875China
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6
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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:S0006-3495(24)00287-X. [PMID: 38664967 DOI: 10.1016/j.bpj.2024.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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7
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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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8
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Dudas EF, Tully MD, Foldes T, Kelly G, Tartaglia GG, Pastore A. The structural properties of full-length annexin A11. Front Mol Biosci 2024; 11:1347741. [PMID: 38516187 PMCID: PMC10955470 DOI: 10.3389/fmolb.2024.1347741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/17/2024] [Indexed: 03/23/2024] Open
Abstract
Annexin A11 (ANXA11) is a calcium-dependent phospholipid-binding protein belonging to the annexin protein family and implicated in the neurodegenerative amyotrophic lateral sclerosis. Structurally, ANXA11 contains a conserved calcium-binding C-terminal domain common to all annexins and a putative intrinsically unfolded N-terminus specific for ANXA11. Little is known about the structure and functions of this region of the protein. By analogy with annexin A1, it was suggested that residues 38 to 59 within the ANXA11 N-terminus could form a helical region that would be involved in interactions. Interestingly, this region contains residues that, when mutated, may lead to clinical manifestations. In the present study, we have studied the structural features of the full-length protein with special attention to the N-terminal region using a combination of biophysical techniques which include nuclear magnetic resonance and small angle X-ray scattering. We show that the N-terminus is intrinsically disordered and that the overall features of the protein are not markedly affected by the presence of calcium. We also analyzed the 38-59 helix hypothesis using synthetic peptides spanning both the wild-type sequence and clinically relevant mutations. We show that the peptides have a remarkable character typical of a native helix and that mutations do not alter the behaviour suggesting that they are required for interactions rather than being structurally important. Our work paves the way to a more thorough understanding of the ANXA11 functions.
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Affiliation(s)
- Erika F. Dudas
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- European Synchrotron Radiation Facility, Grenoble, France
| | - Mark D. Tully
- European Synchrotron Radiation Facility, Grenoble, France
| | - Tamas Foldes
- University College London, Department of Physics and Astronomy, University College London, London, United Kingdom
- Institut de Biologie Structurale (IBS), Institut Laue-Langevin, University Grenoble Alpes, Grenoble, France
| | - Geoff Kelly
- MRC Biomedical NMR Centre, The Francis Crick Institute, London, United Kingdom
| | | | - Annalisa Pastore
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- European Synchrotron Radiation Facility, Grenoble, France
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9
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Szasz A. Peto's "Paradox" and Six Degrees of Cancer Prevalence. Cells 2024; 13:197. [PMID: 38275822 PMCID: PMC10814230 DOI: 10.3390/cells13020197] [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: 11/24/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Peto's paradox and the epidemiologic observation of the average six degrees of tumor prevalence are studied and hypothetically solved. A simple consideration, Petho's paradox challenges our intuitive understanding of cancer risk and prevalence. Our simple consideration is that the more a cell divides, the higher the chance of acquiring cancerous mutations, and so the larger or longer-lived organisms have more cells and undergo more cell divisions over their lifetime, expecting to have a higher risk of developing cancer. Paradoxically, it is not supported by the observations. The allometric scaling of species could answer the Peto paradox. Another paradoxical human epidemiology observation in six average mutations is necessary for cancer prevalence, despite the random expectations of the tumor causes. To solve this challenge, game theory could be applied. The inherited and random DNA mutations in the replication process nonlinearly drive cancer development. The statistical variance concept does not reasonably describe tumor development. Instead, the Darwinian natural selection principle is applied. The mutations in the healthy organism's cellular population can serve the species' evolutionary adaptation by the selective pressure of the circumstances. Still, some cells collect multiple uncorrected mutations, adapt to the extreme stress in the stromal environment, and develop subclinical phases of cancer in the individual. This process needs extensive subsequent DNA replications to heritage and collect additional mutations, which are only marginal alone. Still, together, they are preparing for the first stage of the precancerous condition. In the second stage, when one of the caretaker genes is accidentally mutated, the caused genetic instability prepares the cell to fight for its survival and avoid apoptosis. This can be described as a competitive game. In the third stage, the precancerous cell develops uncontrolled proliferation with the damaged gatekeeper gene and forces the new game strategy with binary cooperation with stromal cells for alimentation. In the fourth stage, the starving conditions cause a game change again, starting a cooperative game, where the malignant cells cooperate and force the cooperation of the stromal host, too. In the fifth stage, the resetting of homeostasis finishes the subclinical stage, and in the fifth stage, the clinical phase starts. The prevention of the development of mutated cells is more complex than averting exposure to mutagens from the environment throughout the organism's lifetime. Mutagenic exposure can increase the otherwise random imperfect DNA reproduction, increasing the likelihood of cancer development, but mutations exist. Toxic exposure is more challenging; it may select the tolerant cells on this particular toxic stress, so these mutations have more facility to avoid apoptosis in otherwise collected random mutational states.
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Affiliation(s)
- Andras Szasz
- Department of Biotechnics, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary
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10
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Cherayil BJ. Survival probabilities and first-passage distributions of self-propelled particles in spherical cavities. Phys Rev E 2023; 108:054607. [PMID: 38115486 DOI: 10.1103/physreve.108.054607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/05/2023] [Indexed: 12/21/2023]
Abstract
A model of self-propelled motion in a closed compartment containing simple or complex fluids is formulated in this paper in terms of the dynamics of a point particle moving in a spherical cavity under the action of random thermal forces and exponentially correlated noise. The particle's time evolution is governed by a generalized Langevin equation (GLE) in which the memory function, connected to the thermal forces by a fluctuation-dissipation relation, is described by Jeffrey's model of viscoelasticity (which reduces to a model of ordinary viscous dynamics in a suitable limit). The GLE is transformed exactly to a Fokker-Planck equation that in spherical polar coordinates is in turn found to admit of an exact solution for the particle's probability density function under absorbing boundary conditions at the surface of the sphere. The solution is used to derive an expression (that is also exact) for the survival probability of the particle in the sphere, starting from its center, which is then used to calculate the distribution of the particle's first-passage times to the boundary. The behavior of these quantities is investigated as a function of the Péclet number and the persistence time of the athermal forces, providing insight into the effects of nonequilibrium fluctuations on confined particle motion in three dimensions.
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Affiliation(s)
- Binny J Cherayil
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
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11
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Wu J, Xu C, Ye Z, Chen H, Wang Y, Yang K, Yuan B. Transition between Different Diffusion Modes of Individual Lipids during the Membrane-Specific Action of As-CATH4 Peptides. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2301713. [PMID: 37093200 DOI: 10.1002/smll.202301713] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/02/2023] [Indexed: 05/03/2023]
Abstract
The cell membrane permeabilization ability of immune defense antimicrobial peptides (AMPs) is widely applied in biomedicine. Although the mechanisms of peptide-membrane interactions have been widely investigated, analyses at the molecular level are still lacking. Herein, the membrane-specific action of a native AMP, As-CATH4, is investigated using a single-lipid tracking method in combination with live cell and model membrane assays conducted at different scales. The peptide-membrane interaction process is characterized by analyzing single-lipid diffusion behaviors. As-CATH4 exhibits potent antimicrobial activity through bacterial membrane permeabilization, with moderate cytotoxicity against mammalian cells. In-plane diffusion analyses of individual lipids show that the lipid molecules exhibit non-Gaussian and heterogeneous diffusion behaviors in both pristine and peptide-treated membranes, which can be decomposed into two Gaussian subgroups corresponding to normal- and slow-diffusive lipids. Assessment of the temporal evolution of these two diffusion modes of lipids reveal that the peptide action states of As-CATH4 include surface binding, transmembrane defect formation, and dynamic equilibrium. The action mechanisms of As-CATH4 at varying concentrations and against different membranes are distinguished. This work resolves the simultaneous mixed diffusion mechanisms of single lipids in biomimetic cell membranes, especially during dynamic membrane permeabilization by AMPs.
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Affiliation(s)
- Jinfeng Wu
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, 215006, P. R. China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, P. R. China
| | - Cheng Xu
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, 215006, P. R. China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, P. R. China
| | - Zifan Ye
- Department of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, P. R. China
| | - Haibo Chen
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, 215006, P. R. China
| | - Yipeng Wang
- Department of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, P. R. China
| | - Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, 215006, P. R. China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, P. R. China
| | - Bing Yuan
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, P. R. China
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12
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Wohl I, Sajman J, Sherman E. Cell Surface Vibrations Distinguish Malignant from Benign Cells. Cells 2023; 12:1901. [PMID: 37508565 PMCID: PMC10378100 DOI: 10.3390/cells12141901] [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: 06/23/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
The mechanical properties of living cells, including their shape, rigidity, and internal dynamics play a crucial role in their physiology and pathology. Still, the relations between the physiological cell state and its rigidity and surface vibrations remain poorly understood. Here, we have employed AFM measurements on T cells and found a negative relation between cell surface stiffness and its vibrations. Blocking T-type Ca++-channels using Mibefradil reduced cortical actin tension in these cells and enhanced their membrane vibrations and dissipation of intracellular mechanical work to the cell surroundings. We also found increased vibrations of cell membranes in five different malignant cells lines derived from T cell leukemia, lung, prostate, bladder, and melanoma cancers, as compared to their corresponding benign cells. This was demonstrated by utilizing TIRF microscopy in single cells and dynamic laser speckles measurements in an in vitro model of multiple cells in a tissue. Our results show that cell membrane vibrations and dissipation of mechanical work are higher in malignant cells relative to benign cells. Accordingly, these properties may be used to detect and monitor cellular and tissue malignancies.
