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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] [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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2
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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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3
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Woolley L, Burbidge A, Vermant J, Christakopoulos F. A microrheological examination of insulin-secreting β-cells in healthy and diabetic-like conditions. SOFT MATTER 2024; 20:3464-3472. [PMID: 38573072 DOI: 10.1039/d3sm01141k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Pancreatic β-cells regulate glucose homeostasis through glucose-stimulated insulin secretion, which is hindered in type-2 diabetes. Transport of the insulin vesicles is expected to be affected by changes in the viscoelastic and transport properties of the cytoplasm. These are evaluated in situ through particle-tracking measurements using a rat insulinoma β-cell line. The use of inert probes assists in decoupling the material properties of the cytoplasm from the active transport through cellular processes. The effect of glucose-stimulated insulin secretion is examined, and the subsequent remodeling of the cytoskeleton, at constant effects of cell activity, is shown to result in reduced mobility of the tracer particles. Induction of diabetic-like conditions is identified to alter the mean-squared displacement of the passive particles in the cytoplasm and diminish its reaction to glucose stimulation.
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Affiliation(s)
- Lukas Woolley
- Department of Materials, ETH Zurich, Vladimir-Prelog-Weg 5, 8093 Zurich, Switzerland.
| | - Adam Burbidge
- Nestlé Research, Route de Jorat 57, vers-chez-les Blanc, 1000 Lausanne, Switzerland
| | - Jan Vermant
- Department of Materials, ETH Zurich, Vladimir-Prelog-Weg 5, 8093 Zurich, Switzerland.
| | - Fotis Christakopoulos
- Department of Materials, ETH Zurich, Vladimir-Prelog-Weg 5, 8093 Zurich, Switzerland.
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4
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Campàs O, Noordstra I, Yap AS. Adherens junctions as molecular regulators of emergent tissue mechanics. Nat Rev Mol Cell Biol 2024; 25:252-269. [PMID: 38093099 DOI: 10.1038/s41580-023-00688-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2023] [Indexed: 03/28/2024]
Abstract
Tissue and organ development during embryogenesis relies on the collective and coordinated action of many cells. Recent studies have revealed that tissue material properties, including transitions between fluid and solid tissue states, are controlled in space and time to shape embryonic structures and regulate cell behaviours. Although the collective cellular flows that sculpt tissues are guided by tissue-level physical changes, these ultimately emerge from cellular-level and subcellular-level molecular mechanisms. Adherens junctions are key subcellular structures, built from clusters of classical cadherin receptors. They mediate physical interactions between cells and connect biochemical signalling to the physical characteristics of cell contacts, hence playing a fundamental role in tissue morphogenesis. In this Review, we take advantage of the results of recent, quantitative measurements of tissue mechanics to relate the molecular and cellular characteristics of adherens junctions, including adhesion strength, tension and dynamics, to the emergent physical state of embryonic tissues. We focus on systems in which cell-cell interactions are the primary contributor to morphogenesis, without significant contribution from cell-matrix interactions. We suggest that emergent tissue mechanics is an important direction for future research, bridging cell biology, developmental biology and mechanobiology to provide a holistic understanding of morphogenesis in health and disease.
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Affiliation(s)
- Otger Campàs
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology Dresden, Dresden, Germany.
| | - Ivar Noordstra
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Alpha S Yap
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia.
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5
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Li M. Harnessing atomic force microscopy-based single-cell analysis to advance physical oncology. Microsc Res Tech 2024; 87:631-659. [PMID: 38053519 DOI: 10.1002/jemt.24467] [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: 08/22/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023]
Abstract
Single-cell analysis is an emerging and promising frontier in the field of life sciences, which is expected to facilitate the exploration of fundamental laws of physiological and pathological processes. Single-cell analysis allows experimental access to cell-to-cell heterogeneity to reveal the distinctive behaviors of individual cells, offering novel opportunities to dissect the complexity of severe human diseases such as cancers. Among the single-cell analysis tools, atomic force microscopy (AFM) is a powerful and versatile one which is able to nondestructively image the fine topographies and quantitatively measure multiple mechanical properties of single living cancer cells in their native states under aqueous conditions with unprecedented spatiotemporal resolution. Over the past few decades, AFM has been widely utilized to detect the structural and mechanical behaviors of individual cancer cells during the process of tumor formation, invasion, and metastasis, yielding numerous unique insights into tumor pathogenesis from the biomechanical perspective and contributing much to the field of cancer mechanobiology. Here, the achievements of AFM-based analysis of single cancer cells to advance physical oncology are comprehensively summarized, and challenges and future perspectives are also discussed. RESEARCH HIGHLIGHTS: Achievements of AFM in characterizing the structural and mechanical behaviors of single cancer cells are summarized, and future directions are discussed. AFM is not only capable of visualizing cellular fine structures, but can also measure multiple cellular mechanical properties as well as cell-generated mechanical forces. There is still plenty of room for harnessing AFM-based single-cell analysis to advance physical oncology.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
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6
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Shen Y, Ori-McKenney KM. Microtubule-associated protein MAP7 promotes tubulin posttranslational modifications and cargo transport to enable osmotic adaptation. Dev Cell 2024:S1534-5807(24)00190-4. [PMID: 38574732 DOI: 10.1016/j.devcel.2024.03.022] [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: 06/23/2023] [Revised: 09/11/2023] [Accepted: 03/12/2024] [Indexed: 04/06/2024]
Abstract
Cells remodel their cytoskeletal networks to adapt to their environment. Here, we analyze the mechanisms utilized by the cell to tailor its microtubule landscape in response to changes in osmolarity that alter macromolecular crowding. By integrating live-cell imaging, ex vivo enzymatic assays, and in vitro reconstitution, we probe the impact of cytoplasmic density on microtubule-associated proteins (MAPs) and tubulin posttranslational modifications (PTMs). We find that human epithelial cells respond to fluctuations in cytoplasmic density by modulating microtubule acetylation, detyrosination, or MAP7 association without differentially affecting polyglutamylation, tyrosination, or MAP4 association. These MAP-PTM combinations alter intracellular cargo transport, enabling the cell to respond to osmotic challenges. We further dissect the molecular mechanisms governing tubulin PTM specification and find that MAP7 promotes acetylation and inhibits detyrosination. Our data identify MAP7 in modulating the tubulin code, resulting in microtubule cytoskeleton remodeling and alteration of intracellular transport as an integrated mechanism of cellular adaptation.
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Affiliation(s)
- Yusheng Shen
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Kassandra M Ori-McKenney
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA.
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7
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Stilgoe A, Favre-Bulle IA, Watson ML, Gomez-Godinez V, Berns MW, Preece D, Rubinsztein-Dunlop H. Shining Light in Mechanobiology: Optical Tweezers, Scissors, and Beyond. ACS PHOTONICS 2024; 11:917-940. [PMID: 38523746 PMCID: PMC10958612 DOI: 10.1021/acsphotonics.4c00064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/26/2024]
Abstract
Mechanobiology helps us to decipher cell and tissue functions by looking at changes in their mechanical properties that contribute to development, cell differentiation, physiology, and disease. Mechanobiology sits at the interface of biology, physics and engineering. One of the key technologies that enables characterization of properties of cells and tissue is microscopy. Combining microscopy with other quantitative measurement techniques such as optical tweezers and scissors, gives a very powerful tool for unraveling the intricacies of mechanobiology enabling measurement of forces, torques and displacements at play. We review the field of some light based studies of mechanobiology and optical detection of signal transduction ranging from optical micromanipulation-optical tweezers and scissors, advanced fluorescence techniques and optogenentics. In the current perspective paper, we concentrate our efforts on elucidating interesting measurements of forces, torques, positions, viscoelastic properties, and optogenetics inside and outside a cell attained when using structured light in combination with optical tweezers and scissors. We give perspective on the field concentrating on the use of structured light in imaging in combination with tweezers and scissors pointing out how novel developments in quantum imaging in combination with tweezers and scissors can bring to this fast growing field.
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Affiliation(s)
- Alexander
B. Stilgoe
- School of
Mathematics and Physics, The University
of Queensland, Brisbane, 4074, Australia
- ARC
CoE for Engineered Quantum Systems, The
University of Queensland, Brisbane, 4074, Australia
- ARC
CoE in Quantum Biotechnology, The University
of Queensland, 4074, Brisbane, Australia
| | - Itia A. Favre-Bulle
- School of
Mathematics and Physics, The University
of Queensland, Brisbane, 4074, Australia
- Queensland
Brain Institute, The University of Queensland, Brisbane, 4074, Australia
| | - Mark L. Watson
- School of
Mathematics and Physics, The University
of Queensland, Brisbane, 4074, Australia
- ARC
CoE for Engineered Quantum Systems, The
University of Queensland, Brisbane, 4074, Australia
| | - Veronica Gomez-Godinez
- Institute
of Engineering and Medicine, University
of California San Diego, San Diego, California 92093, United States
| | - Michael W. Berns
- Institute
of Engineering and Medicine, University
of California San Diego, San Diego, California 92093, United States
- Beckman
Laser Institute, University of California
Irvine, Irvine, California 92612, United States
| | - Daryl Preece
- Beckman
Laser Institute, University of California
Irvine, Irvine, California 92612, United States
| | - Halina Rubinsztein-Dunlop
- School of
Mathematics and Physics, The University
of Queensland, Brisbane, 4074, Australia
- ARC
CoE for Engineered Quantum Systems, The
University of Queensland, Brisbane, 4074, Australia
- ARC
CoE in Quantum Biotechnology, The University
of Queensland, 4074, Brisbane, Australia
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8
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Li P, Chen P, Qi F, Shi J, Zhu W, Li J, Zhang P, Xie H, Li L, Lei M, Ren X, Wang W, Zhang L, Xiang X, Zhang Y, Gao Z, Feng X, Du W, Liu X, Xia L, Liu BF, Li Y. High-throughput and proteome-wide discovery of endogenous biomolecular condensates. Nat Chem 2024:10.1038/s41557-024-01485-1. [PMID: 38499848 DOI: 10.1038/s41557-024-01485-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/23/2024] [Indexed: 03/20/2024]
Abstract
Phase separation inside mammalian cells regulates the formation of the biomolecular condensates that are related to gene expression, signalling, development and disease. However, a large population of endogenous condensates and their candidate phase-separating proteins have yet to be discovered in a quantitative and high-throughput manner. Here we demonstrate that endogenously expressed biomolecular condensates can be identified across a cell's proteome by sorting proteins across varying oligomeric states. We employ volumetric compression to modulate the concentrations of intracellular proteins and the degree of crowdedness, which are physical regulators of cellular biomolecular condensates. The changes in degree of the partition of proteins into condensates or phase separation led to varying oligomeric states of the proteins, which can be detected by coupling density gradient ultracentrifugation and quantitative mass spectrometry. In total, we identified 1,518 endogenous condensate proteins, of which 538 have not been reported before. Furthermore, we demonstrate that our strategy can identify condensate proteins that respond to specific biological processes.
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Affiliation(s)
- Pengjie Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Fukang Qi
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Jinyun Shi
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Wenjie Zhu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Jiashuo Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Peng Zhang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Han Xie
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Lina Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Mengcheng Lei
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xueqing Ren
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Wenhui Wang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Liang Zhang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xufu Xiang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yiwei Zhang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Zhaolong Gao
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xiaojun Feng
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Wei Du
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xin Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Limin Xia
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China.
| | - Yiwei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei Province, China.
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9
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Fujii Y, Ikenouchi J. Cytoplasmic zoning in membrane blebs. J Biochem 2024; 175:133-140. [PMID: 37943501 DOI: 10.1093/jb/mvad084] [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: 09/11/2023] [Revised: 10/23/2023] [Indexed: 11/10/2023] Open
Abstract
Blebs are membrane structures formed by the detachment of the plasma membrane from the underlying actin cytoskeleton. It is now clear that a wide variety of cells, including cancer cells, actively form blebs for cell migration and cell survival. The expansion of blebs has been regarded as the passive ballooning of the plasma membrane by an abrupt increase in intracellular pressure. However, recent studies revealed the importance of 'cytoplasmic zoning', i.e. local changes in the hydrodynamic properties and the ionic and protein content of the cytoplasm. In this review, we summarize the current understanding of the molecular mechanisms behind cytoplasmic zoning and its role in bleb expansion.
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Affiliation(s)
- Yuki Fujii
- Department of Biology, Faculty of Sciences, Kyushu University, Nishi-Ku, Fukuoka 819-0395, Japan
| | - Junichi Ikenouchi
- Department of Biology, Faculty of Sciences, Kyushu University, Nishi-Ku, Fukuoka 819-0395, Japan
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10
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Das R, Sakaue T, Shivashankar GV, Prost J, Hiraiwa T. Chromatin Remodeling Due to Transient-Link-and-Pass Activity Enhances Subnuclear Dynamics. PHYSICAL REVIEW LETTERS 2024; 132:058401. [PMID: 38364140 DOI: 10.1103/physrevlett.132.058401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/02/2024] [Indexed: 02/18/2024]
Abstract
Spatiotemporal coordination of chromatin and subnuclear compartments is crucial for cells. Numerous enzymes act inside nucleus-some of those transiently link and pass two chromatin segments. Here, we study how such an active perturbation affects fluctuating dynamics of an inclusion in the chromatic medium. Using numerical simulations and a versatile effective model, we categorize inclusion dynamics into three distinct modes. The transient-link-and-pass activity speeds up inclusion dynamics by affecting a slow mode related to chromatin remodeling, viz., size and shape of the chromatin meshes.
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Affiliation(s)
- Rakesh Das
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, Kanagawa 252-5258, Japan
| | - G V Shivashankar
- Department of Health Sciences and Technology (D-HEST), ETH Zurich, Villigen 8092, Switzerland
- Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Jacques Prost
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
- Laboratoire Physico Chimie Curie, Institut Curie, Paris Science et Lettres Research University, 75005 Paris, France
| | - Tetsuya Hiraiwa
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
- Institute of Physics, Academia Sinica, Taipei City 115201, Taiwan
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11
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Shen YF, Hu HX, Luo MB. Adsorption of active polymers on attractive nanoparticles. SOFT MATTER 2024; 20:621-628. [PMID: 38131641 DOI: 10.1039/d3sm01380d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The adsorption of active polymers on an attractive nanoparticle (NP) is studied using Langevin dynamics simulations. The active polymers consist of an active Brownian particle (ABP) at the head and a subsequent passive polymer chain. The ABP experiences an active force of magnitude Fa. The interactions between the active polymer and NP are modeled as Lennard-Jones potential with a strength εpn. We find the critical adsorption point εpn* increases with increasing the active force Fa. The increment of εpn*, denoted as Δεpn*, due to Fa can be expressed approximately as Δεpn* ∝ Fa2.5 for the restricted rotating active polymer (RRAP) where the rotation of the head ABP is restricted and Δεpn* ∝ Fa1.7 for the freely rotating active polymer (FRAP) where the ABP rotates freely. Meanwhile, the conformation of the adsorbed polymer, such as adsorbed trains on NP and the tail near the ABP, are also dependent on Fa. When the tail near the ABP is short, the adsorption is significantly affected by the active force. However, when the tail is long, the whole polymer can be viewed as a long tail stretched by the active force and unperturbed adsorption monomers. Simulation results show that the active force has a direct and significant effect on εpn* and the structure of the adsorbed active polymers.
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Affiliation(s)
- Yi-Fan Shen
- School of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Han-Xian Hu
- School of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Meng-Bo Luo
- School of Physics, Zhejiang University, Hangzhou 310027, China.
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12
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Seelbinder B, Wagner S, Jain M, Erben E, Klykov S, Stoev ID, Krishnaswamy VR, Kreysing M. Probe-free optical chromatin deformation and measurement of differential mechanical properties in the nucleus. eLife 2024; 13:e76421. [PMID: 38214505 PMCID: PMC10786458 DOI: 10.7554/elife.76421] [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: 12/15/2021] [Accepted: 11/29/2023] [Indexed: 01/13/2024] Open
Abstract
The nucleus is highly organized to facilitate coordinated gene transcription. Measuring the rheological properties of the nucleus and its sub-compartments will be crucial to understand the principles underlying nuclear organization. Here, we show that strongly localized temperature gradients (approaching 1°C/µm) can lead to substantial intra-nuclear chromatin displacements (>1 µm), while nuclear area and lamina shape remain unaffected. Using particle image velocimetry (PIV), intra-nuclear displacement fields can be calculated and converted into spatio-temporally resolved maps of various strain components. Using this approach, we show that chromatin displacements are highly reversible, indicating that elastic contributions are dominant in maintaining nuclear organization on the time scale of seconds. In genetically inverted nuclei, centrally compacted heterochromatin displays high resistance to deformation, giving a rigid, solid-like appearance. Correlating spatially resolved strain maps with fluorescent reporters in conventional interphase nuclei reveals that various nuclear compartments possess distinct mechanical identities. Surprisingly, both densely and loosely packed chromatin showed high resistance to deformation, compared to medium dense chromatin. Equally, nucleoli display particularly high resistance and strong local anchoring to heterochromatin. Our results establish how localized temperature gradients can be used to drive nuclear compartments out of mechanical equilibrium to obtain spatial maps of their material responses.
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Affiliation(s)
- Benjamin Seelbinder
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Centre for Systems BiologyDresdenGermany
| | - Susan Wagner
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Institute of Biological and Chemical Systems-Biological Information Processing, Karlsruhe Institute of TechnologyEggenstein-LeopoldshafenGermany
| | - Manavi Jain
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Centre for Systems BiologyDresdenGermany
| | - Elena Erben
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Centre for Systems BiologyDresdenGermany
| | - Sergei Klykov
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Centre for Systems BiologyDresdenGermany
| | - Iliya Dimitrov Stoev
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Centre for Systems BiologyDresdenGermany
| | | | - Moritz Kreysing
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Centre for Systems BiologyDresdenGermany
- Institute of Biological and Chemical Systems-Biological Information Processing, Karlsruhe Institute of TechnologyEggenstein-LeopoldshafenGermany
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13
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Sittewelle M, Royle SJ. Passive diffusion accounts for the majority of intracellular nanovesicle transport. Life Sci Alliance 2024; 7:e202302406. [PMID: 37857498 PMCID: PMC10587482 DOI: 10.26508/lsa.202302406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023] Open
Abstract
During membrane trafficking, a vesicle formed at the donor compartment must travel to the acceptor membrane before fusing. For large carriers, it is established that this transport is motor-driven; however, the mode by which small vesicles, which outnumber larger carriers, are transported is poorly characterized. Here, we show that intracellular nanovesicles (INVs), a substantial class of small vesicles, are highly mobile within cells and that this mobility depends almost entirely on passive diffusion (0.1-0.3 μm2 s-1). Using single particle tracking, we describe how other small trafficking vesicles have a similar diffusive mode of transport that contrasts with the motor-dependent movement of larger endolysosomal carriers. We also demonstrate that a subset of INVs is involved in exocytosis and that delivery of cargo to the plasma membrane during exocytosis is decreased when diffusion of INVs is specifically restricted. Our results suggest that passive diffusion is sufficient to explain the majority of small vesicle transport.