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Affiliation(s)
- Ishay Wohl
- Racah Institute of Physics, The Hebrew University, Jerusalem 91904, Israel
| | - Julia Sajman
- Racah Institute of Physics, The Hebrew University, Jerusalem 91904, Israel
| | - Eilon Sherman
- Racah Institute of Physics, The Hebrew University, Jerusalem 91904, Israel
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13
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Goychuk A, Kannan D, Chakraborty AK, Kardar M. Polymer folding through active processes recreates features of genome organization. Proc Natl Acad Sci U S A 2023; 120:e2221726120. [PMID: 37155885 PMCID: PMC10194017 DOI: 10.1073/pnas.2221726120] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 04/02/2023] [Indexed: 05/10/2023] Open
Abstract
From proteins to chromosomes, polymers fold into specific conformations that control their biological function. Polymer folding has long been studied with equilibrium thermodynamics, yet intracellular organization and regulation involve energy-consuming, active processes. Signatures of activity have been measured in the context of chromatin motion, which shows spatial correlations and enhanced subdiffusion only in the presence of adenosine triphosphate. Moreover, chromatin motion varies with genomic coordinate, pointing toward a heterogeneous pattern of active processes along the sequence. How do such patterns of activity affect the conformation of a polymer such as chromatin? We address this question by combining analytical theory and simulations to study a polymer subjected to sequence-dependent correlated active forces. Our analysis shows that a local increase in activity (larger active forces) can cause the polymer backbone to bend and expand, while less active segments straighten out and condense. Our simulations further predict that modest activity differences can drive compartmentalization of the polymer consistent with the patterns observed in chromosome conformation capture experiments. Moreover, segments of the polymer that show correlated active (sub)diffusion attract each other through effective long-ranged harmonic interactions, whereas anticorrelations lead to effective repulsions. Thus, our theory offers nonequilibrium mechanisms for forming genomic compartments, which cannot be distinguished from affinity-based folding using structural data alone. As a first step toward exploring whether active mechanisms contribute to shaping genome conformations, we discuss a data-driven approach.
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Affiliation(s)
- Andriy Goychuk
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Deepti Kannan
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Arup K. Chakraborty
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Mehran Kardar
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
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14
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Xu S, Wang J, Dong J. Nonspecific interaction and overlap concentration influence macromolecular crowding effect on glucose oxidase activity. Int J Biol Macromol 2023; 241:124525. [PMID: 37086776 DOI: 10.1016/j.ijbiomac.2023.124525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 04/24/2023]
Abstract
Macromolecular crowding can change kinetics of enzyme catalysis. How interaction between enzymes and neighboring macromolecules contributes to the crowding effect on enzyme catalysis has not been quantitatively revealed. In this study, crowding effects of dextran and poly(ethylene glycol) (PEG) on glucose oxidase (GOx) are studied. Fluorescence resonance energy transfer experiments show the high transfer efficiency and stable interaction between the dextran and GOx. Further fluorescence quenching analysis also proves that the association of the dextran-GOx pair can become stronger than that of the PEG-GOx pair. Dextrans with concentrations above or below their chain overlap concentrations (c*) reduce Michaelis constants (Km) of GOx catalysis by 90 % or 45 %, respectively, through volume exclusion mechanism, and in the meantime elevate the enzymatic efficiency (kcat/Km) by 8-fold or by 3-fold, respectively, which is more dramatic than that found in other enzymes before. Strong association between the enzyme and the dextran results in slow turnover rates (kcat). Intermediate crowding with weak to moderate affinity to the enzyme below the c* can tune the kcat higher than in the free state. Catalysis under crowded conditions is a joint effect of the enzyme-crowder nonspecific interaction, volume exclusion and overlap condition of the crowders.
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Affiliation(s)
- Siyuan Xu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, Zhejiang Province 312000, China
| | - Jie Wang
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, Zhejiang Province 312000, China
| | - Jian Dong
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, Zhejiang Province 312000, China.
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15
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Kang YG, Canoy RJE, Jang Y, Santos ARMP, Son I, Kim BM, Park Y. Optical coherence microscopy with a split-spectrum image reconstruction method for temporal-dynamics contrast-based imaging of intracellular motility. BIOMEDICAL OPTICS EXPRESS 2023; 14:577-592. [PMID: 36874497 PMCID: PMC9979675 DOI: 10.1364/boe.478264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Biomedical researchers use optical coherence microscopy (OCM) for its high resolution in real-time label-free tomographic imaging. However, OCM lacks bioactivity-related functional contrast. We developed an OCM system that can measure changes in intracellular motility (indicating cellular process states) via pixel-wise calculations of intensity fluctuations from metabolic activity of intracellular components. To reduce image noise, the source spectrum is split into five using Gaussian windows with 50% of the full bandwidth. The technique verified that F-actin fiber inhibition by Y-27632 reduces intracellular motility. This finding could be used to search for other intracellular-motility-associated therapeutic strategies for cardiovascular diseases.
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Affiliation(s)
- Yong Guk Kang
- BK21 Four Institute of Precision Public Health, Korea University, Seoul 02841, Republic of Korea
- These authors contributed equally to this work
| | - Raymart Jay E. Canoy
- Department of Biomicro System Technology, College of Engineering, Korea University, Seoul 02841, Republic of Korea
- These authors contributed equally to this work
| | - Yongjun Jang
- Department of Biomedical Science, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Ana Rita M. P. Santos
- Department of Biomedical Science, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Inwoo Son
- Department of Biomedical Science, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Beop-Min Kim
- BK21 Four Institute of Precision Public Health, Korea University, Seoul 02841, Republic of Korea
- Department of Biomedical Engineering, College of Health Science, Korea University, Seoul 02841, Republic of Korea
| | - Yongdoo Park
- Department of Biomedical Science, College of Medicine, Korea University, Seoul 02841, Republic of Korea
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16
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Zills G, Datta T, Malmi-Kakkada AN. Enhanced mechanical heterogeneity of cell collectives due to temporal fluctuations in cell elasticity. Phys Rev E 2023; 107:014401. [PMID: 36797877 DOI: 10.1103/physreve.107.014401] [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: 03/25/2022] [Accepted: 12/08/2022] [Indexed: 06/18/2023]
Abstract
Cells are dynamic systems characterized by temporal variations in biophysical properties such as stiffness and contractility. Recent studies show that the recruitment and release of actin filaments into and out of the cell cortex-a network of proteins underneath the cell membrane-leads to cell stiffening prior to division and softening immediately afterward. In three-dimensional (3D) cell collectives, it is unclear whether the stiffness change during division at the single-cell scale controls the spatial structure and dynamics at the multicellular scale. This is an important question to understand because cell stiffness variations impact cell spatial organization and cancer progression. Using a minimal 3D model incorporating cell birth, death, and cell-to-cell elastic and adhesive interactions, we investigate the effect of mechanical heterogeneity-variations in individual cell stiffnesses that make up the cell collective-on tumor spatial organization and cell dynamics. We discover that spatial mechanical heterogeneity characterized by a spheroid core composed of stiffer cells and softer cells in the periphery emerges within dense 3D cell collectives, which may be a general feature of multicellular tumor growth. We show that heightened spatial mechanical heterogeneity enhances single-cell dynamics and volumetric tumor growth driven by fluctuations in cell elasticity. Our results could have important implications in understanding how spatiotemporal variations in single-cell stiffness determine tumor growth and spread.
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Affiliation(s)
- Garrett Zills
- Department of Chemistry and Physics, Augusta University, 1120 15th Street, Augusta, Georgia 30912, USA
| | - Trinanjan Datta
- Department of Chemistry and Physics, Augusta University, 1120 15th Street, Augusta, Georgia 30912, USA
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106, USA
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17
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Pompa-García I, Castilla R, Metzler R, Dagdug L. First-passage times in conical varying-width channels biased by a transverse gravitational force: Comparison of analytical and numerical results. Phys Rev E 2022; 106:064137. [PMID: 36671151 DOI: 10.1103/physreve.106.064137] [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: 09/02/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
We study the crossing time statistic of diffusing point particles between the two ends of expanding and narrowing two-dimensional conical channels under a transverse external gravitational field. The theoretical expression for the mean first-passage time for such a system is derived under the assumption that the axial diffusion in a two-dimensional channel of smoothly varying geometry can be approximately described as a one-dimensional diffusion in an entropic potential with position-dependent effective diffusivity in terms of the modified Fick-Jacobs equation. We analyze the channel crossing dynamics in terms of the mean first-passage time, combining our analytical results with extensive two-dimensional Brownian dynamics simulations, allowing us to find the range of applicability of the one-dimensional approximation. We find that the effective particle diffusivity decreases with increasing amplitude of the external potential. Remarkably, the mean first-passage time for crossing the channel is shown to assume a minimum at finite values of the potential amplitude.