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Affiliation(s)
- Méghane Sittewelle
- https://ror.org/01a77tt86 Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Stephen J Royle
- https://ror.org/01a77tt86 Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
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14
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Fujii K, Kondo T, Kimura A. Enucleation of the C. elegans embryo revealed dynein-dependent spacing between microtubule asters. Life Sci Alliance 2024; 7:e202302427. [PMID: 37931957 PMCID: PMC10627822 DOI: 10.26508/lsa.202302427] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/08/2023] Open
Abstract
The intracellular positioning of the centrosome, a major microtubule-organizing center, is important for cellular functions. One of the features of centrosome positioning is the spacing between centrosomes; however, the underlying mechanisms are not fully understood. To characterize the spacing activity in Caenorhabditis elegans embryos, a genetic setup was developed to produce enucleated embryos. The centrosome was duplicated multiple times in the enucleated embryo, which enabled us to characterize the chromosome-independent spacing activity between sister and non-sister centrosome pairs. We found that the timely spacing depended on cytoplasmic dynein, and we propose a stoichiometric model of cortical and cytoplasmic pulling forces for the spacing between centrosomes. We also observed dynein-independent but non-muscle myosin II-dependent movement of centrosomes in the later cell cycle phase. The spacing mechanisms revealed in this study are expected to function between centrosomes in general, regardless of the presence of a chromosome/nucleus between them, including centrosome separation and spindle elongation.
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Affiliation(s)
- Ken Fujii
- https://ror.org/0516ah480 Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies) Mishima, Japan
- https://ror.org/02xg1m795 Cell Architecture Laboratory, National Institute of Genetics, Mishima, Japan
| | - Tomo Kondo
- https://ror.org/02xg1m795 Cell Architecture Laboratory, National Institute of Genetics, Mishima, Japan
| | - Akatsuki Kimura
- https://ror.org/0516ah480 Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies) Mishima, Japan
- https://ror.org/02xg1m795 Cell Architecture Laboratory, National Institute of Genetics, Mishima, Japan
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15
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Roy N, Sood AK, Ganapathy R. Harnessing Viscoelasticity to Suppress Irreversibility Buildup in a Colloidal Stirling Engine. PHYSICAL REVIEW LETTERS 2023; 131:238201. [PMID: 38134791 DOI: 10.1103/physrevlett.131.238201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/18/2023] [Accepted: 11/08/2023] [Indexed: 12/24/2023]
Abstract
Typically, the rate at which a heat engine can produce useful work is constrained by the buildup of irreversibility with increasing operating speed. Here, using a recently developed reservoir engineering technique, we designed and quantified the performance of a colloidal Stirling engine operating in a viscoelastic bath. While the bath acts like a viscous fluid in the quasistatic limit, and the engine's performance agrees with equilibrium predictions, on reducing the cycle time to the bath's structural relaxation time, the increasingly elastic response of the bath aids suppress the buildup of irreversibility. We show that the elastic energy stored during the isothermal compression step of the Stirling cycle facilitates quick equilibration in the isothermal expansion step. This results in equilibriumlike efficiencies even for cycle times shorter than the equilibration time of the colloidal particle.
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Affiliation(s)
- Niloyendu Roy
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore-560064, India
| | - A K Sood
- Department of Physics, Indian Institute of Science, Bangalore-560012, India
- International Centre for Materials Science, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore-560064, India
| | - Rajesh Ganapathy
- International Centre for Materials Science, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore-560064, India
- School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore-560064, India
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16
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Atia L, Fredberg JJ. A life off the beaten track in biomechanics: Imperfect elasticity, cytoskeletal glassiness, and epithelial unjamming. BIOPHYSICS REVIEWS 2023; 4:041304. [PMID: 38156333 PMCID: PMC10751956 DOI: 10.1063/5.0179719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023]
Abstract
Textbook descriptions of elasticity, viscosity, and viscoelasticity fail to account for certain mechanical behaviors that typify soft living matter. Here, we consider three examples. First, strong empirical evidence suggests that within lung parenchymal tissues, the frictional stresses expressed at the microscale are fundamentally not of viscous origin. Second, the cytoskeleton (CSK) of the airway smooth muscle cell, as well as that of all eukaryotic cells, is more solid-like than fluid-like, yet its elastic modulus is softer than the softest of soft rubbers by a factor of 104-105. Moreover, the eukaryotic CSK expresses power law rheology, innate malleability, and fluidization when sheared. For these reasons, taken together, the CSK of the living eukaryotic cell is reminiscent of the class of materials called soft glasses, thus likening it to inert materials such as clays, pastes slurries, emulsions, and foams. Third, the cellular collective comprising a confluent epithelial layer can become solid-like and jammed, fluid-like and unjammed, or something in between. Esoteric though each may seem, these discoveries are consequential insofar as they impact our understanding of bronchospasm and wound healing as well as cancer cell invasion and embryonic development. Moreover, there are reasons to suspect that certain of these phenomena first arose in the early protist as a result of evolutionary pressures exerted by the primordial microenvironment. We have hypothesized, further, that each then became passed down virtually unchanged to the present day as a conserved core process. These topics are addressed here not only because they are interesting but also because they track the journey of one laboratory along a path less traveled by.
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Affiliation(s)
- Lior Atia
- Ben Gurion University of the Negev, Beer Sheva, Israel
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17
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Arjona MI, Najafi J, Minc N. Cytoplasm mechanics and cellular organization. Curr Opin Cell Biol 2023; 85:102278. [PMID: 37979412 DOI: 10.1016/j.ceb.2023.102278] [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: 07/13/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/20/2023]
Abstract
As cells organize spatially or divide, they translocate many micron-scale organelles in their cytoplasm. These include endomembrane vesicles, nuclei, microtubule asters, mitotic spindles, or chromosomes. Organelle motion is powered by cytoskeleton forces but is opposed by viscoelastic forces imparted by the surrounding crowded cytoplasm medium. These resistive forces associated to cytoplasm physcial properties remain generally underappreciated, yet reach significant values to slow down organelle motion or even limit their displacement by springing them back towards their original position. The cytoplasm may also be itself organized in time and space, being for example stiffer or more fluid at certain locations or during particular cell cycle phases. Thus, cytoplasm mechanics may be viewed as a labile module that contributes to organize cells. We here review emerging methods, mechanisms, and concepts to study cytoplasm mechanical properties and their function in organelle positioning, cellular organization and division.
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Affiliation(s)
- María Isabel Arjona
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, France
| | - Javad Najafi
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, France
| | - Nicolas Minc
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, France.
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18
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Hu S, Zhang Y, Yi Q, Yang C, Liu Y, Bai Y. Time-resolved proteomic profiling reveals compositional and functional transitions across the stress granule life cycle. Nat Commun 2023; 14:7782. [PMID: 38012130 PMCID: PMC10682001 DOI: 10.1038/s41467-023-43470-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
Stress granules (SGs) are dynamic, membrane-less organelles. With their formation and disassembly processes characterized, it remains elusive how compositional transitions are coordinated during prolonged stress to meet changing functional needs. Here, using time-resolved proteomic profiling of the acute to prolonged heat-shock SG life cycle, we identify dynamic SG proteins, further segregated into early and late proteins. Comparison of different groups of SG proteins suggests that their biochemical properties help coordinate SG compositional and functional transitions. In particular, early proteins, with high phase-separation-propensity, drive the rapid formation of the initial SG platform, while late proteins are subsequently recruited as discrete modules to further functionalize SGs. This model, supported by immunoblotting and immunofluorescence imaging, provides a conceptual framework for the compositional transitions throughout the acute to prolonged SG life cycle. Additionally, an early SG constituent, non-muscle myosin II, is shown to promote SG formation by increasing SG fusion, underscoring the strength of this dataset in revealing the complexity of SG regulation.
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Affiliation(s)
- Shuyao Hu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
| | - Yufeng Zhang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Qianqian Yi
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Cuiwei Yang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Yanfen Liu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
| | - Yun Bai
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
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19
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Umeda K, Nishizawa K, Nagao W, Inokuchi S, Sugino Y, Ebata H, Mizuno D. Activity-dependent glassy cell mechanics II: Nonthermal fluctuations under metabolic activity. Biophys J 2023; 122:4395-4413. [PMID: 37865819 PMCID: PMC10698330 DOI: 10.1016/j.bpj.2023.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/28/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023] Open
Abstract
The glassy cytoplasm, crowded with bio-macromolecules, is fluidized in living cells by mechanical energy derived from metabolism. Characterizing the living cytoplasm as a nonequilibrium system is crucial in elucidating the intricate mechanism that relates cell mechanics to metabolic activities. In this study, we conducted active and passive microrheology in eukaryotic cells, and quantified nonthermal fluctuations by examining the violation of the fluctuation-dissipation theorem. The power spectral density of active force generation was estimated following the Langevin theory extended to nonequilibrium systems. However, experiments performed while regulating cellular metabolic activity showed that the nonthermal displacement fluctuation, rather than the active nonthermal force, is linked to metabolism. We discuss that mechano-enzymes in living cells do not act as microscopic objects. Instead, they generate meso-scale collective fluctuations with displacements controlled by enzymatic activity. The activity induces structural relaxations in glassy cytoplasm. Even though the autocorrelation of nonthermal fluctuations is lost at long timescales due to the structural relaxations, the nonthermal displacement fluctuation remains regulated by metabolic reactions. Our results therefore demonstrate that nonthermal fluctuations serve as a valuable indicator of a cell's metabolic activities, regardless of the presence or absence of structural relaxations.
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Affiliation(s)
| | | | - Wataru Nagao
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Shono Inokuchi
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Yujiro Sugino
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Ebata
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Daisuke Mizuno
- Department of Physics, Kyushu University, Fukuoka, Japan.
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20
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Xin Y, Li K, Huang M, Liang C, Siemann D, Wu L, Tan Y, Tang X. Biophysics in tumor growth and progression: from single mechano-sensitive molecules to mechanomedicine. Oncogene 2023; 42:3457-3490. [PMID: 37864030 PMCID: PMC10656290 DOI: 10.1038/s41388-023-02844-x] [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: 02/23/2023] [Revised: 09/08/2023] [Accepted: 09/15/2023] [Indexed: 10/22/2023]
Abstract
Evidence from physical sciences in oncology increasingly suggests that the interplay between the biophysical tumor microenvironment and genetic regulation has significant impact on tumor progression. Especially, tumor cells and the associated stromal cells not only alter their own cytoskeleton and physical properties but also remodel the microenvironment with anomalous physical properties. Together, these altered mechano-omics of tumor tissues and their constituents fundamentally shift the mechanotransduction paradigms in tumorous and stromal cells and activate oncogenic signaling within the neoplastic niche to facilitate tumor progression. However, current findings on tumor biophysics are limited, scattered, and often contradictory in multiple contexts. Systematic understanding of how biophysical cues influence tumor pathophysiology is still lacking. This review discusses recent different schools of findings in tumor biophysics that have arisen from multi-scale mechanobiology and the cutting-edge technologies. These findings range from the molecular and cellular to the whole tissue level and feature functional crosstalk between mechanotransduction and oncogenic signaling. We highlight the potential of these anomalous physical alterations as new therapeutic targets for cancer mechanomedicine. This framework reconciles opposing opinions in the field, proposes new directions for future cancer research, and conceptualizes novel mechanomedicine landscape to overcome the inherent shortcomings of conventional cancer diagnosis and therapies.
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Grants
- R35 GM150812 NIGMS NIH HHS
- This work was financially supported by National Natural Science Foundation of China (Project no. 11972316, Y.T.), Shenzhen Science and Technology Innovation Commission (Project no. JCYJ20200109142001798, SGDX2020110309520303, and JCYJ20220531091002006, Y.T.), General Research Fund of Hong Kong Research Grant Council (PolyU 15214320, Y. T.), Health and Medical Research Fund (HMRF18191421, Y.T.), Hong Kong Polytechnic University (1-CD75, 1-ZE2M, and 1-ZVY1, Y.T.), the Cancer Pilot Research Award from UF Health Cancer Center (X. T.), the National Institute of General Medical Sciences of the National Institutes of Health under award number R35GM150812 (X. T.), the National Science Foundation under grant number 2308574 (X. T.), the Air Force Office of Scientific Research under award number FA9550-23-1-0393 (X. T.), the University Scholar Program (X. T.), UF Research Opportunity Seed Fund (X. T.), the Gatorade Award (X. T.), and the National Science Foundation REU Site at UF: Engineering for Healthcare (Douglas Spearot and Malisa Sarntinoranont). We are deeply grateful for the insightful discussions with and generous support from all members of Tang (UF)’s and Tan (PolyU)’s laboratories and all staff members of the MAE/BME/ECE/Health Cancer Center at UF and BME at PolyU.
- National Natural Science Foundation of China (National Science Foundation of China)
- Shenzhen Science and Technology Innovation Commission
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Affiliation(s)
- Ying Xin
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China
| | - Keming Li
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China
| | - Miao Huang
- Department of Mechanical and Aerospace Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
| | - Chenyu Liang
- Department of Mechanical and Aerospace Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
| | - Dietmar Siemann
- UF Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Lizi Wu
- UF Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Youhua Tan
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China.
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong, China.
- Research Institute of Smart Ageing, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Xin Tang
- Department of Mechanical and Aerospace Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA.
- UF Health Cancer Center, University of Florida, Gainesville, FL, USA.
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA.
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL, USA.
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21
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Gu Q, Shanahan L, Hart JW, Belser S, Shofer N, Atatüre M, Knowles HS. Simultaneous Nanorheometry and Nanothermometry Using Intracellular Diamond Quantum Sensors. ACS NANO 2023; 17:20034-20042. [PMID: 37791968 PMCID: PMC10604098 DOI: 10.1021/acsnano.3c05285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023]
Abstract
The viscoelasticity of the cytoplasm plays a critical role in cell morphology, cell division, and intracellular transport. Viscoelasticity is also interconnected with other biophysical properties, such as temperature, which is known to influence cellular bioenergetics. Probing the connections between intracellular temperature and cytoplasmic viscoelasticity provides an exciting opportunity for the study of biological phenomena, such as metabolism and disease progression. The small length scales and transient nature of changes in these parameters combined with their complex interdependencies pose a challenge for biosensing tools, which are often limited to a single readout modality. Here, we present a dual-mode quantum sensor capable of performing simultaneous nanoscale thermometry and rheometry in dynamic cellular environments. We use nitrogen-vacancy centers in diamond nanocrystals as biocompatible sensors for in vitro measurements. We combine subdiffraction resolution single-particle tracking in a fluidic environment with optically detected magnetic resonance spectroscopy to perform simultaneous sensing of viscoelasticity and temperature. We use our sensor to demonstrate probing of the temperature-dependent viscoelasticity in complex media at the nanoscale. We then investigate the interplay between intracellular forces and the cytoplasmic rheology in live cells. Finally, we identify different rheological regimes and reveal evidence of active trafficking and details of the nanoscale viscoelasticity of the cytoplasm.
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Affiliation(s)
| | | | | | - Sophia Belser
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United
Kingdom
| | - Noah Shofer
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United
Kingdom
| | - Mete Atatüre
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United
Kingdom
| | - Helena S. Knowles
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United
Kingdom
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22
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Wang H, Zhang H, Tamura R, Da B, Abdellatef SA, Watanabe I, Ishida N, Fujita D, Hanagata N, Nakagawa T, Nakanishi J. Mapping stress inside living cells by atomic force microscopy in response to environmental stimuli. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2023; 24:2265434. [PMID: 37867575 PMCID: PMC10586080 DOI: 10.1080/14686996.2023.2265434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/26/2023] [Indexed: 10/24/2023]
Abstract
The response of cells to environmental stimuli, under either physiological or pathological conditions, plays a key role in determining cell fate toward either adaptive survival or controlled death. The efficiency of such a feedback mechanism is closely related to the most challenging human diseases, including cancer. Since cellular responses are implemented through physical forces exerted on intracellular components, more detailed knowledge of force distribution through modern imaging techniques is needed to ensure a mechanistic understanding of these forces. In this work, we mapped these intracellular forces at a whole-cell scale and with submicron resolution to correlate intracellular force distribution to the cytoskeletal structures. Furthermore, we visualized dynamic mechanical responses of the cells adapting to environmental modulations in situ. Such task was achieved by using an informatics-assisted atomic force microscope (AFM) indentation technique where a key step was Markov-chain Monte Carlo optimization to search for both the models used to fit indentation force-displacement curves and probe geometry descriptors. We demonstrated force dynamics within cytoskeleton, as well as nucleoskeleton in living cells which were subjected to mechanical state modulation: myosin motor inhibition, micro-compression stimulation and geometrical confinement manipulation. Our results highlight the alteration in the intracellular prestress to attenuate environmental stimuli; to involve in cellular survival against mechanical signal-initiated death during cancer growth and metastasis; and to initiate cell migration.
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Affiliation(s)
- Hongxin Wang
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, Tsukuba, Ibaraki, Japan
| | - Han Zhang
- Center for Basic Research on Materials, National Institute for Materials Science, Tsukuba, Ibaraki, Japan
| | - Ryo Tamura
- Center for Basic Research on Materials, National Institute for Materials Science, Tsukuba, Ibaraki, Japan
| | - Bo Da
- Center for Basic Research on Materials, National Institute for Materials Science, Tsukuba, Ibaraki, Japan
| | - Shimaa A. Abdellatef
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, Tsukuba, Ibaraki, Japan
| | - Ikumu Watanabe
- Center for Basic Research on Materials, National Institute for Materials Science, Tsukuba, Ibaraki, Japan
| | - Nobuyuki Ishida
- Center for Basic Research on Materials, National Institute for Materials Science, Tsukuba, Ibaraki, Japan
| | - Daisuke Fujita
- Center for Basic Research on Materials, National Institute for Materials Science, Tsukuba, Ibaraki, Japan
| | - Nobutaka Hanagata
- Research Network and Facility Services Division, National Institute for Materials Science, Tsukuba, Ibaraki, Japan
| | - Tomoki Nakagawa
- Department of Diagnostic Pathology, University of Tsukuba Hospital, Tsukuba, Ibaraki, Japan
| | - Jun Nakanishi
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, Tsukuba, Ibaraki, Japan
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23
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Mogilner A, Savinov M. Crawling, waving, inch worming, dilating, and pivoting mechanics of migrating cells: Lessons from Ken Jacobson. Biophys J 2023; 122:3551-3559. [PMID: 36934300 PMCID: PMC10541468 DOI: 10.1016/j.bpj.2023.03.023] [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: 01/28/2023] [Revised: 03/07/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Research on the locomotion of single cells on hard, flat surfaces brought insight into the mechanisms of leading-edge protrusion, spatially graded adhesion, front-rear coordination, and how intracellular and traction forces are harnessed to execute various maneuvers. Here, we highlight how, by studying a variety of cell types, shapes, and movements, Ken Jacobson and his collaborators made several discoveries that triggered the mechanistic understanding of cell motility. We then review the recent advancements and current perspectives in this field.
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Affiliation(s)
- Alex Mogilner
- Courant Institute of Mathematical Sciences, New York University, New York, New York; Department of Biology, New York University, New York, New York.
| | - Mariya Savinov
- Courant Institute of Mathematical Sciences, New York University, New York, New York
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24
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Jiang C, Luo HY, Xu X, Dou SX, Li W, Guan D, Ye F, Chen X, Guo M, Wang PY, Li H. Switch of cell migration modes orchestrated by changes of three-dimensional lamellipodium structure and intracellular diffusion. Nat Commun 2023; 14:5166. [PMID: 37620390 PMCID: PMC10449835 DOI: 10.1038/s41467-023-40858-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
Cell migration plays important roles in many biological processes, but how migrating cells orchestrate intracellular molecules and subcellular structures to regulate their speed and direction is still not clear. Here, by characterizing the intracellular diffusion and the three-dimensional lamellipodium structures of fish keratocyte cells, we observe a strong positive correlation between the intracellular diffusion and cell migration speed and, more importantly, discover a switching of cell migration modes with reversible intracellular diffusion variation and lamellipodium structure deformation. Distinct from the normal fast mode, cells migrating in the newly-found slow mode have a deformed lamellipodium with swollen-up front and thinned-down rear, reduced intracellular diffusion and compartmentalized macromolecule distribution in the lamellipodium. Furthermore, in turning cells, both lamellipodium structure and intracellular diffusion dynamics are also changed, with left-right symmetry breaking. We propose a mechanism involving the front-localized actin polymerization and increased molecular crowding in the lamellipodium to explain how cells spatiotemporally coordinate the intracellular diffusion dynamics and the lamellipodium structure in regulating their migrations.