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Affiliation(s)
- Ivan Pompa-García
- Physics Department, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Ciudad de México, 09340, México
| | - Rodrigo Castilla
- Engineering Faculty, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, 04510, México
| | - Ralf Metzler
- Institute of Physics and Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany
- Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea
| | - Leonardo Dagdug
- Physics Department, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Ciudad de México, 09340, México
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18
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Liu J, Jin Y, Bao JD, Chen X. Coexistence of ergodicity and nonergodicity in the aging two-state random walks. SOFT MATTER 2022; 18:8687-8699. [PMID: 36349834 DOI: 10.1039/d2sm01093c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The two-state stochastic phenomenon is observed in various systems and is attracting more interest, and it can be described by the two-state random walk (TSRW) model. The TSRW model is a typical two-state renewal process alternating between the continuous-time random walk state and the Lévy walk state, in both of which the sojourn time distributions follow a power law. In this paper, by discussing the statistical properties and calculating the ensemble averaged and time averaged mean squared displacement, the ergodic property and the ultimate diffusive behavior of the aging TSRW is studied. Results reveal that because of the two-state intermittent feature, ergodicity and nonergodicity can coexist in the aging TSRW, which behave as the time scalings of the time averages and ensemble averages not being identically equal. In addition, we find that the unique state occupation mechanism caused by the diverging mean of the sojourn times of one state, determines the aging TSRW's ultimate diffusive behavior at extremely large timescales, i.e., instead of the term with the larger diffusion exponent, the diffusion is surprisingly characterized by the term with the smaller one, which is distinctly different from previous conclusions and known results. At last, we note that the Lévy walk with rests model which also displays aging and ergodicity breaking, can be generalized by the TSRW model.
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Affiliation(s)
- Jian Liu
- Department of Physics, Beijing Technology and Business University, Beijing, 100048, China.
- Institute of Systems Science, Beijing Technology and Business University, Beijing, 100048, China
- Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Yuliang Jin
- Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Jing-Dong Bao
- Department of Physics, Beijing Normal University, Beijing, 100875, China
| | - Xiaosong Chen
- School of Systems Science, Beijing Normal University, Beijing, 100875, China
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19
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Sheung JY, Garamella J, Kahl SK, Lee BY, McGorty RJ, Robertson-Anderson RM. Motor-driven advection competes with crowding to drive spatiotemporally heterogeneous transport in cytoskeleton composites. FRONTIERS IN PHYSICS 2022; 10:1055441. [PMID: 37547053 PMCID: PMC10403238 DOI: 10.3389/fphy.2022.1055441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The cytoskeleton-a composite network of biopolymers, molecular motors, and associated binding proteins-is a paradigmatic example of active matter. Particle transport through the cytoskeleton can range from anomalous and heterogeneous subdiffusion to superdiffusion and advection. Yet, recapitulating and understanding these properties-ubiquitous to the cytoskeleton and other out-of-equilibrium soft matter systems-remains challenging. Here, we combine light sheet microscopy with differential dynamic microscopy and single-particle tracking to elucidate anomalous and advective transport in actomyosin-microtubule composites. We show that particles exhibit multi-mode transport that transitions from pronounced subdiffusion to superdiffusion at tunable crossover timescales. Surprisingly, while higher actomyosin content increases the range of timescales over which transport is superdiffusive, it also markedly increases the degree of subdiffusion at short timescales and generally slows transport. Corresponding displacement distributions display unique combinations of non-Gaussianity, asymmetry, and non-zero modes, indicative of directed advection coupled with caged diffusion and hopping. At larger spatiotemporal scales, particles in active composites exhibit superdiffusive dynamics with scaling exponents that are robust to changing actomyosin fractions, in contrast to normal, yet faster, diffusion in networks without actomyosin. Our specific results shed important new light on the interplay between non-equilibrium processes, crowding and heterogeneity in active cytoskeletal systems. More generally, our approach is broadly applicable to active matter systems to elucidate transport and dynamics across scales.
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Affiliation(s)
- Janet Y. Sheung
- W. M. Keck Science Department, Scripps College, Claremont, CA, United States
- W. M. Keck Science Department, Pitzer College, Claremont, CA, United States
| | - Jonathan Garamella
- Physics and Biophysics Department, University of San Diego, San Diego, CA, United States
| | - Stella K. Kahl
- W. M. Keck Science Department, Scripps College, Claremont, CA, United States
| | - Brian Y. Lee
- W. M. Keck Science Department, Pitzer College, Claremont, CA, United States
| | - Ryan J. McGorty
- Physics and Biophysics Department, University of San Diego, San Diego, CA, United States
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20
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van Tartwijk FW, Kaminski CF. Protein Condensation, Cellular Organization, and Spatiotemporal Regulation of Cytoplasmic Properties. Adv Biol (Weinh) 2022; 6:e2101328. [PMID: 35796197 DOI: 10.1002/adbi.202101328] [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: 12/31/2021] [Revised: 05/15/2022] [Indexed: 01/28/2023]
Abstract
The cytoplasm is an aqueous, highly crowded solution of active macromolecules. Its properties influence the behavior of proteins, including their folding, motion, and interactions. In particular, proteins in the cytoplasm can interact to form phase-separated assemblies, so-called biomolecular condensates. The interplay between cytoplasmic properties and protein condensation is critical in a number of functional contexts and is the subject of this review. The authors first describe how cytoplasmic properties can affect protein behavior, in particular condensate formation, and then describe the functional implications of this interplay in three cellular contexts, which exemplify how protein self-organization can be adapted to support certain physiological phenotypes. The authors then describe the formation of RNA-protein condensates in highly polarized cells such as neurons, where condensates play a critical role in the regulation of local protein synthesis, and describe how different stressors trigger extensive reorganization of the cytoplasm, both through signaling pathways and through direct stress-induced changes in cytoplasmic properties. Finally, the authors describe changes in protein behavior and cytoplasmic properties that may occur in extremophiles, in particular organisms that have adapted to inhabit environments of extreme temperature, and discuss the implications and functional importance of these changes.
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Affiliation(s)
- Francesca W van Tartwijk
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
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21
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Moran SJ, Puckett S, Ornelles DA, Macosko JC, Holzwarth G, Lyles DS. Dynamic Actin Filament Traps Mediate Active Diffusion of Vesicular Stomatitis Virus Ribonucleoproteins. J Virol 2022; 96:e0093422. [PMID: 36135365 PMCID: PMC9555154 DOI: 10.1128/jvi.00934-22] [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: 06/20/2022] [Accepted: 09/06/2022] [Indexed: 11/20/2022] Open
Abstract
A recently developed variational Bayesian analysis using pattern recognition and machine learning of single viral ribonucleoprotein (RNP) particle tracks in the cytoplasm of living cells provides a quantitative molecular explanation for active diffusion, a concept previously "explained" largely by hypothetical models based on indirect analyses such as continuum microrheology. Machine learning shows that vesicular stomatitis virus (VSV) RNP particles are temporarily confined to dynamic traps or pores made up of cytoskeletal elements. Active diffusion occurs when the particles escape from one trap to a nearby trap. In this paper, we demonstrate that actin filament disruption increased RNP mobility by increasing trap size. Inhibition of nonmuscle myosin II ATPase decreased mobility by decreasing trap size. Trap sizes were observed to fluctuate with time, dependent on nonmuscle myosin II activity. This model for active diffusion is likely to account for the dominant motion of other viral and cellular elements. IMPORTANCE RNA virus ribonucleoproteins (RNPs) are too large to freely diffuse in the host cytoplasm, yet their dominant motions consist of movements in random directions that resemble diffusion. We show that vesicular stomatitis virus (VSV) RNPs overcome limitations on diffusion in the host cytoplasm by hopping between traps formed in part by actin filaments and that these traps expand and contract by nonmuscle myosin II ATPase activity. ATP-dependent random motion of cellular particles has been termed "active diffusion." Thus, these mechanisms are applicable to active diffusion of other cellular and viral elements.
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Affiliation(s)
- Steven J. Moran
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Shelby Puckett
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - David A. Ornelles
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jed C. Macosko
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina, USA
| | - George Holzwarth
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Douglas S. Lyles
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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22
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Zamir A, Li G, Chase K, Moskovitch R, Sun B, Zaritsky A. Emergence of synchronized multicellular mechanosensing from spatiotemporal integration of heterogeneous single-cell information transfer. Cell Syst 2022; 13:711-723.e7. [PMID: 35921844 PMCID: PMC9509451 DOI: 10.1016/j.cels.2022.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/14/2021] [Accepted: 07/07/2022] [Indexed: 01/26/2023]
Abstract
Multicellular synchronization is a ubiquitous phenomenon in living systems. However, how noisy and heterogeneous behaviors of individual cells are integrated across a population toward multicellular synchronization is unclear. Here, we study the process of multicellular calcium synchronization of the endothelial cell monolayer in response to mechanical stimuli. We applied information theory to quantify the asymmetric information transfer between pairs of cells and defined quantitative measures to how single cells receive or transmit information within a multicellular network. Our analysis revealed that multicellular synchronization was established by gradual enhancement of information spread from the single cell to the multicellular scale. Synchronization was associated with heterogeneity in the cells' communication properties, reinforcement of the cells' state, and information flow. Altogether, we suggest a phenomenological model where cells gradually learn their local environment, adjust, and reinforce their internal state to stabilize the multicellular network architecture to support information flow from local to global scales toward multicellular synchronization.
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Affiliation(s)
- Amos Zamir
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Guanyu Li
- Department of Physics, Oregon State University, Corvallis, OR 97331, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Katelyn Chase
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Robert Moskovitch
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bo Sun
- Department of Physics, Oregon State University, Corvallis, OR 97331, USA.
| | - Assaf Zaritsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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23
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Hibbard JVK, Vázquez N, Wallingford JB. Cilia proteins getting to work - how do they commute from the cytoplasm to the base of cilia? J Cell Sci 2022; 135:jcs259444. [PMID: 36073764 PMCID: PMC9482345 DOI: 10.1242/jcs.259444] [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] [Indexed: 11/20/2022] Open
Abstract
Cilia are multifunctional organelles that originated with the last eukaryotic common ancestor and play central roles in the life cycles of diverse organisms. The motile flagella that move single cells like sperm or unicellular organisms, the motile cilia on animal multiciliated cells that generate fluid flow in organs, and the immotile primary cilia that decorate nearly all cells in animals share many protein components in common, yet each also requires specialized proteins to perform their specialized functions. Despite a now-advanced understanding of how such proteins are transported within cilia, we still know very little about how they are transported from their sites of synthesis through the cytoplasm to the ciliary base. Here, we review the literature concerning this underappreciated topic in ciliary cell biology. We discuss both general mechanisms, as well as specific examples of motor-driven active transport and passive transport via diffusion-and-capture. We then provide deeper discussion of specific, illustrative examples, such as the diverse array of protein subunits that together comprise the intraflagellar transport (IFT) system and the multi-protein axonemal dynein motors that drive beating of motile cilia. We hope this Review will spur further work, shedding light not only on ciliogenesis and ciliary signaling, but also on intracellular transport in general.
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Affiliation(s)
| | | | - John B. Wallingford
- Department of Molecular Biosciences, University of Texas, Austin, TX 78751, USA
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24
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Jiang C, Yang M, Li W, Dou SX, Wang PY, Li H. Spatiotemporal three-dimensional transport dynamics of endocytic cargos and their physical regulations in cells. iScience 2022; 25:104210. [PMID: 35479412 PMCID: PMC9035719 DOI: 10.1016/j.isci.2022.104210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/14/2022] [Accepted: 04/04/2022] [Indexed: 11/21/2022] Open
Abstract
Intracellular transport, regulated by complex cytoarchitectures and active driving forces, is crucial for biomolecule translocations and relates to many cellular functions. Despite extensive knowledge obtained from two-dimensional (2D) experiments, the real three-dimensional (3D) spatiotemporal characteristics of intracellular transport is still unclear. With 3D single-particle tracking, we comprehensively studied the transport dynamics of endocytic cargos. With varying timescale, the intracellular transport changes from thermal-dominated 3D-constrained motion to active-dominated quasi-2D motion. Spatially, the lateral motion is heterogeneous with peripheral regions being faster than perinuclear regions, while the axial motion is homogeneous across the cells. We further confirmed that such anisotropy and heterogeneity of vesicle transport result from actively directed motion on microtubules. Strikingly, inside the vesicles, we observed endocytic nanoparticles make diffusive motions on their inner membranes when microtubules are absent, suggesting endocytic cargos are normally localized at the inner vesicle membranes through a physical connection to the microtubules outside during transport.
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Affiliation(s)
- Chao Jiang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing 100875, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingcheng Yang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Wei Li
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng-Ye Wang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Hui Li
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing 100875, China
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25
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Patteson AE, Asp ME, Janmey PA. Materials science and mechanosensitivity of living matter. APPLIED PHYSICS REVIEWS 2022; 9:011320. [PMID: 35392267 PMCID: PMC8969880 DOI: 10.1063/5.0071648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Living systems are composed of molecules that are synthesized by cells that use energy sources within their surroundings to create fascinating materials that have mechanical properties optimized for their biological function. Their functionality is a ubiquitous aspect of our lives. We use wood to construct furniture, bacterial colonies to modify the texture of dairy products and other foods, intestines as violin strings, bladders in bagpipes, and so on. The mechanical properties of these biological materials differ from those of other simpler synthetic elastomers, glasses, and crystals. Reproducing their mechanical properties synthetically or from first principles is still often unattainable. The challenge is that biomaterials often exist far from equilibrium, either in a kinetically arrested state or in an energy consuming active state that is not yet possible to reproduce de novo. Also, the design principles that form biological materials often result in nonlinear responses of stress to strain, or force to displacement, and theoretical models to explain these nonlinear effects are in relatively early stages of development compared to the predictive models for rubberlike elastomers or metals. In this Review, we summarize some of the most common and striking mechanical features of biological materials and make comparisons among animal, plant, fungal, and bacterial systems. We also summarize some of the mechanisms by which living systems develop forces that shape biological matter and examine newly discovered mechanisms by which cells sense and respond to the forces they generate themselves, which are resisted by their environment, or that are exerted upon them by their environment. Within this framework, we discuss examples of how physical methods are being applied to cell biology and bioengineering.
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Affiliation(s)
- Alison E. Patteson
- Physics Department and BioInspired Institute, Syracuse University, Syracuse NY, 13244, USA
| | - Merrill E. Asp
- Physics Department and BioInspired Institute, Syracuse University, Syracuse NY, 13244, USA
| | - Paul A. Janmey
- Institute for Medicine and Engineering and Departments of Physiology and Physics & Astronomy, University of Pennsylvania, Philadelphia PA, 19104, USA
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26
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Chakraborty R, Maiti A, Sharma N, Dey KK. Active matter dynamics in confined microfluidic environments. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 186:245-265. [PMID: 35033287 DOI: 10.1016/bs.pmbts.2021.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The field of active matter is a nascent area of research in soft condensed matter physics, which is drawing on the expertise of researchers from diverse disciplines. Small scale active particles-both inorganic and biological-display non-trivial emergent dynamics and interactions that could help us understand complex biological processes and phenomena. Recently, using microfluidic technologies, several research groups have performed important experimental and theoretical studies to understand the behavior of self-propelled particles and molecular active matter within confined environments-to glean a fundamental understanding of the cellular processes occurring under ultra-low Reynolds number conditions. In this chapter, we would like to review applications of microfluidics in active matter research, highlighting a few important theoretical and experimental investigations. We will conclude the discussion with a note on the future of this field mentioning a few open questions that are at the forefront of our minds.
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Affiliation(s)
- Rik Chakraborty
- Discipline of Physics, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India
| | - Arnab Maiti
- Discipline of Physics, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India
| | - Nikita Sharma
- Discipline of Physics, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India
| | - Krishna Kanti Dey
- Discipline of Physics, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India.
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27
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Liu J, Zhu P, Bao JD, Chen X. Strong anomalous diffusive behaviors of the two-state random walk process. Phys Rev E 2022; 105:014122. [PMID: 35193269 DOI: 10.1103/physreve.105.014122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
The phenomenon of the two-state process is observed in various systems and is increasingly attracting attention, such that there is a need for a theoretical model of the process. In this paper, we present a prototypal two-state random walk (TSRW) model of a renewal process alternating between the continuous-time random walk (CTRW) state and Lévy walk (LW) state. The jump length distribution of the CTRW state is assumed to be Gaussian whereas the time distributions of the two states are both considered to follow a power law. The diffusive behavior is analyzed and discussed by calculating the mean squared displacement (MSD) analytically and numerically. The results reveal that it displays strong anomalous diffusive behaviors caused by random motions of both states, i.e., two anomalous diffusion terms coexist in the expression of the MSD, and the time distribution which has the heavier tail determines their forms. Moreover, because the two diffusion terms originate from different mechanisms, we find that the diffusion can be characterized by either the term with the largest diffusion exponent or the term with the largest diffusion coefficient at long timescales, which shows very different properties from the single-state process. In addition, the two-state nature of the process of the particle moving in a velocity field makes the TSRW model applicable to describe it. Results obtained from the two-state model reveal that the diffusion can even exhibit subdiffusive behavior, which is significantly different from known results obtained using the single-state model.
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Affiliation(s)
- Jian Liu
- Department of Physics, Institute of Systems Science, Beijing Technology and Business University, Beijing 100048, China
| | - Ping Zhu
- Department of Physics, Institute of Systems Science, Beijing Technology and Business University, Beijing 100048, China
| | - Jing-Dong Bao
- Department of Physics, Beijing Normal University, Beijing 100875, China
| | - Xiaosong Chen
- School of Systems Science, Beijing Normal University, Beijing 100875, China
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Yu X, Sha L, Liu Q, Zhao Y, Fang H, Cao Y, Zhao J. Recent advances in cell membrane camouflage-based biosensing application. Biosens Bioelectron 2021; 194:113623. [PMID: 34530371 DOI: 10.1016/j.bios.2021.113623] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 01/04/2023]
Abstract
Cell membrane, a semi-permeable membrane composed of phospholipid bilayers, is a natural barrier to prevent extracellular substances from freely entering the cell. Cell membrane with selective permeability and fluidity ensures the relative stability of the intracellular environment and enables various biochemical reactions to smoothly operate in an orderly manner. Inspired by the natural composition and transport process, various cell membranes and synthetic bionic films as the mimics of cell membranes have emerged as appealing camouflage materials for biosensing applications. The membranes are devoted to surface modification and substance delivery, and realize the detection or in situ analysis of multiple biomarkers, such as glucose, nucleic acids, virus, and circulating tumor cells. In this review, we summarize the recent advances in cell membrane camouflage-based biosensing applications, mainly focusing on the use of the membranes extracted from natural cells (e.g., blood cells and cancer cells) as well as biomimetic membranes. Materials and surfaces camouflaged with cell membranes are shown to have superior stability and biocompatibility as well as intrinsic properties of original cells, which greatly facilitate their use in biosensing. In specific, camouflage with blood cell membranes bestows low immunogenicity and prolonged blood circulation time, camouflage with cancer cell membranes provides homologous targeting ability, and camouflage with biomimetic membranes endows considerable plasticity for functionalization. Further research is expected to focus on the deeper understanding of cell-specific properties of membranes and the exploration of hybrid membranes, which might provide new development opportunities for cell membrane camouflage-based biosensing application.
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Affiliation(s)
- Xiaomeng Yu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, PR China; Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Lingjun Sha
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Qi Liu
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Yingyan Zhao
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Huan Fang
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Ya Cao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, PR China; Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China.
| | - Jing Zhao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, PR China; Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China.