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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 and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Yu Luo
- 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 and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinpeng Xu
- Physics Program, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China
- Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - 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 and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, 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
| | - Dongshi Guan
- School of Physical Sciences and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Fangfu Ye
- 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 and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325001, China
| | - Xiaosong Chen
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing, 100875, China
| | - Ming Guo
- Department of Mechanical Engineering, MIT, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - 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 and School of Engineering 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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Bacanu A, Pelletier JF, Jung Y, Fakhri N. Inferring scale-dependent non-equilibrium activity using carbon nanotubes. NATURE NANOTECHNOLOGY 2023; 18:905-911. [PMID: 37157022 DOI: 10.1038/s41565-023-01395-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 04/04/2023] [Indexed: 05/10/2023]
Abstract
In living systems, irreversible, yet stochastic, molecular interactions form multiscale structures (such as cytoskeletal networks), which mediate processes (such as cytokinesis and cellular motility) in a close relationship between the structure and function. However, owing to a lack of methods to quantify non-equilibrium activity, their dynamics remain poorly characterized. Here, by measuring the time-reversal asymmetry encoded in the conformational dynamics of filamentous single-walled carbon nanotubes embedded in the actomyosin network of Xenopus egg extract, we characterize the multiscale dynamics of non-equilibrium activity encoded in bending-mode amplitudes. Our method is sensitive to distinct perturbations to the actomyosin network and the concentration ratio of adenosine triphosphate to adenosine diphosphate. Thus, our method can dissect the functional coupling of microscopic dynamics to the emergence of larger scale non-equilibrium activity. We relate the spatiotemporal scales of non-equilibrium activity to the key physical parameters of a semiflexible filament embedded in a non-equilibrium viscoelastic environment. Our analysis provides a general tool to characterize steady-state non-equilibrium activity in high-dimensional spaces.
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Affiliation(s)
- Alexandru Bacanu
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - James F Pelletier
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
| | - Yoon Jung
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nikta Fakhri
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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26
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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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27
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Shen Y, Ori-McKenney KM. Macromolecular Crowding Tailors the Microtubule Cytoskeleton Through Tubulin Modifications and Microtubule-Associated Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544846. [PMID: 37398431 PMCID: PMC10312695 DOI: 10.1101/2023.06.14.544846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cells remodel their cytoskeletal networks to adapt to their environment. Here, we analyze the mechanisms utilized by the cell to tailor its microtubule landscape in response to changes in osmolarity that alter macromolecular crowding. By integrating live cell imaging, ex vivo enzymatic assays, and in vitro reconstitution, we probe the impact of acute perturbations in cytoplasmic density on microtubule-associated proteins (MAPs) and tubulin posttranslational modifications (PTMs), unraveling the molecular underpinnings of cellular adaptation via the microtubule cytoskeleton. We find that cells respond to fluctuations in cytoplasmic density by modulating microtubule acetylation, detyrosination, or MAP7 association, without differentially affecting polyglutamylation, tyrosination, or MAP4 association. These MAP-PTM combinations alter intracellular cargo transport, enabling the cell to respond to osmotic challenges. We further dissect the molecular mechanisms governing tubulin PTM specification, and find that MAP7 promotes acetylation by biasing the conformation of the microtubule lattice, and directly inhibits detyrosination. Acetylation and detyrosination can therefore be decoupled and utilized for distinct cellular purposes. Our data reveal that the MAP code dictates the tubulin code, resulting in remodeling of the microtubule cytoskeleton and alteration of intracellular transport as an integrated mechanism of cellular adaptation.
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Affiliation(s)
- Yusheng Shen
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Kassandra M Ori-McKenney
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
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28
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Ebata H, Umeda K, Nishizawa K, Nagao W, Inokuchi S, Sugino Y, Miyamoto T, Mizuno D. Activity-dependent glassy cell mechanics Ⅰ: Mechanical properties measured with active microrheology. Biophys J 2023; 122:1781-1793. [PMID: 37050875 PMCID: PMC10209042 DOI: 10.1016/j.bpj.2023.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 01/27/2023] [Accepted: 04/07/2023] [Indexed: 04/14/2023] Open
Abstract
Active microrheology was conducted in living cells by applying an optical-trapping force to vigorously fluctuating tracer beads with feedback-tracking technology. The complex shear modulus G(ω)=G'(ω)-iG″(ω) was measured in HeLa cells in an epithelial-like confluent monolayer. We found that G(ω)∝(-iω)1/2 over a wide range of frequencies (1 Hz < ω/2π < 10 kHz). Actin disruption and cell-cycle progression from G1 to S and G2 phases only had a limited effect on G(ω) in living cells. On the other hand, G(ω) was found to be dependent on cell metabolism; ATP-depleted cells showed an increased elastic modulus G'(ω) at low frequencies, giving rise to a constant plateau such that G(ω)=G0+A(-iω)1/2. Both the plateau and the additional frequency dependency ∝(-iω)1/2 of ATP-depleted cells are consistent with a rheological response typical of colloidal jamming. On the other hand, the plateau G0 disappeared in ordinary metabolically active cells, implying that living cells fluidize their internal states such that they approach the critical jamming point.
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Affiliation(s)
- Hiroyuki Ebata
- Department of Physics, Kyushu University, Fukuoka, Japan
| | | | - Kenji Nishizawa
- Institute of Developmental Biology of Marseille, Marseille, France
| | - Wataru Nagao
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Shono Inokuchi
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Yujiro Sugino
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Takafumi Miyamoto
- Department of Endocrinology and Metabolism, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan; Transborder Medical Research Center, University of Tsukuba, Ibaraki, Japan
| | - Daisuke Mizuno
- Department of Physics, Kyushu University, Fukuoka, Japan.
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29
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Higgins G, Higgins F, Peres J, Lang DM, Abdalrahman T, Zaman MH, Prince S, Franz T. Intracellular mechanics and TBX3 expression jointly dictate the spreading mode of melanoma cells in 3D environments. Exp Cell Res 2023; 428:113633. [PMID: 37172754 DOI: 10.1016/j.yexcr.2023.113633] [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: 03/21/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023]
Abstract
Cell stiffness and T-box transcription factor 3 (TBX3) expression have been identified as biomarkers of melanoma metastasis in 2D environments. This study aimed to determine how mechanical and biochemical properties of melanoma cells change during cluster formation in 3D environments. Vertical growth phase (VGP) and metastatic (MET) melanoma cells were embedded in 3D collagen matrices of 2 and 4 mg/ml collagen concentrations, representing low and high matrix stiffness. Mitochondrial fluctuation, intracellular stiffness, and TBX3 expression were quantified before and during cluster formation. In isolated cells, mitochondrial fluctuation decreased and intracellular stiffness increased with increase in disease stage from VGP to MET and increased matrix stiffness. TBX3 was highly expressed in soft matrices but diminished in stiff matrices for VGP and MET cells. Cluster formation of VGP cells was excessive in soft matrices but limited in stiff matrices, whereas for MET cells it was limited in soft and stiff matrices. In soft matrices, VGP cells did not change the intracellular properties, whereas MET cells exhibited increased mitochondrial fluctuation and decreased TBX3 expression. In stiff matrices, mitochondrial fluctuation and TBX3 expression increased in VGP and MET, and intracellular stiffness increased in VGP but decreased in MET cells. The findings suggest that soft extracellular environments are more favourable for tumour growth, and high TBX3 levels mediate collective cell migration and tumour growth in the earlier VGP disease stage but play a lesser role in the later metastatic stage of melanoma.
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Affiliation(s)
- Ghodeejah Higgins
- Biomedical Engineering Research Centre, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Faatiemah Higgins
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Jade Peres
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Dirk M Lang
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Tamer Abdalrahman
- Biomedical Engineering Research Centre, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Muhammad H Zaman
- Department of Biomedical Engineering, Boston University, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Sharon Prince
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Thomas Franz
- Biomedical Engineering Research Centre, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Observatory, South Africa; Bioengineering Science Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK.
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30
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Corci B, Hooiveld O, Dolga AM, Åberg C. Extending the analogy between intracellular motion in mammalian cells and glassy dynamics. SOFT MATTER 2023; 19:2529-2538. [PMID: 36939775 DOI: 10.1039/d2sm01672a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
How molecules, organelles, and foreign objects move within living cells has been studied in organisms ranging from bacteria to human cells. In mammalian cells, in particular, cellular vesicles move across the cell using motor proteins that carry the vesicle down the cytoskeleton to their destination. We have recently noted several similarities between the motion of such vesicles and that in disordered, "glassy", systems, but the generality of this observation remains unclear. Here we follow the motion of mitochondria, the organelles responsible for cell energy production, in mammalian cells over timescales from 50 ms to 70 s. Qualitative observations show that single mitochondria remain within a spatially limited region for extended periods of time, before moving longer distances relatively quickly. The displacement distribution is roughly Gaussian for shorter distances (≲0.05 μm) but exhibits exponentially decaying tails at longer distances (up to 0.40 μm). This behaviour is well-described by a model developed to describe the motion in glassy systems. These observations are extended to in total 3 different objects (mitochondria, lysosomes and nano-sized beads enclosed in vesicles), 3 different mammalian cell types (HEK 293, HeLa, and HT22), from 2 different organisms (human and mouse). Further evidence that supports glass-like characteristics of the motion is a difference between the time it takes to move a longer distance for the first time and subsequent times, as well as a weak ergodicity breaking of the motion. Overall, we demonstrate the ubiquity of glass-like motion in mammalian cells, providing a different perspective on intracellular motion.
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Affiliation(s)
- Beatrice Corci
- Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Oscar Hooiveld
- Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Amalia M Dolga
- Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Christoffer Åberg
- Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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31
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Lee WS, Enomoto T, Akimoto AM, Yoshida R. Capsule self-oscillating gels showing cell-like nonthermal membrane/shape fluctuations. MATERIALS HORIZONS 2023; 10:1332-1341. [PMID: 36722870 DOI: 10.1039/d2mh01490d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A primary interest in cell membrane and shape fluctuations is establishing experimental models reflecting only nonthermal active contributions. Here we report a millimeter-scaled capsule self-oscillating gel model mirroring the active contribution effect on cell fluctuations. In the capsule self-oscillating gels, the propagating chemical signals during a Belousov-Zhabotinsky (BZ) reaction induce simultaneous local deformations in the various regions, showing cell-like shape fluctuations. The capsule self-oscillating gels do not fluctuate without the BZ reaction, implying that only the active chemical parameter induces the gel fluctuations. The period and amplitude depend on the gel layer thickness and the concentration of the chemical substrate for the BZ reaction. Our results allow for a solid experimental platform showing actively driven cell-like fluctuations, which can potentially contribute to investigating the active parameter effect on cell fluctuations.
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Affiliation(s)
- Won Seok Lee
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Takafumi Enomoto
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Aya Mizutani Akimoto
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Ryo Yoshida
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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32
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Lee S, Jung I, Lee S, Shin J, Cho E, Jung S, Ih S, Kim YG, Hong S, Choi YL, Park S. Plasmonic-Magnetic Active Nanorheology for Intracellular Viscosity. NANO LETTERS 2023; 23:2031-2038. [PMID: 36695563 DOI: 10.1021/acs.nanolett.2c04761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We demonstrate active plasmonic systems where plasmonic signals are repeatedly modulated by changing the orientation of nanoprobes under an external magnetic field, which is a prerequisite for in situ active nanorheology in intracellular viscosity measurements. Au/Ni/Au nanorods act as "nanotransmitters", which transmit the mechanical motion of nanorods to an electromagnetic radiation signal as a periodic sine function. This fluctuating optical response is transduced to frequency peaks via Fourier transform surface plasmon resonance (FTSPR). As a driving frequency of the external magnetic field applied to the Au/Ni/Au nanorods increases and reaches above a critical threshold, there is a transition from the synchronous motion of nanorods to asynchronous responses, leading to the disappearance of the FTSPR peak, which allows us to measure the local viscosity of the complex fluids. Using this ensemble-based method with plasmonic functional nanomaterials, we measure the intracellular viscosity of cancer cells and normal cells in a reliable and reproducible manner.
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Affiliation(s)
- Sungwoo Lee
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
- Institute of Basic Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Insub Jung
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
- Institute of Basic Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Soohyun Lee
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Junghyun Shin
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University (SNU), Seoul 08826, Republic of Korea
| | - Eunbyeol Cho
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Sangbaek Jung
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Seongkeun Ih
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Yang-Gyun Kim
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Seunghun Hong
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University (SNU), Seoul 08826, Republic of Korea
| | - Yoon-La Choi
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University (SKKU), Seoul 06355, Republic of Korea
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Sungho Park
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
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Zhu X, Qin R, Qu K, Wang Z, Zhao X, Xu W. Atomic force microscopy-based assessment of multimechanical cellular properties for classification of graded bladder cancer cells and cancer early diagnosis using machine learning analysis. Acta Biomater 2023; 158:358-373. [PMID: 36581006 DOI: 10.1016/j.actbio.2022.12.035] [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: 06/14/2022] [Revised: 12/10/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022]
Abstract
Cellular mechanical properties (CMPs) have been frequently reported as biomarkers for cell cancerization to assist objective cytology, compared to the current subjective method dependent on cytomorphology. However, single or dual CMPs cannot always successfully distinguish every kind of malignant cell from its benign counterpart. In this work, we extract 4 CMPs of four different graded bladder cancer (BC) cell lines by AFM (atomic force microscopy)-based nanoindentation to generate a CMP database, which is used to train a cancerization-grade classifier by machine learning. The classifier is tested on 4 categories of BC cells at different cancer grades. The classification shows split-independent robustness and an accuracy of 91.25% with an AUC-ROC (ROC stands for receiver operating characteristic, and ROC curve is a graphical plot which illustrates the performance of a binary classifier system as its discrimination threshold is varied) value of 97.98%. Finally, we also compare our proposed method with traditional invasive diagnosis and noninvasive cancer diagnosis relying on cytomorphology, in terms of accuracy, sensitivity and specificity. Unlike former studies focusing on the discrimination between normal and cancerous cells, our study fulfills the classification of 4 graded cell lines at different cancerization stages, and thus provides a potential method for early detection of cancerization. STATEMENT OF SIGNIFICANCE: We measured four cellular mechanical properties (CMPs) of 4 graded bladder cancer (BC) cell lines using AFM (atomic force microscopy). We found that single or dual CMPs cannot fulfill the task of BC cell classification. Instead, we employ MLA (Machine Learning Algorithm)-based analysis whose inputs are BC CMPs. Compared with traditional cytomorphology-based prognoses, the non-invasive method proposed in this study has higher accuracy but with many fewer cellular properties as inputs. The proposed non-invasive prognosis is characterized with high sensitivity and specificity, and thus provides a potential tumor-grading means to identify cancer cells with different metastatic potential. Moreover, our study proposes an objective grading method based on quantitative characteristics desirable for avoiding misdiagnosis induced by ambiguous subjectivity.
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Affiliation(s)
- Xinyao Zhu
- Key Laboratory of Mechanism Theory and Equipment Design of Ministry of Education, Tianjin University, Tianjin 300350, China.
| | - Rui Qin
- Key Laboratory of Mechanism Theory and Equipment Design of Ministry of Education, Tianjin University, Tianjin 300350, China
| | - Kaige Qu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China; JR3CN & IRAC, University of Bedfordshire, Luton LU1 3JU, UK
| | - Zuobin Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China; JR3CN & IRAC, University of Bedfordshire, Luton LU1 3JU, UK
| | - Xuexia Zhao
- College of Mechanical and Vehicle Engineering, Taiyuan University of Technology, Taiyuan 030000, China
| | - Wei Xu
- Faculty of Engineering and Physical Sciences, University of Surrey, Guilford GU2 7XH, UK
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34
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Shaiken TE, Grimm SL, Siam M, Williams A, Rezaeian AH, Kraushaar D, Ricco E, Robertson MJ, Coarfa C, Jain A, Malovannaya A, Stossi F, Opekun AR, Price AP, Dubrulle J. Transcriptome, proteome, and protein synthesis within the intracellular cytomatrix. iScience 2023; 26:105965. [PMID: 36824274 PMCID: PMC9941065 DOI: 10.1016/j.isci.2023.105965] [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: 03/03/2022] [Revised: 11/07/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
Despite the knowledge that protein translation and various metabolic reactions that create and sustain cellular life occur in the cytoplasm, the structural organization within the cytoplasm remains unclear. Recent models indicate that cytoplasm contains viscous fluid and elastic solid phases. We separated these viscous fluid and solid elastic compartments, which we call the cytosol and cytomatrix, respectively. The distinctive composition of the cytomatrix included structural proteins, ribosomes, and metabolome enzymes. High-throughput analysis revealed unique biosynthetic pathways within the cytomatrix. Enrichment of biosynthetic pathways in the cytomatrix indicated the presence of immobilized biocatalysis. Enzymatic immobilization and segregation can surmount spatial impediments, and the local pathway segregation may form cytoplasmic organelles. Protein translation was reprogrammed within the cytomatrix under the restriction of protein synthesis by drug treatment. The cytosol and cytomatrix are an elaborately interconnected network that promotes operational flexibility in healthy cells and the survival of malignant cells.
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Affiliation(s)
- Tattym E. Shaiken
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
- PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA
| | - Sandra L. Grimm
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mohamad Siam
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
- PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA
| | - Amanda Williams
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
- PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA
| | - Abdol-Hossein Rezaeian
- PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Daniel Kraushaar
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily Ricco
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Cristian Coarfa
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antrix Jain
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Malovannaya
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fabio Stossi
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antone R. Opekun
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alyssa P. Price
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julien Dubrulle
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
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35
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Roy S, Vaippully R, Lokesh M, Nalupurackal G, Edwina P, Bajpai S, Roy B. Comparison of translational and rotational modes towards passive rheology of the cytoplasm of MCF-7 cells using optical tweezers. FRONTIERS IN PHYSICS 2023; 10:1099958. [PMID: 36685106 PMCID: PMC7614090 DOI: 10.3389/fphy.2022.1099958] [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: 06/17/2023]
Abstract
A colloidal particle placed inside the cell cytoplasm is enmeshed within a network of cytoskeletal fibres immersed in the cytosolic fluid. The translational mode is believed to yield different rheological parameters than the rotational mode, given that these modes stretch the fibers differently. We compare the parameters for Michigan Cancer Foundation-7 (MCF-7) cells in this manuscript and find that the results are well comparable to each other. At low values of 0 Hz viscosity, the rotational and translational viscoelasticity matches well. However, discrepancies appear at higher values which may indicate that the cytoskeletal modes involved in rotation and translation of the particle are getting invoked. We also show that the 0 Hz viscosity increases as the cell ages under the conditions of constant room temperature of 25°C on the sample chamber.