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29
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Pompa-García I, Dagdug L. Two-dimensional diffusion biased by a transverse gravitational force in an asymmetric channel: Reduction to an effective one-dimensional description. Phys Rev E 2021; 104:044118. [PMID: 34781435 DOI: 10.1103/physreve.104.044118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/01/2021] [Indexed: 11/07/2022]
Abstract
We focus on the derivation of a general position-dependent effective diffusion coefficient to describe two-dimensional (2D) diffusion in a narrow and smoothly asymmetric channel of varying width under a transverse gravitational external field, a generalization of the symmetric channel case using the projection method introduced earlier by Kalinay and Percus [P. Kalinay and J. K. Percus, J. Chem. Phys. 122, 204701 (2005)10.1063/1.1899150]. To this end, we project the 2D Smoluchowski equation into an effective one-dimensional generalized Fick-Jacobs equation in the presence of constant force in the transverse direction. The expression for the diffusion coefficient given in Eq. (34) is our main result. This expression is a more general effective diffusion coefficient for narrow 2D channels in the presence of constant transverse force, which contains the well-known previous results for a symmetric channel obtained by Kalinay, as well as the limiting cases when the transverse gravitational external field goes to zero and infinity. Finally, we show that diffusivity can be described by the interpolation formula proposed by Kalinay, D_{0}/[1+(1/4)w^{'2}(x)]^{-η}, where spatial confinement, asymmetry, and the presence of a constant transverse force can be encoded in η, which is a function of channel width (w), channel centerline, and transverse force. The interpolation formula also reduces to well-known previous results, namely, those obtained by Reguera and Rubi [D. Reguera and J. M. Rubi, Phys. Rev. E 64, 061106 (2001)10.1103/PhysRevE.64.061106] and by Kalinay [P. Kalinay, Phys. Rev. E 84, 011118 (2011)10.1103/PhysRevE.84.011118].
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Affiliation(s)
- Ivan Pompa-García
- Physics Department, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Ciudad de México 09340, Mexico
| | - Leonardo Dagdug
- Physics Department, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Ciudad de México 09340, Mexico
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30
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Mogre SS, Christensen JR, Reck-Peterson SL, Koslover EF. Optimizing microtubule arrangements for rapid cargo capture. Biophys J 2021; 120:4918-4931. [PMID: 34687720 DOI: 10.1016/j.bpj.2021.10.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/05/2021] [Accepted: 10/18/2021] [Indexed: 10/20/2022] Open
Abstract
Cellular functions such as autophagy, cell signaling, and vesicular trafficking involve the retrograde transport of motor-driven cargo along microtubules. Typically, newly formed cargo engages in slow undirected movement from its point of origin before attaching to a microtubule. In some cell types, cargo destined for delivery to the perinuclear region relies on capture at dynein-enriched loading zones located near microtubule plus ends. Such systems include extended cell regions of neurites and fungal hyphae, where the efficiency of the initial diffusive loading process depends on the axial distribution of microtubule plus ends relative to the initial cargo position. We use analytic mean first-passage time calculations and numerical simulations to model diffusive capture processes in tubular cells, exploring how the spatial arrangement of microtubule plus ends affects the efficiency of retrograde cargo transport. Our model delineates the key features of optimal microtubule arrangements that minimize mean cargo capture times. Namely, we show that configurations with a single microtubule plus end abutting the distal tip and broadly distributed other plus ends allow for efficient capture in a variety of different scenarios for retrograde transport. Live-cell imaging of microtubule plus ends in Aspergillus nidulans hyphae indicates that their distributions exhibit these optimal qualitative features. Our results highlight important coupling effects between the distribution of microtubule tips and retrograde cargo transport, providing guiding principles for the spatial arrangement of microtubules within tubular cell regions.
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Affiliation(s)
- Saurabh S Mogre
- Department of Physics, University of California San Diego, La Jolla, California
| | - Jenna R Christensen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California; Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, California; Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Elena F Koslover
- Department of Physics, University of California San Diego, La Jolla, California.
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31
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Liu J, Zhang C, Bao JD, Chen X. Correlated continuous-time random walk in the velocity field: the role of velocity and weak asymptotics. SOFT MATTER 2021; 17:9786-9798. [PMID: 34657952 DOI: 10.1039/d1sm00995h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Within the framework of a space-time correlated continuous-time random walk model, anomalous diffusion of particles moving in the velocity field is studied in this paper. The weak asymptotic form ω(t) ∼ t-(1+α), 1 < α < 2 for large t, is considered to be the waiting time distribution. The analytical results reveal that the diffusion in the velocity field, i.e., the mean squared displacement, can display a multi-fractional form caused by dispersive bias and space-time correlation. The numerical results indicate that the multi-fractional diffusion leads to a crossover phenomenon in-between the process at an intermediate timescale, followed by a steady state which is always determined by the largest diffusion exponent term. In addition, the role of velocity and weak asymptotics is discussed. The extremely small fluid velocity can characterize the diffusion by a diffusion coefficient instead of diffusion exponent, which is distinctly different from the former definition. In particular, for the waiting time displaying a weak asymptotic property, if the anomalous part is suppressed by the normal part, a second crossover phenomenon appears at an intermediate timescale, followed by a steady normal diffusion, which implies that the anomalies underlying the process are smoothed out at large timescales. Moreover, we discuss that the consideration of bias and correlation could help to avoid a possible not readily noticeable mistake in studying the topic concerned in this paper, which may be helpful in the relevant experimental research.
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Affiliation(s)
- Jian Liu
- Department of Physics, Beijing Technology and Business University, Beijing, 100048, China.
- Institute of Systems Science, Beijing Technology and Business University, Beijing, 100048, China
| | - Caiyun Zhang
- Department of Physics, Beijing Technology and Business University, Beijing, 100048, China.
- Institute of Systems Science, Beijing Technology and Business University, Beijing, 100048, China
| | - Jing-Dong Bao
- Department of Physics, Beijing Normal University, Beijing, 100875, China
| | - Xiaosong Chen
- School of Systems Science, Beijing Normal University, Beijing, 100875, China
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32
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Huang DE, Zia RN. Toward a flow-dependent phase-stability criterion: Osmotic pressure in sticky flowing suspensions. J Chem Phys 2021; 155:134113. [PMID: 34624990 DOI: 10.1063/5.0058676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Equilibrium phase instability of colloids is robustly predicted by the Vliegenthart-Lekkerkerker (VL) critical value of the second virial efficient, but no such general criterion has been established for suspensions undergoing flow. A transition from positive to negative osmotic pressure is one mechanical hallmark of a change in phase stability in suspensions and provides a natural extension of the equilibrium osmotic pressure encoded in the second virial coefficient. Here, we propose to study the non-Newtonian rheology of an attractive colloidal suspension using the active microrheology framework as a model for focusing on the pair trajectories that underlie flow stability. We formulate and solve a Smoluchowski relation to understand the interplay between attractions, hydrodynamics, Brownian motion, and flow on particle microstructure in a semi-dilute suspension and utilize the results to study the viscosity and particle-phase osmotic pressure. We find that an interplay between attractions and hydrodynamics leads to dramatic changes in the nonequilibrium microstructure, which produces a two-stage flow-thinning of viscosity and leads to pronounced flow-induced negative osmotic pressure. We summarize these findings with an osmotic pressure heat map that predicts where hydrodynamic enhancement of attractive bonds encourages flow-induced aggregation or phase separation. We identify a critical isobar-a flow-induced critical pressure consistent with phase instability and a nonequilibrium extension of the VL criterion.
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Affiliation(s)
- Derek E Huang
- Department of Chemical Engineering, Stanford University, Stanford, California 94302, USA
| | - Roseanna N Zia
- Department of Chemical Engineering, Stanford University, Stanford, California 94302, USA
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33
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Wohl I, Sherman E. Reducing Myosin II and ATP-Dependent Mechanical Activity Increases Order and Stability of Intracellular Organelles. Int J Mol Sci 2021; 22:10369. [PMID: 34638710 PMCID: PMC8508806 DOI: 10.3390/ijms221910369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
Organization of intracellular content is affected by multiple simultaneous processes, including diffusion in a viscoelastic and structured environment, intracellular mechanical work and vibrations. The combined effects of these processes on intracellular organization are complex and remain poorly understood. Here, we studied the organization and dynamics of a free Ca++ probe as a small and mobile tracer in live T cells. Ca++, highlighted by Fluo-4, is localized in intracellular organelles. Inhibiting intracellular mechanical work by myosin II through blebbistatin treatment increased cellular dis-homogeneity of Ca++-rich features in length scale < 1.1 μm. We detected a similar effect in cells imaged by label-free bright-field (BF) microscopy, in mitochondria-highlighted cells and in ATP-depleted cells. Blebbistatin treatment also reduced the dynamics of the Ca++-rich features and generated prominent negative temporal correlations in their signals. Following Guggenberger et al. and numerical simulations, we suggest that diffusion in the viscoelastic and confined medium of intracellular organelles may promote spatial dis-homogeneity and stability of their content. This may be revealed only after inhibiting intracellular mechanical work and related cell vibrations. Our described mechanisms may allow the cell to control its organization via balancing its viscoelasticity and mechanical activity, with implications to cell physiology in health and disease.
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Affiliation(s)
| | - Eilon Sherman
- Racah Institute of Physics, The Hebrew University, Jerusalem 9190401, Israel;
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34
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Gildor T, Winter MR, Layous M, Hijaze E, Ben-Tabou de-Leon S. The biological regulation of sea urchin larval skeletogenesis - From genes to biomineralized tissue. J Struct Biol 2021; 213:107797. [PMID: 34530133 DOI: 10.1016/j.jsb.2021.107797] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/02/2021] [Accepted: 09/07/2021] [Indexed: 10/20/2022]
Abstract
Biomineralization is the process in which soft organic tissues use minerals to produce shells, skeletons and teeth for various functions such as protection and physical support. The ability of the cells to control the time and place of crystal nucleation as well as crystal orientation and stiffness is far beyond the state-of-the art of human technologies. Thus, understanding the biological control of biomineralization will promote our understanding of embryo development as well as provide novel approaches for material engineering. Sea urchin larval skeletogenesis offers an excellent platform for functional analyses of both the molecular control system and mineral uptake and deposition. Here we describe the current understanding of the genetic, molecular and cellular processes that underlie sea urchin larval skeletogenesis. We portray the regulatory genes that define the specification of the skeletogenic cells and drive the various morphogenetic processes that occur in the skeletogenic lineage, including: epithelial to mesenchymal transition, cell migration, spicule cavity formation and mineral deposition into the spicule cavity. We describe recent characterizations of the size, motion and mineral concentration of the calcium-bearing vesicles in the skeletogenic cells. We review the distinct specification states within the skeletogenic lineage that drive localized skeletal growth at the tips of the spicules. Finally, we discuss the surprising similarity between the regulatory network and cellular processes that drive sea urchin skeletogenesis and those that control vertebrate vascularization. Overall, we illustrate the novel insights on the biological regulation and evolution of biomineralization, gained from studies of the sea urchin larval skeletogenesis.
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Affiliation(s)
- Tsvia Gildor
- Marine Biology Department, Charney School of Marine Sciences, the University of Haifa, Haifa, Israel
| | - Mark R Winter
- Marine Biology Department, Charney School of Marine Sciences, the University of Haifa, Haifa, Israel
| | - Majed Layous
- Marine Biology Department, Charney School of Marine Sciences, the University of Haifa, Haifa, Israel
| | - Eman Hijaze
- Marine Biology Department, Charney School of Marine Sciences, the University of Haifa, Haifa, Israel
| | - Smadar Ben-Tabou de-Leon
- Marine Biology Department, Charney School of Marine Sciences, the University of Haifa, Haifa, Israel.
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35
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Xiang Y, Surovtsev IV, Chang Y, Govers SK, Parry BR, Liu J, Jacobs-Wagner C. Interconnecting solvent quality, transcription, and chromosome folding in Escherichia coli. Cell 2021; 184:3626-3642.e14. [PMID: 34186018 DOI: 10.1016/j.cell.2021.05.037] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/09/2020] [Accepted: 05/25/2021] [Indexed: 12/12/2022]
Abstract
All cells fold their genomes, including bacterial cells, where the chromosome is compacted into a domain-organized meshwork called the nucleoid. How compaction and domain organization arise is not fully understood. Here, we describe a method to estimate the average mesh size of the nucleoid in Escherichia coli. Using nucleoid mesh size and DNA concentration estimates, we find that the cytoplasm behaves as a poor solvent for the chromosome when the cell is considered as a simple semidilute polymer solution. Monte Carlo simulations suggest that a poor solvent leads to chromosome compaction and DNA density heterogeneity (i.e., domain formation) at physiological DNA concentration. Fluorescence microscopy reveals that the heterogeneous DNA density negatively correlates with ribosome density within the nucleoid, consistent with cryoelectron tomography data. Drug experiments, together with past observations, suggest the hypothesis that RNAs contribute to the poor solvent effects, connecting chromosome compaction and domain formation to transcription and intracellular organization.
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Affiliation(s)
- Yingjie Xiang
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, CT 06520, USA; Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
| | - Ivan V Surovtsev
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Yunjie Chang
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sander K Govers
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA; Department of Biology and Institute of Chemistry, Engineering and Medicine for Human Health, Stanford University, Palo Alto, CA 94305, USA
| | - Bradley R Parry
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Jun Liu
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA; Department of Biology and Institute of Chemistry, Engineering and Medicine for Human Health, Stanford University, Palo Alto, CA 94305, USA.
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36
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Basu H, Ding L, Pekkurnaz G, Cronin M, Schwarz TL. Kymolyzer, a Semi-Autonomous Kymography Tool to Analyze Intracellular Motility. ACTA ACUST UNITED AC 2021; 87:e107. [PMID: 32530579 DOI: 10.1002/cpcb.107] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The movement of intracellular cargo, such as transcripts, proteins, and organelles, is fundamental to cellular function. Neurons, due to their long axons and dendrites, are particularly dependent on proper intracellular trafficking and vulnerable to defects in the movement of intracellular cargo that are noted in neurodegenerative and neurodevelopmental disorders. Accurate quantification of intracellular transport is therefore needed for studying the mechanisms of cargo trafficking, the influence of mutations, and the effects of potentially therapeutic pharmaceuticals. In this article, we introduce an algorithm called "Kymolyzer." The algorithm can quantify intracellular trafficking along a defined path, such as that formed by the aligned microtubules of axons and dendrites. Kymolyzer works as a semi-autonomous kymography software application. It constructs and analyzes kymographs to measure the movement and distribution of fluorescently tagged objects along a user-defined path. The algorithm can be used under a wide variety of experimental conditions and can extract a diverse array of motility parameters describing intracellular movement, including time spent in motion, percentage of objects in motion, percentage of objects that are stationary, and velocities of motile objects. This article serves as a user manual describing the design of Kymolyzer, providing a stepwise protocol for its use and illustrating its functions with common examples. © 2020 Wiley Periodicals LLC Basic Protocol: Kymolyzer, a semi-autonomous kymography tool to analyze intracellular motility.
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Affiliation(s)
- Himanish Basu
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts.,Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts
| | - Lai Ding
- Harvard NeuroDiscovery Center, Boston, Massachusetts.,Present Address: Brigham and Women's Hospital, Boston, Massachusetts
| | - Gulcin Pekkurnaz
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts.,Department of Neurobiology, Harvard Medical School, Boston, Massachusetts.,Present Address: Division of Biological Sciences, University of California, San Diego, California
| | - Michelle Cronin
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts.,Present Address: Addgene, Watertown, Massachusetts
| | - Thomas L Schwarz
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts.,Department of Neurobiology, Harvard Medical School, Boston, Massachusetts
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37
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Wohl I, Sherman E. Spectral Analysis of ATP-Dependent Mechanical Vibrations in T Cells. Front Cell Dev Biol 2021; 9:590655. [PMID: 34178972 PMCID: PMC8222795 DOI: 10.3389/fcell.2021.590655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 04/27/2021] [Indexed: 11/13/2022] Open
Abstract
Mechanical vibrations affect multiple cell properties, including its diffusivity, entropy, internal content organization, and thus-function. Here, we used Differential Interference Contrast (DIC), confocal, and Total Internal Reflection Fluorescence (TIRF) microscopies to study mechanical vibrations in live (Jurkat) T cells. Vibrations were measured via the motion of intracellular particles and plasma membrane. These vibrations depend on adenosine triphosphate (ATP) consumption and on Myosin II activity. We then used spectral analysis of these vibrations to distinguish the effects of thermal agitation, ATP-dependent mechanical work and cytoskeletal visco-elasticity. Parameters of spectral analyses could be related to mean square displacement (MSD) analyses with specific advantages in characterizing intracellular mechanical work. We identified two spectral ranges where mechanical work dominated vibrations of intracellular components: 0-3 Hz for intracellular particles and the plasma-membrane, and 100-150 Hz for the plasma-membrane. The 0-3 Hz vibrations of the cell membrane that we measured in an experimental model of immune synapse (IS) are expected to affect the IS formation and function in effector cells. It may also facilitate immunological escape of extensively vibrating malignant cells.
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Affiliation(s)
| | - Eilon Sherman
- Racah Institute of Physics, The Hebrew University, Jerusalem, Israel
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38
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Ashraf S, Tay YD, Kelly DA, Sawin KE. Microtubule-independent movement of the fission yeast nucleus. J Cell Sci 2021; 134:jcs.253021. [PMID: 33602740 PMCID: PMC8015250 DOI: 10.1242/jcs.253021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 02/09/2021] [Indexed: 12/14/2022] Open
Abstract
Movement of the cell nucleus typically involves the cytoskeleton and either polymerization-based pushing forces or motor-based pulling forces. In the fission yeast Schizosaccharomyces pombe, nuclear movement and positioning are thought to depend on microtubule polymerization-based pushing forces. Here, we describe a novel, microtubule-independent, form of nuclear movement in fission yeast. Microtubule-independent nuclear movement is directed towards growing cell tips, and it is strongest when the nucleus is close to a growing cell tip, and weakest when the nucleus is far from that tip. Microtubule-independent nuclear movement requires actin cables but does not depend on actin polymerization-based pushing or myosin V-based pulling forces. The vesicle-associated membrane protein (VAMP)-associated proteins (VAPs) Scs2 and Scs22, which are critical for endoplasmic reticulum-plasma membrane contact sites in fission yeast, are also required for microtubule-independent nuclear movement. We also find that in cells in which microtubule-based pushing forces are present, disruption of actin cables leads to increased fluctuations in interphase nuclear positioning and subsequent altered septation. Our results suggest two non-exclusive mechanisms for microtubule-independent nuclear movement, which may help illuminate aspects of nuclear positioning in other cells.