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Affiliation(s)
- Srestha Roy
- Department of Physics, Indian Institute of Technology Madras, Chennai, India
| | - Rahul Vaippully
- Department of Physics, Indian Institute of Technology Madras, Chennai, India
| | - Muruga Lokesh
- Department of Physics, Indian Institute of Technology Madras, Chennai, India
| | - Gokul Nalupurackal
- Department of Physics, Indian Institute of Technology Madras, Chennai, India
| | - Privita Edwina
- Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai, India
| | - Saumendra Bajpai
- Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai, India
| | - Basudev Roy
- Department of Physics, Indian Institute of Technology Madras, Chennai, India
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36
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Erkamp NA, Qi R, Welsh TJ, Knowles TPJ. Microfluidics for multiscale studies of biomolecular condensates. LAB ON A CHIP 2022; 23:9-24. [PMID: 36269080 PMCID: PMC9764808 DOI: 10.1039/d2lc00622g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/04/2022] [Indexed: 05/12/2023]
Abstract
Membraneless organelles formed through condensation of biomolecules in living cells have become the focus of sustained efforts to elucidate their mechanisms of formation and function. These condensates perform a range of vital functions in cells and are closely connected to key processes in functional and aberrant biology. Since these systems occupy a size scale intermediate between single proteins and conventional protein complexes on the one hand, and cellular length scales on the other hand, they have proved challenging to probe using conventional approaches from either protein science or cell biology. Additionally, condensate can form, solidify and perform functions on various time-scales. From a physical point of view, biomolecular condensates are colloidal soft matter systems, and microfluidic approaches, which originated in soft condensed matter research, have successfully been used to study biomolecular condensates. This review explores how microfluidics have aided condensate research into the thermodynamics, kinetics and other properties of condensates, by offering high-throughput and novel experimental setups.
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Affiliation(s)
- Nadia A Erkamp
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Runzhang Qi
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Timothy J Welsh
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, CB3 0HE, UK
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Tripathi AK, Tlusty T. Gauging Nanoswimmer Dynamics via the Motion of Large Bodies. PHYSICAL REVIEW LETTERS 2022; 129:254502. [PMID: 36608228 DOI: 10.1103/physrevlett.129.254502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Nanoswimmers are ubiquitous in biotechnology and nanotechnology but are extremely challenging to measure due to their minute size and driving forces. A simple method is proposed for detecting the elusive physical features of nanoswimmers by observing how they affect the motion of much larger, easily traceable particles. Modeling the swimmers as hydrodynamic force dipoles, we find direct, easy-to-calibrate relations between the observable power spectrum and diffusivity of the tracers and the dynamic characteristics of the swimmers-their force dipole moment and correlation times.
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Affiliation(s)
- Ashwani Kr Tripathi
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Tsvi Tlusty
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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38
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Blache U, Ford EM, Ha B, Rijns L, Chaudhuri O, Dankers PY, Kloxin AM, Snedeker JG, Gentleman E. Engineered hydrogels for mechanobiology. NATURE REVIEWS. METHODS PRIMERS 2022; 2:98. [PMID: 37461429 PMCID: PMC7614763 DOI: 10.1038/s43586-022-00179-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 07/20/2023]
Abstract
Cells' local mechanical environment can be as important in guiding cellular responses as many well-characterized biochemical cues. Hydrogels that mimic the native extracellular matrix can provide these mechanical cues to encapsulated cells, allowing for the study of their impact on cellular behaviours. Moreover, by harnessing cellular responses to mechanical cues, hydrogels can be used to create tissues in vitro for regenerative medicine applications and for disease modelling. This Primer outlines the importance and challenges of creating hydrogels that mimic the mechanical and biological properties of the native extracellular matrix. The design of hydrogels for mechanobiology studies is discussed, including appropriate choice of cross-linking chemistry and strategies to tailor hydrogel mechanical cues. Techniques for characterizing hydrogels are explained, highlighting methods used to analyze cell behaviour. Example applications for studying fundamental mechanobiological processes and regenerative therapies are provided, along with a discussion of the limitations of hydrogels as mimetics of the native extracellular matrix. The article ends with an outlook for the field, focusing on emerging technologies that will enable new insights into mechanobiology and its role in tissue homeostasis and disease.
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Affiliation(s)
- Ulrich Blache
- Fraunhofer Institute for Cell Therapy and Immunology and Fraunhofer Cluster of Excellence for Immune-Mediated Disease, Leipzig, Germany
| | - Eden M. Ford
- Department of Chemical and Biomolecular Engineering, University of Delaware, DE, USA
| | - Byunghang Ha
- Department of Mechanical Engineering, Stanford University, CA, USA
| | - Laura Rijns
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Laboratory of Chemical Biology, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Ovijit Chaudhuri
- Department of Mechanical Engineering, Stanford University, CA, USA
| | - Patricia Y.W. Dankers
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Laboratory of Chemical Biology, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - April M. Kloxin
- Department of Chemical and Biomolecular Engineering, University of Delaware, DE, USA
- Department of Material Science and Engineering, University of Delaware, DE, USA
| | - Jess G. Snedeker
- University Hospital Balgrist and ETH Zurich, Zurich, Switzerland
| | - Eileen Gentleman
- Centre for Craniofacial and Regenerative Biology, King’s College London, London SE1 9RT, UK
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39
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Jardat M, Dahirel V, Illien P. Diffusion of a tracer in a dense mixture of soft particles connected to different thermostats. Phys Rev E 2022; 106:064608. [PMID: 36671123 DOI: 10.1103/physreve.106.064608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022]
Abstract
We study the dynamics of a tracer in a dense mixture of particles connected to different thermostats. Starting from the overdamped Langevin equations that describe the evolution of the system, we derive the expression of the self-diffusion coefficient of a tagged particle in the suspension, in the limit of soft interactions between the particles. Our derivation, which relies on the linearization of the Dean-Kawasaki equations obeyed by the density fields and on a path-integral representation of the dynamics of the tracer, extends previous derivations that held for tracers in contact with a single bath. Our analytical result is confronted to results from Brownian dynamics simulations. The agreement with numerical simulations is very good even for high densities. We show how the diffusivity of tracers can be affected by the activity of a dense environment of soft particles that may represent polymer coils-a result that could be of relevance in the interpretation of measurements of diffusivity in biological media. Finally, our analytical result is general and can be applied to the diffusion of tracers coupled to different types of fluctuating environments, provided that their evolution equations are linear and that the coupling between the tracer and the bath is weak.
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Affiliation(s)
- Marie Jardat
- Sorbonne Université, CNRS, Laboratoire PHENIX (Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX), 4 Place Jussieu, 75005 Paris, France
| | - Vincent Dahirel
- Sorbonne Université, CNRS, Laboratoire PHENIX (Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX), 4 Place Jussieu, 75005 Paris, France
| | - Pierre Illien
- Sorbonne Université, CNRS, Laboratoire PHENIX (Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX), 4 Place Jussieu, 75005 Paris, France
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40
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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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41
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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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42
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Kiwanuka M, Higgins G, Ngcobo S, Nagawa J, Lang DM, Zaman MH, Davies NH, Franz T. Effect of paclitaxel treatment on cellular mechanics and morphology of human oesophageal squamous cell carcinoma in 2D and 3D environments. Integr Biol (Camb) 2022; 14:zyac013. [PMID: 36244059 PMCID: PMC9585394 DOI: 10.1093/intbio/zyac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 08/14/2022] [Accepted: 09/10/2022] [Indexed: 06/16/2023]
Abstract
During chemotherapy, structural and mechanical changes in malignant cells have been observed in several cancers, including leukaemia and pancreatic and prostate cancer. Such cellular changes may act as physical biomarkers for chemoresistance and cancer recurrence. This study aimed to determine how exposure to paclitaxel affects the intracellular stiffness of human oesophageal cancer of South African origin in vitro. A human oesophageal squamous cell carcinoma cell line WHCO1 was cultured on glass substrates (2D) and in collagen gels (3D) and exposed to paclitaxel for up to 48 h. Cellular morphology and stiffness were assessed with confocal microscopy, visually aided morpho-phenotyping image recognition and mitochondrial particle tracking microrheology at 24 and 48 h. In the 2D environment, the intracellular stiffness was higher for the paclitaxel-treated than for untreated cells at 24 and 48 h. In the 3D environment, the paclitaxel-treated cells were stiffer than the untreated cells at 24 h, but no statistically significant differences in stiffness were observed at 48 h. In 2D, paclitaxel-treated cells were significantly larger at 24 and 48 h and more circular at 24 but not at 48 h than the untreated controls. In 3D, there were no significant morphological differences between treated and untreated cells. The distribution of cell shapes was not significantly different across the different treatment conditions in 2D and 3D environments. Future studies with patient-derived primary cancer cells and prolonged drug exposure will help identify physical cellular biomarkers to detect chemoresistance onset and assess therapy effectiveness in oesophageal cancer patients.
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Affiliation(s)
- Martin Kiwanuka
- Biomedical Engineering Research Centre, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Ghodeejah Higgins
- Biomedical Engineering Research Centre, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Silindile Ngcobo
- Cardiovascular Research Unit, Christiaan Barnard Division of Cardiothoracic Surgery, University of Cape Town, Observatory, South Africa
| | - Juliet Nagawa
- Biomedical Engineering Research Centre, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Dirk M Lang
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Muhammad H Zaman
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Neil H Davies
- Cardiovascular Research Unit, Christiaan Barnard Division of Cardiothoracic Surgery, University of Cape Town, Observatory, South Africa
| | - Thomas Franz
- Biomedical Engineering Research Centre, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Observatory, South Africa
- Bioengineering Science Research Group, Engineering Sciences, University of Southampton, Southampton, UK
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43
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Huang WYC, Cheng X, Ferrell JE. Cytoplasmic organization promotes protein diffusion in Xenopus extracts. Nat Commun 2022; 13:5599. [PMID: 36151204 PMCID: PMC9508076 DOI: 10.1038/s41467-022-33339-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
Abstract
The cytoplasm is highly organized. However, the extent to which this organization influences the dynamics of cytoplasmic proteins is not well understood. Here, we use Xenopus laevis egg extracts as a model system to study diffusion dynamics in organized versus disorganized cytoplasm. Such extracts are initially homogenized and disorganized, and self-organize into cell-like units over the course of tens of minutes. Using fluorescence correlation spectroscopy, we observe that as the cytoplasm organizes, protein diffusion speeds up by about a factor of two over a length scale of a few hundred nanometers, eventually approaching the diffusion time measured in organelle-depleted cytosol. Even though the ordered cytoplasm contained organelles and cytoskeletal elements that might interfere with diffusion, the convergence of protein diffusion in the cytoplasm toward that in organelle-depleted cytosol suggests that subcellular organization maximizes protein diffusivity. The effect of organization on diffusion varies with molecular size, with the effects being largest for protein-sized molecules, and with the time scale of the measurement. These results show that cytoplasmic organization promotes the efficient diffusion of protein molecules in a densely packed environment. Cytoplasmic organization is a hallmark of living cells. Here, the authors make use of self-organizing cell extracts to examine how the emergence of large-scale organizations influences the microscopic diffusion of protein molecules in the cytoplasm.