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39
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Lin C, Ashwin P, Steinberg G. Modelling the motion of organelles in an elongated cell via the coordination of heterogeneous drift-diffusion and long-range transport. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:10. [PMID: 33683507 DOI: 10.1140/epje/s10189-020-00007-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Cellular distribution of organelles in living cells is achieved via a variety of transport mechanisms, including directed motion, mediated by molecular motors along microtubules (MTs), and diffusion which is predominantly heterogeneous in space. In this paper, we introduce a model for particle transport in elongated cells that couples poleward drift, long-range bidirectional transport and diffusion with spatial heterogeneity in a three-dimensional space. Using stochastic simulations and analysis of a related population model, we find parameter regions where the three-dimensional model can be reduced to a coupled one-dimensional model or even a one-dimensional scalar model. We explore the efficiency with which individual model components can overcome drift towards one of the cell poles to reach an approximately even distribution. In particular, we find that if lateral movement is well mixed, then increasing the binding ability of particles to MTs is an efficient way to overcome a poleward drift, whereas if lateral motion is not well mixed, then increasing the axial diffusivity away from MTs becomes an efficient way to overcome the poleward drift. Our three-dimensional model provides a new tool that will help to understand the mechanisms by which eukaryotic cells organize their organelles in an elongated cell, and in particular when the one-dimensional models are applicable.
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Affiliation(s)
- Congping Lin
- School of Mathematics and Statistics, Huazhong University of Science and Technology, Wuhan, China.
- Center for Mathematical Sciences, Huazhong University of Science and Technology, Wuhan, China.
- Hubei Key Lab of Engineering Modeling and Scientific Computing, Huazhong University of Science and Technology, Wuhan, China.
| | - Peter Ashwin
- Department of Mathematics, University of Exeter, Exeter, UK
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40
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Winter MR, Morgulis M, Gildor T, Cohen AR, Ben-Tabou de-Leon S. Calcium-vesicles perform active diffusion in the sea urchin embryo during larval biomineralization. PLoS Comput Biol 2021; 17:e1008780. [PMID: 33617532 PMCID: PMC7932551 DOI: 10.1371/journal.pcbi.1008780] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 03/04/2021] [Accepted: 02/08/2021] [Indexed: 11/18/2022] Open
Abstract
Biomineralization is the process by which organisms use minerals to harden their tissues and provide them with physical support. Biomineralizing cells concentrate the mineral in vesicles that they secret into a dedicated compartment where crystallization occurs. The dynamics of vesicle motion and the molecular mechanisms that control it, are not well understood. Sea urchin larval skeletogenesis provides an excellent platform for investigating the kinetics of mineral-bearing vesicles. Here we used lattice light-sheet microscopy to study the three-dimensional (3D) dynamics of calcium-bearing vesicles in the cells of normal sea urchin embryos and of embryos where skeletogenesis is blocked through the inhibition of Vascular Endothelial Growth Factor Receptor (VEGFR). We developed computational tools for displaying 3D-volumetric movies and for automatically quantifying vesicle dynamics. Our findings imply that calcium vesicles perform an active diffusion motion in both, calcifying (skeletogenic) and non-calcifying (ectodermal) cells of the embryo. The diffusion coefficient and vesicle speed are larger in the mesenchymal skeletogenic cells compared to the epithelial ectodermal cells. These differences are possibly due to the distinct mechanical properties of the two tissues, demonstrated by the enhanced f-actin accumulation and myosinII activity in the ectodermal cells compared to the skeletogenic cells. Vesicle motion is not directed toward the biomineralization compartment, but the vesicles slow down when they approach it, and probably bind for mineral deposition. VEGFR inhibition leads to an increase of vesicle volume but hardly changes vesicle kinetics and doesn’t affect f-actin accumulation and myosinII activity. Thus, calcium vesicles perform an active diffusion motion in the cells of the sea urchin embryo, with diffusion length and speed that inversely correlate with the strength of the actomyosin network. Overall, our studies provide an unprecedented view of calcium vesicle 3D-dynamics and point toward cytoskeleton remodeling as an important effector of the motion of mineral-bearing vesicles. Biomineralization is a widespread, fundamental process by which organisms use minerals to harden their tissues. Mineral-bearing vesicles were observed in biomineralizing cells and play an essential role in biomineralization, yet little is known about their three-dimensional (3D) dynamics. Here we quantify 3D-vesicle-dynamics during calcite skeleton formation in sea urchin larvae, using lattice-light-sheet microscopy. We discover that calcium vesicles perform a diffusive motion in both calcifying and non-calcifying cells of the embryo. The diffusion coefficient and vesicle speed are higher in the mesenchymal skeletogenic cells compared to the epithelial ectodermal cells. This difference is possibly due to the higher rigidity of the ectodermal cells as demonstrated by the enhanced signal of f-actin and myosinII activity in these cells compared to the skeletogenic cells. The motion of the vesicles in the skeletogenic cells, is not directed toward the biomineralization compartment but the vesicles slow down near it, possibly to deposit their content. Blocking skeletogenesis through the inhibition of Vascular Endothelial Growth Factor Receptor (VEGFR), increases vesicle volume but doesn’t change the diffusion mode and the cytoskeleton markers in the cells. Our studies reveal the active diffusive motion of mineral bearing vesicles that is apparently defined by the mechanical properties of the cells.
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Affiliation(s)
- Mark R. Winter
- Marine Biology Department, Charney School of Marine Sciences, the University of Haifa, Haifa, Israel
- * E-mail: (MRW); (SBD)
| | - Miri Morgulis
- Marine Biology Department, Charney School of Marine Sciences, the University of Haifa, Haifa, Israel
| | - Tsvia Gildor
- Marine Biology Department, Charney School of Marine Sciences, the University of Haifa, Haifa, Israel
| | - Andrew R. Cohen
- Dept of Electrical Engineering, Drexel University, Pennsylvania, United States of America
| | - Smadar Ben-Tabou de-Leon
- Marine Biology Department, Charney School of Marine Sciences, the University of Haifa, Haifa, Israel
- * E-mail: (MRW); (SBD)
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41
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Liu J, Bao JD, Chen X. Correlated continuous-time random walk in a velocity field: Anomalous bifractional crossover. Phys Rev E 2021; 102:062122. [PMID: 33465995 DOI: 10.1103/physreve.102.062122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/23/2020] [Indexed: 11/06/2022]
Abstract
The diffusion of space-time correlated continuous-time random walk moving in the velocity field, which includes the fluid flowing freely and the fluid flowing through porous media, is investigated in this paper. Results reveal that it presents anomalous diffusion merely caused by space-time correlation in the freely flowing fluid, and the bias from the velocity field only supplies a standard advection, which is verified by the corresponding generalized diffusion equation which includes a standard advection term. However, the diffusion in the fluid flowing through porous media, i.e., the mean squared displacement, can display a bifractional form of which one originates from space-time correlation and the other one originates from dispersive bias caused by sticking of the porous media. The fractional advection term emerging in the corresponding generalized diffusion equation confirms the results. Moreover, the coexistence of correlation and dispersive bias result in crossover phenomenon in-between the diffusive process at an intermediate timescale, but just as the definition of diffusion, the one owning the largest diffusion exponent always prevails at large timescales. However, since the two fractional diffusions originate from a different mechanism, even if it owns the smaller diffusion exponent, that one can dominate the diffusion if it fluctuates much stronger than the other one, which no longer obeys the previous conclusion.
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Affiliation(s)
- Jian Liu
- Department of Physics, Beijing Technology and Business University, Beijing, 100048, China Institute of Systems Science, Beijing Technology and Business University, Beijing, 100048, China
| | - Jing-Dong Bao
- Department of Physics, Beijing Normal University, Beijing, 100875, China
| | - Xiaosong Chen
- School of Systems Science, Beijing Normal University, Beijing, 100875, China
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42
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Macropinocytosis-mediated membrane recycling drives neural crest migration by delivering F-actin to the lamellipodium. Proc Natl Acad Sci U S A 2020; 117:27400-27411. [PMID: 33087579 PMCID: PMC7959501 DOI: 10.1073/pnas.2007229117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Membrane and cytoskeletal dynamics are critical to cell motility. Extensively studied in cell culture, their roles in cell movement in vivo are less understood, especially in higher vertebrates. We use dynamic imaging to visualize membrane and cytoskeletal behavior in migrating neural crest cells in living tissue. We found that forward movement of individual neural crest cells is accompanied by circular membrane flow, from anterior-to-posterior apically and posterior-to-anterior basally, coupled with internalization of lipid vesicles via macropinocytosis in the soma. Macropinosomes become wrapped with actin, then undergo anterograde translocation via microtubules toward the lamellipodium, resulting in its expansion. We elucidate how actin dynamics and membrane flow are interacted to drive forward locomotion of individual cells. Individual cell migration requires front-to-back polarity manifested by lamellipodial extension. At present, it remains debated whether and how membrane motility mediates this cell morphological change. To gain insights into these processes, we perform live imaging and molecular perturbation of migrating chick neural crest cells in vivo. Our results reveal an endocytic loop formed by circular membrane flow and anterograde movement of lipid vesicles, resulting in cell polarization and locomotion. Rather than clathrin-mediated endocytosis, macropinosomes encapsulate F-actin in the cell body, forming vesicles that translocate via microtubules to deliver actin to the anterior. In addition to previously proposed local conversion of actin monomers to polymers, we demonstrate a surprising role for shuttling of F-actin across cells for lamellipodial expansion. Thus, the membrane and cytoskeleton act in concert in distinct subcellular compartments to drive forward cell migration.
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43
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S Mogre S, Brown AI, Koslover EF. Getting around the cell: physical transport in the intracellular world. Phys Biol 2020; 17:061003. [PMID: 32663814 DOI: 10.1088/1478-3975/aba5e5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eukaryotic cells face the challenging task of transporting a variety of particles through the complex intracellular milieu in order to deliver, distribute, and mix the many components that support cell function. In this review, we explore the biological objectives and physical mechanisms of intracellular transport. Our focus is on cytoplasmic and intra-organelle transport at the whole-cell scale. We outline several key biological functions that depend on physically transporting components across the cell, including the delivery of secreted proteins, support of cell growth and repair, propagation of intracellular signals, establishment of organelle contacts, and spatial organization of metabolic gradients. We then review the three primary physical modes of transport in eukaryotic cells: diffusive motion, motor-driven transport, and advection by cytoplasmic flow. For each mechanism, we identify the main factors that determine speed and directionality. We also highlight the efficiency of each transport mode in fulfilling various key objectives of transport, such as particle mixing, directed delivery, and rapid target search. Taken together, the interplay of diffusion, molecular motors, and flows supports the intracellular transport needs that underlie a broad variety of biological phenomena.
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Affiliation(s)
- Saurabh S Mogre
- Department of Physics, University of California, San Diego, San Diego, California 92093, United States of America
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44
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Park J, Bailey EJ, Composto RJ, Winey KI. Single-Particle Tracking of Nonsticky and Sticky Nanoparticles in Polymer Melts. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00457] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jinseok Park
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Eric J. Bailey
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Russell J. Composto
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Karen I. Winey
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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45
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Leung HM, Wang ML, Osman H, Abouei E, MacAulay C, Follen M, Gardecki JA, Tearney GJ. Imaging intracellular motion with dynamic micro-optical coherence tomography. BIOMEDICAL OPTICS EXPRESS 2020; 11:2768-2778. [PMID: 32499959 PMCID: PMC7249806 DOI: 10.1364/boe.390782] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 05/12/2023]
Abstract
This paper describes a new technology that uses 1-µm-resolution optical coherence tomography (µOCT) to obtain cross-sectional images of intracellular dynamics with dramatically enhanced image contrast. This so-called dynamic µOCT (d-µOCT) is accomplished by acquiring a time series of µOCT images and conducting power frequency analysis of the temporal fluctuations that arise from intracellular motion on a pixel-per-pixel basis. Here, we demonstrate d-µOCT imaging of freshly excised human esophageal and cervical biopsy samples. Depth-resolved d-µOCT images of intact tissue show that intracellular dynamics provides a new contrast mechanism for µOCT that highlights subcellular morphology and activity in epithelial surface maturation patterns.
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Affiliation(s)
- Hui Min Leung
- Wellman Center for Photomedicine, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
- Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
| | - Michelle L. Wang
- Wellman Center for Photomedicine, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Hany Osman
- Wellman Center for Photomedicine, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
- Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
| | - Elham Abouei
- University of British Columbia, Department of Physics and Astronomy, Vancouver, BC V6 T 1Z1, Canada
- British Columbia Cancer Research Center, Department of Integrative Oncology, Vancouver, BC V5Z 1L3, Canada
| | - Calum MacAulay
- British Columbia Cancer Research Center, Department of Integrative Oncology, Vancouver, BC V5Z 1L3, Canada
| | - Michele Follen
- NYC Health + Hospitals/Kings County, Cancer Prevention and Cancer Services for Kings County Hospital, 451 Clarkson Avenue, C-Building, Suite 4104, Brooklyn, NY 11203, USA
| | - Joseph A. Gardecki
- Wellman Center for Photomedicine, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
- Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
| | - Guillermo J. Tearney
- Wellman Center for Photomedicine, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
- Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
- Harvard-MIT Division of Heath Sciences and Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Department of Pathology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
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46
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Cao X, Zhang B, Zhao N. Contrastive factors of activity and crowding on conformational properties of a flexible polymer. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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47
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Gray WT, Govers SK, Xiang Y, Parry BR, Campos M, Kim S, Jacobs-Wagner C. Nucleoid Size Scaling and Intracellular Organization of Translation across Bacteria. Cell 2020; 177:1632-1648.e20. [PMID: 31150626 DOI: 10.1016/j.cell.2019.05.017] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/01/2019] [Accepted: 05/08/2019] [Indexed: 01/10/2023]
Abstract
The scaling of organelles with cell size is thought to be exclusive to eukaryotes. Here, we demonstrate that similar scaling relationships hold for the bacterial nucleoid. Despite the absence of a nuclear membrane, nucleoid size strongly correlates with cell size, independent of changes in DNA amount and across various nutrient conditions. This correlation is observed in diverse bacteria, revealing a near-constant ratio between nucleoid and cell size for a given species. As in eukaryotes, the nucleocytoplasmic ratio in bacteria varies greatly among species. This spectrum of nucleocytoplasmic ratios is independent of genome size, and instead it appears linked to the average population cell size. Bacteria with different nucleocytoplasmic ratios have a cytoplasm with different biophysical properties, impacting ribosome mobility and localization. Together, our findings identify new organizational principles and biophysical features of bacterial cells, implicating the nucleocytoplasmic ratio and cell size as determinants of the intracellular organization of translation.
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Affiliation(s)
- William T Gray
- Microbial Sciences Institute, Yale University, West Haven, CT, USA; Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Sander K Govers
- Microbial Sciences Institute, Yale University, West Haven, CT, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Yingjie Xiang
- Microbial Sciences Institute, Yale University, West Haven, CT, USA; Department of Mechanical Engineering and Materials Science, Yale University, New Haven, CT, USA
| | - Bradley R Parry
- Microbial Sciences Institute, Yale University, West Haven, CT, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Manuel Campos
- Microbial Sciences Institute, Yale University, West Haven, CT, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Sangjin Kim
- Microbial Sciences Institute, Yale University, West Haven, CT, USA; Department of Mechanical Engineering and Materials Science, Yale University, New Haven, CT, USA
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA.
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48
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Cao X, Zhang B, Zhao N. Effective temperature scaled dynamics of a flexible polymer in an active bath. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1730992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Xiuli Cao
- College of Chemistry, Sichuan University, Chengdu, China
| | - Bingjie Zhang
- College of Chemistry, Sichuan University, Chengdu, China
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu, China
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49
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Timmermann M, Lukat N, Schneider LP, Shields CW, López GP, Selhuber-Unkel C. Migration of Microparticle-Containing Amoeba through Constricted Environments. ACS Biomater Sci Eng 2020; 6:889-897. [PMID: 32215319 PMCID: PMC7082834 DOI: 10.1021/acsbiomaterials.9b00496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 11/30/2019] [Indexed: 12/28/2022]
Abstract
![]()
In many situations,
cells migrate through tiny orifices.
Examples
include the extravasation of immune cells from the bloodstream for
fighting infections, the infiltration of cancer cells during metastasis,
and the migration of human pathogens. An extremely motile and medically
relevant type of human pathogen is Acanthamoeba castellanii. In the study presented here, we investigated how a combination
of microparticles and microstructured interfaces controls the migration
of A. castellanii trophozoites. The
microinterfaces comprised well-defined micropillar arrays, and the
trophozoites easily migrated through the given constrictions by adapting
the shape and size of their intracellular vacuoles and by adapting
intracellular motion. After feeding the trophozoite cells in microinterfaces
with synthetic, stiff microparticles of various sizes and shapes,
their behavior changed drastically: if the particles were smaller
than the micropillar gap, migration was still possible. If the cells
incorporated particles larger than the pillar gap, they could become
immobilized but could also display remarkable problem-solving capabilities.
For example, they turned rod-shaped microparticles such that their
short axis fit through the pillar gap or they transported the particles
above the structure. As migration is a crucial contribution to A. castellanii pathogenicity and is also relevant
to other biological processes in microenvironments, such as cancer
metastasis, our results provide an interesting strategy for controlling
the migration of cells containing intracellular particles by microstructured
interfaces that serve as migration-limiting environments.
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Affiliation(s)
- Michael Timmermann
- Institute of Materials Science, Biocompatible Nanomaterials, University of Kiel, Kaiserstr. 2, 24143 Kiel, Germany
| | - Nils Lukat
- Institute of Materials Science, Biocompatible Nanomaterials, University of Kiel, Kaiserstr. 2, 24143 Kiel, Germany
| | - Lindsay P Schneider
- Institute of Materials Science, Biocompatible Nanomaterials, University of Kiel, Kaiserstr. 2, 24143 Kiel, Germany
| | - C Wyatt Shields
- NSF Research Triangle Materials Research Science and Engineering Center, Durham, North Carolina 27708, United States.,Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gabriel P López
- NSF Research Triangle Materials Research Science and Engineering Center, Durham, North Carolina 27708, United States.,Center for Biomedical Engineering, Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Christine Selhuber-Unkel
- Institute of Materials Science, Biocompatible Nanomaterials, University of Kiel, Kaiserstr. 2, 24143 Kiel, Germany
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50
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Abstract
Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely integrated in experimental studies or accounted for in modelling. Whilst polymer physics is recognised as an important tool to understand the mechanisms of genome folding, in this commentary we discuss its potential applicability to aspects of TE biology. Based on recent works on the relationship between genome organisation and TE integration, we argue that existing polymer models may be extended to create a predictive framework for the study of TE integration patterns. We suggest that these models may offer orthogonal and generic insights into the integration profiles (or "topography") of TEs across organisms. In addition, we provide simple polymer physics arguments and preliminary molecular dynamics simulations of TEs inserting into heterogeneously flexible polymers. By considering this simple model, we show how polymer folding and local flexibility may generically affect TE integration patterns. The preliminary discussion reported in this commentary is aimed to lay the foundations for a large-scale analysis of TE integration dynamics and topography as a function of the three-dimensional host genome.
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