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Affiliation(s)
- William Y C Huang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Xianrui Cheng
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - James E Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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44
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Li Y, Wong IY, Guo M. Reciprocity of Cell Mechanics with Extracellular Stimuli: Emerging Opportunities for Translational Medicine. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107305. [PMID: 35319155 PMCID: PMC9463119 DOI: 10.1002/smll.202107305] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Human cells encounter dynamic mechanical cues in healthy and diseased tissues, which regulate their molecular and biophysical phenotype, including intracellular mechanics as well as force generation. Recent developments in bio/nanomaterials and microfluidics permit exquisitely sensitive measurements of cell mechanics, as well as spatiotemporal control over external mechanical stimuli to regulate cell behavior. In this review, the mechanobiology of cells interacting bidirectionally with their surrounding microenvironment, and the potential relevance for translational medicine are considered. Key fundamental concepts underlying the mechanics of living cells as well as the extracelluar matrix are first introduced. Then the authors consider case studies based on 1) microfluidic measurements of nonadherent cell deformability, 2) cell migration on micro/nano-topographies, 3) traction measurements of cells in three-dimensional (3D) matrix, 4) mechanical programming of organoid morphogenesis, as well as 5) active mechanical stimuli for potential therapeutics. These examples highlight the promise of disease diagnosis using mechanical measurements, a systems-level understanding linking molecular with biophysical phenotype, as well as therapies based on mechanical perturbations. This review concludes with a critical discussion of these emerging technologies and future directions at the interface of engineering, biology, and medicine.
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Affiliation(s)
- Yiwei Li
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, Hubei, 430074, China
| | - Ian Y Wong
- School of Engineering, Center for Biomedical Engineering, Joint Program in Cancer Biology, Brown University, 184 Hope St Box D, Providence, RI, 02912, USA
| | - Ming Guo
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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45
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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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46
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Cytoplasmic forces functionally reorganize nuclear condensates in oocytes. Nat Commun 2022; 13:5070. [PMID: 36038550 PMCID: PMC9424315 DOI: 10.1038/s41467-022-32675-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/05/2022] [Indexed: 12/21/2022] Open
Abstract
Cells remodel their cytoplasm with force-generating cytoskeletal motors. Their activity generates random forces that stir the cytoplasm, agitating and displacing membrane-bound organelles like the nucleus in somatic and germ cells. These forces are transmitted inside the nucleus, yet their consequences on liquid-like biomolecular condensates residing in the nucleus remain unexplored. Here, we probe experimentally and computationally diverse nuclear condensates, that include nuclear speckles, Cajal bodies, and nucleoli, during cytoplasmic remodeling of female germ cells named oocytes. We discover that growing mammalian oocytes deploy cytoplasmic forces to timely impose multiscale reorganization of nuclear condensates for the success of meiotic divisions. These cytoplasmic forces accelerate nuclear condensate collision-coalescence and molecular kinetics within condensates. Disrupting the forces decelerates nuclear condensate reorganization on both scales, which correlates with compromised condensate-associated mRNA processing and hindered oocyte divisions that drive female fertility. We establish that cytoplasmic forces can reorganize nuclear condensates in an evolutionary conserved fashion in insects. Our work implies that cells evolved a mechanism, based on cytoplasmic force tuning, to functionally regulate a broad range of nuclear condensates across scales. This finding opens new perspectives when studying condensate-associated pathologies like cancer, neurodegeneration and viral infections. Cytoskeletal activity generates mechanical forces known to agitate and displace membrane-bound organelles in the cytoplasm. In oocytes, Al Jord et al. discover that these cytoplasmic forces functionally remodel nuclear RNA-processing condensates across scales for developmental success.
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47
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Extraction of accurate cytoskeletal actin velocity distributions from noisy measurements. Nat Commun 2022; 13:4749. [PMID: 35963858 PMCID: PMC9376101 DOI: 10.1038/s41467-022-31583-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 06/23/2022] [Indexed: 11/09/2022] Open
Abstract
Dynamic remodeling of the actin cytoskeleton is essential for many cellular processes. Tracking the movement of individual actin filaments can in principle shed light on how this complex behavior arises at the molecular level. However, the information that can be extracted from these measurements is often limited by low signal-to-noise ratios. We developed a Bayesian statistical approach to estimate true, underlying velocity distributions from the tracks of individual actin-associated fluorophores with quantified localization uncertainties. We found that the motion of filamentous (F)-actin in fibroblasts and endothelial cells was better described by a statistical jump process than by models in which filaments undergo continuous, diffusive movement. In particular, a model with exponentially distributed jump length- and time-scales recapitulated actin filament velocity distributions measured for the cell cortex, integrin-based adhesions, and stress fibers, suggesting that a common physical model can potentially describe actin filament dynamics in a variety of cellular contexts.
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48
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Koyano Y, Kitahata H. Anomalous diffusion and transport by a reciprocal convective flow. Phys Rev E 2022; 106:024102. [PMID: 36109911 DOI: 10.1103/physreve.106.024102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/10/2022] [Indexed: 06/15/2023]
Abstract
Under low-Reynolds-number conditions, dynamics of convection and diffusion are usually considered separately because their dominant spatial and temporal scales are different, but cooperative effects of convection and diffusion can cause diffusion enhancement [Koyano et al., Phys. Rev. E 102, 033109 (2020)2470-004510.1103/PhysRevE.102.033109]. In this paper, such cooperative effects are investigated in detail. Numerical simulations based on the convection-diffusion equation revealed that anisotropic diffusion and net shift as well as diffusion enhancement occur under a reciprocal flow. Such anomalous diffusion and transport are theoretically derived by the analyses of the Langevin dynamics.
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Affiliation(s)
- Yuki Koyano
- Department of Human Environmental Science, Graduate School of Human Development and Environment, Kobe University, Kobe 657-0011, Japan
| | - Hiroyuki Kitahata
- Department of Physics, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
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Català-Castro F, Schäffer E, Krieg M. Exploring cell and tissue mechanics with optical tweezers. J Cell Sci 2022; 135:jcs259355. [PMID: 35942913 DOI: 10.1242/jcs.259355] [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
Cellular and tissue biosystems emerge from the assembly of their constituent molecules and obtain a set of specific material properties. To measure these properties and understand how they influence cellular function is a central goal of mechanobiology. From a bottoms-up, physics or engineering point-of-view, such systems are a composition of basic mechanical elements. However, the sheer number and dynamic complexity of them, including active molecular machines and their emergent properties, makes it currently intractable to calculate how biosystems respond to forces. Because many diseases result from an aberrant mechanotransduction, it is thus essential to measure this response. Recent advances in the technology of optical tweezers have broadened their scope from single-molecule applications to measurements inside complex cellular environments, even within tissues and animals. Here, we summarize the basic optical trapping principles, implementations and calibration procedures that enable force measurements using optical tweezers directly inside cells of living animals, in combination with complementary techniques. We review their versatility to manipulate subcellular organelles and measure cellular frequency-dependent mechanics in the piconewton force range from microseconds to hours. As an outlook, we address future challenges to fully unlock the potential of optical tweezers for mechanobiology.
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Affiliation(s)
- Frederic Català-Castro
- Neurophotonics and Mechanical Systems Biology, ICFO, Institut de Ciències Fotòniques, 08860 Castelldefels, Spain
| | - Erik Schäffer
- Cellular Nanoscience, ZMBP, University of Tübingen, 72076 Tübingen, Germany
| | - Michael Krieg
- Neurophotonics and Mechanical Systems Biology, ICFO, Institut de Ciències Fotòniques, 08860 Castelldefels, Spain
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Shi Y, Sivarajan S, Crocker JC, Reich DH. Measuring Cytoskeletal Mechanical Fluctuations and Rheology with Active Micropost Arrays. Curr Protoc 2022; 2:e433. [PMID: 35612274 PMCID: PMC9321978 DOI: 10.1002/cpz1.433] [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] [Indexed: 11/07/2022]
Abstract
The dynamics of the cellular actomyosin cytoskeleton are crucial to many aspects of cellular function. Here, we describe techniques that employ active micropost array detectors (AMPADs) to measure cytoskeletal rheology and mechanical force fluctuations. The AMPADS are arrays of flexible poly(dimethylsiloxane) (PDMS) microposts with magnetic nanowires embedded in a subset of microposts to enable actuation of those posts via an externally applied magnetic field. Techniques are described to track the magnetic microposts' motion with nanometer precision at up to 100 video frames per second to measure the local cellular rheology at well-defined positions. Application of these high-precision tracking techniques to the full array of microposts in contact with a cell also enables mapping of the cytoskeletal mechanical fluctuation dynamics with high spatial and temporal resolution. This article describes (1) the fabrication of magnetic micropost arrays, (2) measurement protocols for both local rheology and cytoskeletal force fluctuation mapping, and (3) special-purpose software routines to reduce and analyze these data. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Fabrication of magnetic micropost arrays Basic Protocol 2: Data acquisition for cellular force fluctuations on non-magnetic micropost arrays Basic Protocol 3: Data acquisition for local cellular rheology measurements with magnetic microposts Basic Protocol 4: Data reduction: determining microposts' motion Basic Protocol 5: Data analysis: determining local rheology from magnetic microposts Basic Protocol 6: Data analysis for force fluctuation measurements Support Protocol 1: Fabrication of magnetic Ni nanowires by electrodeposition Support Protocol 2: Configuring Streampix for magnetic rheology measurements.
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Affiliation(s)
- Yu Shi
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland.,Current address: Department of Biomedical Engineering, University of North Carolina, Chapel Hill, North Carolina
| | - Shankar Sivarajan
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland
| | - John C Crocker
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Daniel H Reich
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland
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